The Mega-Important MicroRNAs

Yesterday, when I was writing about the structures found in DNA, I said

Between the genes lie stretches of the main program that calls the subroutines

This is, of course, a gross over-simplification. One of the most interesting discoveries of recent years is that between your common or garden genes there are other structures that do not code for proteins, but for strings of RNA. It turns out that the latter play crucial roles in many biological processes, for example development. Indeed, they are fast emerging as one of genomics' superstars.

So it is only right that Nature Genetics should devote an entire issue to the subject; even better, it's freely available until August 2006. So get downloading now. Admittedly, microRNAs aren't the lightest of subject-matters, but they're mega-important.

Last Night a DVD Saved My Life

Last night, my Windows 2000 box died. To be fair, it was nothing to do with Windows, but a dodgy hard disc. And yes, of course I have backups...it's just that they're not entirely up-to-date, and missing even a few days' data is a pain. I could re-install Windows and hope that gave me access to my data (stored on a separate partition), but this would take a few hours that I don't have, and might not work. Luckily there's a better way.

Booting up the PC with the Knoppix 5.0 Live DVD inside produced not only a working machine in a couple of minutes, with access to all of my data, but a cool 5000 programs at my beck and call. Including K3b, which meant that I could simply burn copies of the data I was missing. Problem solved.

Thanks, Knoppix: you're a gent.

The Personal Genome Part 265

Here's Nick Wade reviewing candidate technologies for the sub-$1000 genome. It's coming, people.

The Future of Media

The Future of Media Report has two main things going for it. First, it comes from an Australian group, which gives it a slightly different perspective on things. Secondly, it is packed full of interesting graphs and charts. Make that three: it's available under a liberal CC licence.

If Not Net Neutrality - What?

That old contrarian curmudgeon, Andrew Orlowski, has found a soul-mate in Richard Bennett: "[t]he veteran engineer played a role in the design of the internet we use today, and helped shaped Wi-Fi" as Orlowski explains before an interview. In addition,

Bennett argues that the measures proposed to 'save' the internet, which in many cases are sincerely held, could hasten its demise. Network congestion is familiar to anyone's whose left a BitTorrent client running at home, and it's the popularity of such new applications that makes better network management an imperative if we expect VoIP to work well. The problem, he says, is that many of the drafts proposed to ensure 'Net Neutrality' would prohibit such network management, and leave VoIP and video struggling.

The conversation that follows is extremely interesting, and certainly hits home. But I have big problems with this part:

They all seem to be worried that ISPs have secret plan to sell top rank - to pick a search engine that loads faster than anyone else's. But it's not clear that a), anyone has done that; b), that it's technically achievable; or c) that it is necessarily abusive; or d) that their customers would stand for it.

These all seems very weak arguments in against net neutrality; I'd rather err on the side of hippy edge-to-edge goodness.

TOPAZ Tarnished

I've written approvingly of PLoS ONE before, and it's also good to see that the underlying software platform will be open source. But I was disappointed to read this post calling for some "help to shape the future":

Now is your chance to get very actively involved in the creation of TOPAZ, the new Open Source publishing platform which PLoS is involved in developing and which will be supporting PLoS ONE when it launches. What we need is some people in the San Francisco area who would be willing to be on a focus group to give us some advice on the feel and functionality that you would like to see. It is a great project and we really do want your views.

Surely a global perspective is absolutely critical to what PLoS ONE is trying to achieve? So limiting focus groups to a very particular part of the anglophone world seems foolish, to say the least.

And it's not as if there aren't other ways that this could be done, taking input from all around the world. For example, I've heard this thing called "The Internet" can be quite handy in these circumstances....

The Other GNU/Linux

Think of GNU/Linux and you probably think of servers, maybe with a smidgeon of desktop thrown in for good measure. In fact, the domain where GNU/Linux utterly dominates is that of high-performance computing.

But it may be that GNU/Linux's finest hour is yet to come - as a mobile phone operating system. After all, it is likely that there will be a mobile phone for most people on this planet one day, but the same cannot be said about conventional PCs.

