castanyes blaves

Random ramblings about some random stuff, and things; but more stuff than things -- all in a mesmerizing and kaleidoscopic soapbox-like flow of words.



Daniel Falush, Department of Microbiology, University College Cork

First third about human population admixture, then e.coli...

Example of admixture -- Barack Obama

Li and Stephens 2003 -- HMM model for genetic variation

HGDP data (Li et al., Science 2008) - 650k ~ 1000 unrelated indvs

Sloppy painting -- african portion more or less remains
african. Brahui (Pakistan) have a lot of admixture.

Hazara admixture -- 22 generations ago -- Mongol era admixture

Kalash -- 630 BC -- Outlier population with the oldest time having no

Aaron Darling in the bacteria side
Didelot did ClonalFrame

phlyopools (not misspelled) -- weak ARGs -- lots of recombination in ecoli set 15
strains -- data doesn't tell much at the very deep branches of the
tree, but the more external branches have a lot of information

group b1 has high recombination rates -- lots of pathogens in it



Curtis Huttenhower, Lewis-Sigler Institute for Integrative Genomics and Department of Computer Science at Princeton University

MEFIT - Complex human diseases analysed at a meta-study level for gene expression datasets

Gene     -> Function
Gene     -> Gene
Data     -> Function
Function -> Function e.g. regulatory cross-talk

Prior knowledge on yeast ~80% whereas human is less than 40%

Sleipnip - 8 hours to 1 minute in yeast -- 30 years to 2 months - 18 hours in parallel

Predicted functional relatedness of a gene against any other gene in the genome

What is the data that relates BRCA1 and BRCA2? Mint, BioGRID, etc.

Genes that are related to a known disease, eg. altzheimer's disease

Is a gene performing X specific function to another group of genes?




Martin Evison, University of Toronto

Measures used nowadays in court to identify faces -- photogrammetry, superimposition and anthroscopy

Face changes with age and differently for each sex. Nostrils are very good landmarks. Ear lobes are the measure that has the most variance. In any age range, females have more generous lips.

Company in Florida giving the police a face profile based on SNPs tagging facial differences on a sample of 200 people (own emploees). Narrows down the profiles police force need to look for.

Oragene saliva sample should last for 1 year. Sampling then correlating with faces. Cool 3D model of faces done by interpolating 8 1Mpx pictures, called geometrix facevision.




Open Source push by the UK government

BBC NEWS | Technology | UK Government backs open source
The UK Government has said it will accelerate the use of open source software in public services.

Tom Watson MP, minister for digital engagement, said open source software would be on a level playing field with proprietary software like Windows.

Open source software will be adopted "when it delivers best value for money", the government said.

It added that public services should where possible avoid being "locked into proprietary software".

Licenses for the use of open source software are generally free of charge and embrace open standards, and the code that powers the programs can be modified without fear of trampling on intellectual property or copyright.

Announcing an open source and open standards action plan, the government said it would:

* ensure that the Government adopts open standards and uses these to communicate with the citizens and businesses that have adopted open source solutions

* ensure that open source solutions are considered properly and, where they deliver best value for money are selected for Government business solutions

* strengthen the skills, experience and capabilities within Government and in its suppliers to use open source to greatest advantage

* embed an open source culture of sharing, re-use and collaborative development across Government and its suppliers

* ensure that systems integrators and proprietary software suppliers demonstrate the same flexibility and ability to re-use their solutions and products as is inherent in open source.

Government departments will be required to adopt open source software when "there is no significant overall cost difference between open and non-open source products" because of its "inherent flexibility".



Text me if you can

BBC NEWS | Technology | Texting 'improves language skill'
Texting is likely to be an important part of a child's learning development, she thinks.

"The more exposure you have to the written word the more literate you become and we tend to get better at things that we do for fun," she said.

The study found no evidence of a detrimental effect of text speak on conventional spelling.

"What we think of as misspellings, don't really break the rules of language and children have a sophisticated understanding of the appropriate use of words," she said.

Other reports have produced similar results. Research from the University of Toronto into how teenagers use instant messaging found that instant messaging had a positive effect on their command of language.




Gramm-Leach-Bliley act of 1999

Gramm-Leach-Bliley Act - Wikipedia, the free encyclopedia
The Gramm-Leach-Bliley Act (GLBA) allowed commercial and investment banks to consolidate. For example, Citibank merged with Travelers Group, an insurance company, and in 1998 formed the conglomerate Citigroup

Economists Robert Ekelund and Mark Thornton have criticized the Act as contributing to the 2007 subprime mortgage financial crisis, arguing that while "in a world regulated by a gold standard, 100% reserve banking, and no FDIC deposit insurance" the Financial Services Modernization Act would have made "perfect sense" as a legitimate act of deregulation, under the present fiat monetary system it "amounts to corporate welfare for financial institutions and a moral hazard that will make taxpayers pay dearly". [14]



Desensitising for peanut allergy. Cool!

BBC NEWS | Health | Hope over peanut allergy 'cure'
It's not a permanent cure, but as long as they go on taking a daily dose they should maintain their tolerance




Not there yet for complicated genomes

BioMed Central | Full text | Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome
[...] the addition of GS FLX Paired End reads vastly improved the capability of 454 pyrosequencing by enabling the assembly of contigs into large scaffolds. Indeed, in terms of the number of scaffolds produced, the GS FLX assembly that included the combined shotgun and paired end reads was comparable to the Sanger assembly. Moreover, the order of the GS FLX scaffolds could be established from information from BAC-end sequences and the Atlantic salmon physical map. However, numerous gaps remained within the scaffolds, which is undesirable when a complete or reference genome sequence is one of the goals. Currently, if the Atlantic salmon genome is to provide a reference sequence for all salmonids, then a substantial proportion of the sequencing will have to be carried out using Sanger technology.




MacBook Pro 17" Unibody First Look
  • There are three tri-wing screws holding the battery to the Unibody case. (A tri-wing screwdriver is shown in the second photo.)
  • Apple did this to intimidate people out of swapping the battery, but a small flathead screwdriver (2mm or so) works fine to remove the screws.



Second Linux phone by Google

It took a long time for Linux to become mainstream in mobile phones, but Google realised they needed a strong platform to develop on the smartphone market, bought the company behind Android and, after a few months, the G1 was born. Now, copying the pervasiveness strategy that Microsoft took for the OS in personal computers, Google is producing an OS that will be massaged into different smartphones with different features, always making sure they provide as many Google services as possible. Why hasn't Microsoft mobile been successful in doing that? Well, first of all, they have been, as you can see in the purple cheese below:

Notice the Linux market share is only 1/4 the size of Microsoft's share. But Microsoft bases their revenue on selling the OS to the phone manufacturer, and don't have much vested interest in what services are provided by the phone. Whereas if you want your services to work on the smartphone, you allocate your resources to make sure they do. Symbian has the same issue Microsoft has: they are not strong in providing services. On the other hand, Apple (red) has successfully been doing very good iPhones previous to the Android birth. They do have a couple of very important services to offer: music and video content. But Apple will always rely on Google's efforts to have maps, mail and docs. So they rely on that in the same funny way they rely on Microsoft's Office, which is a pain to their strive for OS success. Apple in the smartphone sector is what the IBM in the PC sector was before Microsoft and the PC clones...

BBC NEWS | Technology | Second 'Google phone' is unveiled
The touchscreen HTC Magic will feature a 3.2 Megapixel camera, Wi-Fi, and GPS, but no slide-out keyboard.




Amazing Perl profiling with perl -d:NYTProf (updated)

Perl has always been considered a lesser computer language when compared against Java or C. There is always this idea that if a language doesn't have good debugging or profiling tools, it's not really a serious language. And to be fair, open source tools for C weren't even that good at profiling before the advent of valgrind. I had always been rather dissatisfied with the profiling tools in Perl, but last summer I discovered Devel::NYTProf:

Now, I can say that Perl has leap-frogged a fair number of other languages in terms of profiling capabilities. Tim Bunce, who have a talk this fall at the London Perl Mongers meeting, has released a new NYTProf 2.08 version, which incorporates even more optimization tracking goodies.