So news stories like this one, about the doubling of membership of a GNU/Linux phone standards group, are actually rather important.

But dull.

Theses Unbound

OK, I admit it: I chose this for the title again. Well, "consultation on a national e-theses service for the UK" isn't quite so exciting.

The Internet? It's a Series of (You)Tubes

Is it just me, or has the entire VC industry gone utterly bonkers over Internet video? It seems that every day there's a new YouTube me-too launch on TechCrunch - with the usual "I think it's got potential" that seems to accompany every such story - and now, thanks to IP Democracy, we have a neat little table that suggests that VCs are, indeed, barking:

we take a look at the amount of venture money that has flowed into IP video start-ups over the past year and find that over $600 million has been invested in the YouTubes and Sling Medias and MobiTVs of the world since around this time last year. Our list (see table below) doesn’t even include investments for web sites or technology companies that focus a lot — but not primarily — on IP video efforts.

I realise that the Internet is a series of tubes, but as far as video is concerned, things really seem to be going down them.

EU Parliament Gets a Touch of the Opens

Blige, serious goings-on in the EU parliament. In a text recently adopted, it

18. Takes note of the Commissions' view that the EU must acquire a cost-effective, legally watertight and user-friendly system of intellectual property protection so as to attract technologically advanced companies; considers that the protection of intellectual property must not interfere with open access to public goods and public knowledge; urges the Commission to promote a socially inclusive knowledge-based society by supporting, for example, free and open source software and licensing concepts like the General Public License (GPL) and the Public Documentation Licence (PDL);

This is a gauntlet thrown down to the European Commission, particularly Microsoft's friend, Mr McCreevy. I wonder what will happen next. (Via Heise Online.)

Open Source is Better - Ask a Virus Writer

Virus writers are not known for their morals - or for being fanboys: they will use whatever means necessary to achieve their dubious ends. So when MacAfee warns that

Malicious-software writers are increasingly using open-source methodologies when developing their code

you can be pretty sure that this follows an extremely objective evaluation of the various competing development methods.

Maybe not quite the testimonial most free software enthusiasts were looking for, but a testimonial nonetheless.

The World's First Open Source Man

The genome – the totality of DNA found in practically every cell in our body - is a kind of computer program, stored on 23 pairs of biological DVDs, called chromosomes. Within each chromosome, there are thousands of special sub-routines known as genes. Between the genes lie stretches of the main program that calls the subroutines, as well as spacing elements to make the code more legible, and non-functional comments – doubtless deeply cool when they were first written – that have by now lost all their meaning for us.

DNA's digital code – written not in binary, but quaternary (usually represented by the initials of the four chemicals that store it: A, C, G and T) – is run in a wide range of cellular computers, using a central processing unit (known as a ribosome), and with various initial values and time-dependent inputs supplied in a special format, as proteins. The cell computer produces similarly-formatted outputs, which may act on both itself and other cells.

Thanks to a far-sighted agreement known as the Bermuda Principles, the digital code that lies at the heart of life is freely available from three main databases: one each in the US, UK and Japan. As a result, the DNA that was obtained through the Human Genome Project is open source's greatest triumph.

But so far, no human genome can be said to represent any single human being: that of the Human Genome Project is in fact a composite, made up of a couple of dozen anonymous donors. But soon, all that will change; for the first time, the complete genome of a single person will be placed in the public databases for anyone to download and to use, creating in effect the world's first open source man.

His name is Craig Venter, and for nearly two decades he has been simultaneously revered and reviled as one of the most innovative researchers in the world of genomics. He was the person behind the company Celera that sought to sequence the human genome before the public Human Genome Project, with the aim of patenting as much of it as possible. Fortunately, the Human Genome Project managed to stitch together the thousands of DNA fragments it had analysed – not least thanks to some serious hardware running GNU/Linux – and to put its own human genome in the public domain, thus thwarting Celera's plans to make it proprietary.

A nice twist to this story is that it turned out that Celera's DNA sequence was not, as originally claimed, another composite, but came almost entirely from one person: Craig Venter himself. So his latest project is in many ways simply the completion of this earlier attempt to become the first human with a fully-sequenced genome. The difference now, though, it that it will be in the public databases, and hence accessible by anyone.