Never again let your Java/C coworkers make fun or your underrated language: the camel has ass-kicking profiling abilities now!

UPDATE: Not that I don't consider c#, vb, php or javascript as good languages, it's only that I know less of their profiling tools



The wonders of the internet

It's like the statement: "I'm sure a teenager in Singapore has already coded this in his/her bedroom tonight"... BBC NEWS | Technology | Nine-year-old writes iPhone code
A nine-year-old Malaysian boy in Singapore has written a painting application for the Apple iPhone.


And now with a press release

Investor Relations .::. illumina, inc. .::. News Release
Illumina, Inc. (NASDAQ:ILMN) unveiled a development roadmap for its Genome Analyzer system that charts a path to generate greater than 95 Gigabases of high quality data per run in 2009. This roadmap, which was presented at a user-group meeting at this week’s Advances in Genome Biology and Technology (AGBT) conference, outlined advances in chemistry, algorithms, and hardware which will substantially improve accuracy, read length, data density, and ease of use. These developments chart a clear and demonstrable path for researchers to generate 25x coverage of a human genome for less than $10,000 in 2009.

“The demonstrated pace of innovation on the Genome Analyzer has enabled us and end-users to embark on ambitious, new whole-genome sequencing projects that will have a major impact on human health, especially cancer,” said David Bentley, Vice President and Chief Scientist of DNA Sequencing at Illumina. “Currently we can generate greater than 25x coverage of a human genome in three flow cells; a year ago, more than 40 flow cells were used to complete our first African genome. By year’s end, we anticipate generating the same 25x coverage on a single flow cell bringing the cost of acquiring a human genome sequence to below $10,000.”

The current configuration of the Genome Analyzer has the potential to generate in excess of 15 Gigabases of high quality data per run. From this baseline, the performance of the Genome Analyzer is expected to increases greater than six-fold in 2009. The advances to achieve this increase will be commercialized in several phases throughout the year and include the following elements:

* Chemistry advancements including new polymerases for sequencing and cluster generation to enable faster run times and paired reads in excess of 2x100 base pairs each. These advancements also improve sequencing accuracy to greater than 98.5% for 2x100 paired end reads and 99.9% for 2x50 paired end reads.
* Hardware upgrades including improved flow cell holder and larger reagent cooler provide an increase in output and walk-away automation for reads of at least 100 cycles. These hardware components will comprise the Genome AnalyzerIIx Upgrade Kit, which current Genome Analyzer users can order immediately to increase the output and enhance the automation of their system.
* Algorithm improvements including a new approach to cluster detection will increase output up to 80% on high density flow cells and improve basecalling yielding greater accuracy and a larger proportion of perfect reads per run.
* Data density is increased by use of semi-ordered arrays of one micron and subsequently sub-micron features. These ordered arrays, combined with increases in read length, are expected to yield greater than 55 and 95 Gigabases per run respectively.

The combination of these advances will not only increase the output and decrease the cost of sequencing on a Genome Analyzer, but also expand the menu of applications that researchers can perform on the system. Notably, de novo sequencing and assembly of complex genomes, already possible with the Genome Analyzer, is considerably enhanced by the capability to completely sequence DNA fragments of up to 250 base pairs using the Illumina short-insert libraries and 150 base pair reads. The ability to generate contiguous 250 base pair sequences allows researchers to use a variety of existing long read assemblers for de novo sequencing and metagenomics.

“With the largest installed base of next-generation platforms and over 200 peer-reviewed publications to date, the Illumina Genome Analyzer has enabled a variety of scientists worldwide to conduct groundbreaking research rapidly and cost effectively,” said Joel McComb, Senior Vice President and General Manager of Illumina’s Life Sciences Business unit. “With the planned system enhancements in 2009, we anticipate that the Genome Analyzer will continue to provide a scalable and flexible solution for a broad menu of applications, including large scale whole-genome analysis, de novo sequencing, and metagenomics, and accelerate the rate of discoveries leading to novel insights about human health, biodiversity, and the environment.”



The strength of the British pound

The Bank of England (BoE) has slashed interest rates by another 50 points today, leaving the current rate at 1%. This measure is to tackle stimulate the economy at a moment where there is more worry about deflation than inflation. Also today, the European Central Bank (ECB) has decided to keep interest rates at 2%. Even though one would expect the British currency to fall spectacularly against the Euro given these two decisions by the central banks, this hasn't happened. In fact, the British pound hitted bottom 5 weeks ago, and since then it's been pretty obvious than the BoE was more prone to further slashes than the ECB. How is this explained?

Well, in my opinion, the BoE is trying to be more proactive in stimulating the economy than the ECB. This seemed costly 2 months ago, when the pound seemed to be going down the pipe, but now it's recovering. The same can be said for the Federal Reserve in the US, an organ that has been even more aggressive than the BoE and the ECB. The US dollar has already recovered *a lot* of ground to the Euro and the British pound. So with the current situation, one can only predict that both the US dollar and the British pound will gain turf against the Euro in the next few months.

If I am wrong, time will prove me wrong :-p



Another great read

Cambridge University - the Unauthorised History
Cambridge University – the Unauthorised History

Cambridge University is celebrating its 800th anniversary in 2009. The official history tells the tale of the buildings; but what about the ideas?

Down through the years, Oxford has produced many powerful men and Cambridge many iconoclasts – scientists, philosophers and revolutionaries. The polarisation is by no means total: Oxford's alumni include the reformer John Wyclif and the father of economics Adam Smith, while ours include the Prime Minister Charles Grey, who abolished slavery and passed the Great Reform Bill. But we've long produced more of the rebels; way back in the Civil War, for example, we were parliamentarian while Oxford was royalist. Why should this be?

I can't find anyone else trying to tell the tale, so I'll try. This web page explains how disruption has been in our DNA from the very beginning.
Creative disruption

If you want physical objects destroyed, the army can do that. As for badly-run companies, they get trashed when the economy goes into recession; the economist Joseph Schumpeter taught us that this "creative destruction" is vital for progress as it clears away the deadwood and creates space in which new businesses can grow. And it's just the same in ecosystems: from 1911, the USA put a lot of effort into stopping forest fires, but then discovered that although they saved individual plants and animals they were destroying the environment. A forest with a fire brigade is a sad old forest; a lot of plants from sequoias to proteas reproduce only in the aftermath of a fire.

Just as fire regenerates the forest, so a great university regenerates human culture – our view of the world and our understanding of it. We incinerate the rubbish. And Cambridge has long been the hottest flamethrower; we're the most creatively destructive institution in all of human history. And big new things come from that. The ground we cleared made us the cradle of evangelical Christianity in the sixteenth and seventeenth centuries, of science in the seventeenth and eighteenth, of atheism in the nineteenth, and of all sorts of cool new stuff since – including the emerging sciences of life and information.

In the beginning

I believe it goes right back to the beginning. We were founded, eight hundred years ago, by scholars fleeing persecution during a period of conflict between church and state. In 1209 the buring issue of the day was whether King John or Pope Innocent III should appoint the next Archbishop of Canterbury. Such power struggles were going on all over Europe, and had been for years (John's father Henry II had had St Thomas Becket killed). One of the church's reactions was to organise crusades – against infidels abroad and heretics at home. Robert Moore tells the story of how successive popes in the twelfth and thirteenth centuries incited the mob against lepers, gays, Jews and other undesirables, in the process forming a culture of persecution of outgroups and minorities that has blighted Europe ever since.

It was against this background that our founders fled Oxford in 1209 and settled in the newly-chartered town of Cambridge. The townsfolk of Oxford had hanged two clerks for a murder of which they were apparently innocent; the king backed the townsmen, and the scholars dispersed for five years. Some of the refugees came to Cambridge, and established our university. A generation later, in 1231, both Cambridge and Oxford got charters from Henry III which exempted us from taxes; and two years after that a Bull from Pope Gregory IX gave our graduates the right to teach everywhere. Had these men foreseen the role Cambridge would play in later reformation and revolution, they might have been less generous!