This will have profound consequences. Aside from placing his DNA fingerprint out in the open – which will certainly be handy for any police forces that wish to investigate Venter – it means that anyone can analyse his DNA for anything. At the very least, scientists will be able to carry out tests for genetic pre-dispositions to all kinds of common and not-so-common diseases.

So it might happen that a laboratory somewhere discovers that Venter is carrying a genetic variant that has potentially serious health implications. Most of us will be able to choose whether to take such tests and hence whether to know the results, which is just as well. In the case of incurable diseases, for example, the knowledge that there is a high probability – perhaps even certainty – that you will succumb at some point in the future is not very useful unless there is a cure or at least a treatment available. Venter no longer has that choice. Whether he wants it or not, others can carry out the test and announce the result; since Venter is a scientific celebrity and a public figure, he is bound to get to hear about it one way or another.

So while his decision to sequence his genome might be seen as the ultimate act of egotism, by choosing to publish the result he will in fact be providing science with a wonderfully rich resource - the complete code of his life - and at some considerable risk, if only psychological, to himself.

The Dangers of Open Content

Here's a nice story involving Elephant's Dream and Wikipedia - and a reminder that the latter is best regarded as a rough guide or a starting point, to be used with intelligence, not instead of it. (Via Slashdot.)

More Microsoftie FUD

Another comparative "analysis" of security flaws in Windows and Red Hat. The result: Windows is better - the figures prove it. Well, yes, but let's look at those figures at little more. The giveaway is this paragraph:

Because of the nature of the Open Source model, there seems to be a higher tendency (unscientificly speaking) to just copy a piece of code and reuse it in another components. This means that if a piece of code turns out to be flawed, not only must it be fixed, but also that maintainers must find every place they might've reused that blob of code. A visual inspection showed me that many of these were the multiple vulnerabilities affecting firefox, mozilla and thunderbird. In a typical example, firefox packages were fixed, then mozilla packages were fixed 4 days later, then thunderbird was fixed 4 days after that.

Note that it says "In a typical example, firefox packages were fixed, then mozilla packages were fixed 4 days later". So one reason why Red Hat has more vulnerabilities is that it has far more packages included, many of which duplicate functions - like Firefox and Mozilla. The point is, you wouldn't install both Firefox and Mozilla: you'd choose one. So there's only one vulnerability that should be counted. Not only that, but Red Hat is penalised because it actually offers much more than Windows.

I don't know what the other vulnerabilities were, but I'd guess they involved similar over-counting - either through duplication, or simply because Red Hat offered extra packages. By all means compare Windows and Red Hat, but make it a fair comparison.

Wikipeda Does RSS

I amazed this hasn't been done before: you can now track changes to Wikipedia articles through an RSS feed. If you use Firefox, say, to go to the history tab of the page that interests you, you'll find the standard orange radio symbol in the address bar like any other RSS feed.

This is clearly great, because it means that you can watch how pages of interest to you change; it's also clearly terrible, because it means that edit war loonies will be able to engage even more rapidly. (Via Micro Persuasion.)

The Value of the Public Domain

More light reading - this time about the public domain. Or rather, a little beyond the traditional public domain, as the author Rufus Pollock states:

Traditionally, the public domain has been defined as the set of intellectual works that can be copied, used and reused without restriction of any kind. For the purposes of this essay I wish to widen this a little and make the public domain synonymous with ‘open’ knowledge, that is, all ideas and information that can be freely used, redistributed and reused. The word ‘freely’ must be loosely interpreted – for example the requirement of attribution or even that derivative works be re-shared, does not render a work unfree.

It's quite academic in tone, but has some useful references (even if it misses out a crucial one - not that I'm bitter...).

Innovation Happens Elsewhere - Online, Too

Ron Goldman and Richard P. Gabriel have made available an online version of their book Innovation Happens Elsewhere: Open Source as Business Strategy. It's a well-written and highly-approachable introduction to open source, mainly for those thinking about using free software in business.