Early years

By the end of the thirteenth century, Cambridge was already making its mark in philosophy, with Duns Scotus producing disruptive ideas in theology (some of which by the 20th century had become Catholic orthodoxy). After the fall of Constantinople, the Renaissance got going and challenged the curriculum. Cambridge, like other medieval universities, had taught grammar, rhetoric and logic for the BA, then arithmetic, music, geometry and astronomy for the MA; much of the course material came from Aristotle. Suddenly this tradition was under fire, and the big debate was whether to teach Terence as well as Aristotle. In 1488, the rebels won: we started offering a four-year BA with two years in "humane letters" followed by two in logic and philosophy. We prospered amidst this tumult; six new colleges were founded between 1430 and 1496. Another fifteenth-century development was that we started hiring salaried professors, rather than leaving all the teaching to the "Regent masters" or young teaching fellows at the colleges and hostels. The professors mainly taught postgraduate subjects like law and medicine. This was an advance for scholarship, but caused some problems for governance: the university was still run by the Regent masters, but their position was weakened by the professors.

As Renaissance moved toward Reformation, there were Cambridge scholars on both sides of the barricades. One of the most influential of our critical theologians was Erasmus, said to have "laid the egg that Luther hatched". His major act of disruptive scholarship, produced at Cambridge, was a New Testament in parallel Greek and Latin texts. Until then, the church had claimed to be the sole custodian of God's word, whose official text was the Vulgate of St Jerome. By producing the first translation from the original manuscripts for over a thousand years, Erasmus undermined the Vatican's monopoly on biblical authority – although that issue would rumble on and on.

Rebellion and reformation

Thus it was that when Henry VIII needed a theologian to justify rebellion against the Pope, he turned to Cambridge and hired Edward Foxe, the Provost of Kings. Foxe was soon eclipsed by his colleague Thomas Cranmer who became the first protestant Archbishop of Canterbury, wrote the Book of Common Prayer, and was executed by Queen Mary. Another Cambridge martyr was William Tyndale who translated the Bible into English and, like Cranmer, got burned at the stake for his pains. However Tyndale had embraced the printing press. He printed 55,000 copies of the Bible before he was burned, and stoked the fires of the Reformation.

The Cambridge Puritan tradition got traction as our internal rebellion against statutes imposed on us by Queen Elizabeth in 1570, which gave college masters power over academics in the hope that they would curtail heresy. Wishful thinking! Our Puritan tradition drove the settlement of America – the Pilgrim leaders Henry Barrowe, John Greenwood and Robert Browne were all Cambridge men – and culminated in the Civil War the following century. The Cambridge MP Oliver Cromwell defeated and executed King Charles I, supported by many more Cambridge men, such as the poet John Milton and the founder of the Royal Society John Wilkins. Others spread dissent farther afield; John Harvard endowed a university in New England and left it all his books. Cambridge men such as Tyndall, Cranmer and Milton gave a huge push to the process of reining in religion – of turning it from an instrument of state power into a matter of conscience (though that wasn't always what they intended).

Physics, chemistry and biology

In 1665-7, Isaac Newton discovered the laws of motion and gravity, and the calculus. This trashed the medieval idea of a God lurking everywhere in the world, forever interfering to keep the planets in their rightful motions and the destinies of men aligned to his will. By showing that God could simply have wound up the universe and set it running, but didn't need to interfere thereafter, Newton greatly enlarged the space for men to wonder whether supernatural powers dictate our fortunes in this world and the next. He himself was religious – but a dissident. Although a Fellow of Trinity College he did not believe in the doctrine of the Trinity; but no matter. He got a special dispensation from Charles II to be a dissenter.

Francis Bacon had already written about the scientific method in the early 17th century; Newton and his Royal Society colleagues such as Wilkins, Flamsteed and Halley made science a reality. (The word "scientist" was coined much later by William Whewell.) Within a few years, people could doubt in public whether there was a next world, and not go to jail (Halley managed to become a professor at Oxford in 1703 despite being an atheist). The eighteenth-century Enlightenment flourished in the space this created. Unfortunately for Cambridge, our authorities restricted the university to Church of England members through the eighteenth and early nineteenth centuries, and even required many academics to be ordained within a set number of years appointment. There was a long argument with our mathematicians wanting dissenters admitted, without needing the royal dispensation that Newton got, while our theologians dragged their feet. As a result, much of the running in the Enlightenment was made by men from elsewhere, such as Edinburgh's David Hume.

The nineteenth century saw a number of great Cambridge men filling in the gaps in the Newtonian idea of the world as mechanism rather than magic. Charles Babbage came up with the idea of the computer, and although he couldn't really build one with the technology of the time, his idea would eventually challenge the very concept of intelligence at the deepest level. Meanwhile, James Clerk Maxwell explained electromagnetism, and in 1897 JJ Thomson discoved the electron, laying the foundations for modern physics and electronics that would lead to proper computers. We also had great social reformers, such as Henry Mayhew. But the greatest iconoclast of the nineteenth century was undoubtedly another Cambridge scientist, Charles Darwin. By explaining how animals and plants evolve by variation followed by natural selection over long periods of time, he shot down the belief that man had been created specially by God and that we were qualitatively different from other animals.

Twentieth-century troublemakers
The early twentieth century saw not just the full-blown emergence of modern physics, with Cockroft and Walton splitting the atom and theorists like Dirac showing that reality is stranger than anyone could have imagined. It also saw philosophy flourish as people sought to understand this new and scary world. Cambridge philosphers such as Wittgenstein and Russell taught us that many metaphysical problems of the past simply arose from abuse of language (an idea that our medieval logicians had also explored). Russell also came up with Russell's Paradox, and such work in logic led (via Goedel) to Alan Turing's work on the foundations of computing. After Turing went to Manchester another Cambridge man, Maurice Wilkes, built the world's first proper computer, the EDSAC, and established the lab where I work. Shortly aftwards, Watson and Crick discovered the structure of DNA, which led rapidly to the realisation that living things are also self-replicating computational machines. Bioinformatics is now one of our strongpoints; Cambridge did about a third of the Human Genome Project (and John Sulston, who ran our genome project, pushed for the genome to become public domain – disrupting the world of "intellectual property"). And biology is only one of many fields to be turned upside down by computing. Starting in the 1950s, sciences as disparate as astronomy and crystallography have been revolutionised by computing; one science after another has started shifting from the theory-intensive model pioneered by Newton to a more data-intensive way of working. And the disruption caused by computing has spread from one industry after another – from telecomms to bookselling.

As for the humanities, Alfred Marshall synthesised what was known about economics, then Maynard Keynes attacked this classical synthesis and finally Peter Bauer undermined the postwar Keynesian consensus on central planning, price controls and foreign aid. We've also produced many creative and disruptive writers, such as Siegfried Sassoon, EM Forster, Sylvia Plath, Douglas Adams and even Salman Rushdie; meanwhile F.R. Leavis set literary criticism on its head. I'm not an expert on literature; I'm an engineer, and this web page is my own perspective – hey, warts and all, as Cromwell put it. But one thing I do know is that many other Cambridge people have helped to pick apart error in just about every imaginable field of human endeavour.

The next 800 years?
Cambridge scientists and scholars have demolished more ancient superstitions than anyone else. We've not just been a bit more productive than other universities – we've been miles better. No other institution even comes close. Our effect on religion, from reformation to atheism, has been profound: if Dawkins is the Devil's chaplain, Cambridge could be called the Devil's flamethrower! But it's much wider than that. Our talent for creative destruction hasn't just lead to massive advances in liberty and prosperity. It's completely changed the way people think.

The most profound innovation was science itself, which emerged in the seventeeth century among Bacon, Newton, Wilkins, Halley and their contemporaries. Science is not like religion; it's not about finding true doctrines. It's about demolishing wrong ones. Ideas are two a penny; it's the efficient destruction of error that leads us to truth. And we really need such a method. The truths at the heart of Newtonian mechanics, evolution, electromagnetism, quantum mechanics and bioinformatics are often so counterintuitive and disturbing that we only accept them when absolutely every other possibility has been shot down in flames. To understand the mechanism, you first have to burn away the myth.

So there we have it. That's us. Cambridge has been setting cultural forest fires for the last 800 years, and I sure hope we'll be setting them for the next 800 too.

Lessons for the future

So how do we keep Cambridge at the forefront? I believe that the critical lessons from our history are the importance of academic self-government and intellectual freedom. We were a self-governing community of scholars right from the start, unlike universities such as Bologna which started out as communities of students who banded together to hire teachers. Time has proved our model to be the best. And at various times, either church or state has tried to intervene, to centralise power and control us – as with Queen Elizabeth's statutes of 1570. These interventions have never had the desired effect, but have often hobbled us for a while. The worst was in the eighteenth and early nineteenth centuries when we weren't allowed to admit nonconformists. That simply handed the baton for a while to the Scottish universities, and to new institutions such as UCL. And even in the twentieth century we weren't perfect: although we admitted women from 1869 we didn't give them proper degrees and let them vote until 1947. Yet Oxford enfranchised women in 1920. Nostra maxima culpa!

Intellectual freedom is a more modern and difficult concept. Medieval and reformation academics often sought to suppress colleagues whose views they disliked; there were Dominicans training in Cambridge to hunt heretics from 1238, and when King's College was founded in 1441 all the fellows had to take an oath not to follow the teachings of Wyclif. (And who knows – perhaps these tussles left us with a certain edge, a certain wilingness to denounce error!) As for academic freedom, it seems to have put up its first tender shoots in the early 16th century. Erasmus remarked that Cambridge became much more open in the mid-1510s, and when a fellow of John's was accused of heresy in 1527, our chancellor John Fisher changed the statutes so that heretics could be sacked – yet there was great reluctance to do so! The emergence of science in the seventeenth century and the Enlightenment in the eighteenth had a huge effect, but it was the mid-19th century before we broke the stranglehold of the Anglican church. As late as 1813, Charles Babbage's thesis was considered to be blasphemous and he wasn't allowed to graduate! The mid-19th-century liberalisation was not the end of the story, though; Bertrand Russell was sacked by Trinity College in 1916 for being a conscientious objector to World War I, and there were many further tussles until the current wording of our Statute U (which protects academics against arbitrary discipline and dismissal) was drafted in the 1980s by David Williams. Freedom of speech in academia can't be totally separated from the same freedom in the rest of society, of course, but for centuries we academics have led the way.

Academic freedom and institutional self-governance are subtly but deeply linked. They are both still under pressure – from a busybody state and a centralising university bureaucracy. The hot topic in 2009, our octocentenary year, is a proposal to curtail academics' protection by abolishing Statute U and replacing it with a much more malleable Code of Practice. Authority argues that we should treat academic and other staff equally. Fine; let's extend the protections we now enjoy to other university staff too. For more, see the Campaign for Cambridge Freedoms.

Ross Anderson

Acknowledgements: I'm grateful to Elisabeth Leedham-Green, Gillian Evans, Richard Evans, David MacKay and Peter Robinson for comments and corrections. As for the heresies expressed here, I confess! They are mine!



Amazon games to try for free

Amazon moves into casual gaming in a very big way - Ars Technica
For the first week, visitors will even be able to grab three games for free: Jewel Quest 2, Build a Lot, and The Scruffs. That, along with the ability to try every game before you buy, should be enough to entice fans of casual gaming to check out Amazon's offerings. It also looks like this could be Amazon's first step into the world of digital distribution for video games.


UK Treasury's best investment in history?

BBC NEWS | The Reporters | Robert Peston
The Bank of England has provided this £185bn in the form of Treasury Bills - which are short-dated government bonds that can easily be turned into cash. And in return it has received £287bn of collateral from the banks, in the form of loans made by those banks.

All of those loans received from the banks have been securitised or turned into tradable securities. And most of them are residential mortgages converted into mortgage-backed securities.

So the best way of seeing all this is as a three-year loan of £185bn to the banks, made by all of us as taxpayers, for which we've received £287bn of assets.

And, what's more, we've received a fee of 1.15% for our trouble.

For British taxpayers, that doesn't look such a terrible deal. The risk of loss to us, given that we've lent £102bn less than the face value of the collateral we've been given, looks pretty small.

But it shows you quite how serious it was that the commercial market for mortgage-backed securities had collapsed and quite how desperate the banks were to raise cash.


on ack

ack -- better than grep, a power search tool for programmers
Top 10 reasons to use ack instead of grep.

1. It's blazingly fast because it only searches the stuff you want searched.
2. ack is pure Perl, so it runs on Windows just fine.
3. The standalone version uses no non-standard modules, so you can put it in your ~/bin without fear.
4. Searches recursively through directories by default, while ignoring .svn, CVS and other VCS directories.
* Which would you rather type?
$ grep pattern $(find . -type f | grep -v '\.svn')
$ ack pattern
5. ack ignores most of the crap you don't want to search
* VCS directories
* blib, the Perl build directory
* backup files like foo~ and #foo#
* binary files, core dumps, etc
6. Ignoring .svn directories means that ack is faster than grep for searching through trees.
7. Lets you specify file types to search, as in --perl or --nohtml.
* Which would you rather type?
$ grep pattern $(find . -name '*.pl' -or -name '*.pm' -or -name '*.pod' | grep -v .svn)
$ ack --perl pattern
Note that ack's --perl also checks the shebang lines of files without suffixes, which the find command will not.
8. File-filtering capabilities usable without searching with ack -f. This lets you create lists of files of a given type.
$ ack -f --perl > all-perl-files
9. Color highlighting of search results.
10. Uses real Perl regular expressions, not a GNU subset.
11. Allows you to specify output using Perl's special variables
* Example: ack '(Mr|Mr?s)\. (Smith|Jones)' --output='$S'
12. Many command-line switches are the same as in GNU grep:
-w does word-only searching
-c shows counts per file of matches
-l gives the filename instead of matching lines
13. Command name is 25% fewer characters to type! Save days of free-time! Heck, it's 50% shorter compared to grep -r.



News with a pinch of salt

BBC NEWS | Health | 'Hidden salt' in restaurant meals
Consensus Action on Salt and Health (CASH) found that nearly three quarters of the main course dishes had levels in excess of ideal daily limits.



Ubuntu Netbook Installers

The Ubuntu netboot installers - I Still Know What You Learned Last Summer
As I understand it, there are three ways to do a netboot install. I've previously written about installing Ubuntu by booting from files downloaded to your hard disk. It's also easy to do a netboot install from either a CD or a USB key, and the procedures are very similar.

All three methods are nice because they have small initial downloads (~10 MB); they then download the rest of your OS at install time. It's a waste of time to download a ~700MB CD image if you're going to upgrade half of your packages right after installation. (Software is usually out of date by the time you install it!) The netboot installers are also versatile. They will install, at your request, any (or all!) of the following: Ubuntu desktop, Ubuntu server, Kubuntu desktop, Xubuntu desktop, Edubuntu desktop, and many more.

The hard disk method has the advantage that, of course, you don't need to use any external media. However, in my experience, the CD and USB key installers seem to be less flaky. Unlike a hard disk installation, they also work even if you don't have Grub already installed.

For either the CD or USB key methods, you can find the appropriate files here:

(This is for Jaunty/i386. If you want a different release or have a different architecture, adjust the URL accordingly.)

For CD installation: download mini.iso and burn it to your CD.

For USB media installation: download boot.img.gz and follow the instructions here. It will boil down to doing something like this:

# zcat boot.img.gz > /dev/sdX1
# aptitude install mbr
# install-mbr /dev/sdX

Then boot from your new media into the installer.



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