I particularly like the following take:

Open source is fundamentally about people volunteering to work on projects in what could be called the commons; that is, it is about working on things for the public good.

This idea will come as no surprise to readers of this blog, but it's still a novel viewpoint for many. The rest of the book shows a similarly refreshing originality in its approach. (Via Creative Commons blog.)

Net Neutrality and Open Spectrum

David Levine has an interesting post that joins the dots connecting the net neutrality debate with the issue of creating a spectrum commons. I don't share his concerns about imposing net neutrality through legislation, but I certainly agree that breaking the last mile monopoly through wireless is ultimately a better solution. And while we're at it, let's try and get some global wireless meshes going too.

ODF A.G. (After Google)

It's curious the low-key way that Google has joined the ODF Alliance. But there's no mistaking the impact and importance of that move. IBM's Bob Sutor has some interesting observations in this context. Two in particular:

It is up to Google to say what they want about this, but, as I noted last night, ODF Alliance membership jumped by 20 members in the few days following the news of their membership.

and

OpenDocument is bringing on a Renaissance of document creation and publishing. That which we used to know is being rediscovered and combined (mashed together) with what we have learned recently.

The orthodoxy of "this is how you create office documents" is going to fall by the wayside, though there will opposing kingdoms and battles and heretics and maybe even a few heros emerging.

Tripped up for Want of a Commons

I'm not a poddie myself, but the idea behind Griffin Technology's iTrip - being able to broadcast your MP3 files to nearby FM radios - is a great one. A pity, then, that's it's currently against the law in the UK because it "trespasses" on someone else's "property" - the radio spectrum that has been allocated for their use.

The current fix, apparently, is to use the 2003 Wireless Telegraphy (Exemption) Regulations Act. But the real solution is to create a much broader spectrum commons where people can start trying out all sorts of wireless innovation - without having to jump through these kind of hoops.

Update: Wow, that was quick. Here's Ofcom with a consultation on Wireless Telegraphy Licence Exemption that amends the 2003 Wireless Telegraphy (Exemption) Regulations Act. Powerful things, these blogs. (Via openspectrum.info.)

Microsoft the Translator, Microsoft the Traitor

Since I sank to the (oceanic) depths of linking to a fisheries story on the basis of an irresistible headline, I don't see why I shouldn't do the same for this post, winningly entitled "Traduttore, Traditore" - Italian for "Translator, Traitor".

It's an interesting examination of the reality behind Microsoft's much-ballyhooed support for ODF, but what really grabbed my attention was the fact that this translator/traitor word pairing is always close to the surface of my mind whenever I use either: I'm always teetering on the brink of swapping one for the other. Which would be unfortunate. (Via Bob Sutor's Open Blog.)

Making All the Right Connexions

A couple of months back I had the pleasure of interviewing Richard Baraniuk for an article about open content for LWN.net. As I wrote then:

Just as open source avoids re-inventing the wheel by building on existing code, so open courseware aims to save time, effort and money by making educational material freely available for others to re-use, extend and improve.

The first such project, Connexions, came from Rice University. It was the brainchild of Richard Baraniuk, professor of electrical engineering, who was directly inspired by the example of open source. Connexions uses a content creation platform called Rhaptos, which is released under the GNU GPL.

Connexions is a fascinating exercise in re-inventing university course materials, but Baraniuk told me that they were planning to go even further. Now Rice has announced that it is to use print-on-demand technologies to produce academic textbooks in a completely new way. As the press release explains:

Rice University's innovative Connexions today announced an on-demand printing agreement with QOOP Inc. that will allow students and instructors anywhere in the world to order high-quality, hardbound textbooks from Connexions - in most cases for less than $25.

The deal positions Connexions to take the lead in open-source textbook publishing as soon as it completes software needed to feed each of its titles to QOOP's on-demand publishing platform. Connexions plans to offer more than 100 titles for online purchase by year's end.

"From its inception, Connexions has used the Web to go beyond print," said Connexions founder Richard Baraniuk. "Connexions lets pupils and instructors make cross-disciplinary intellectual leaps with a simple mouse click, following knowledge wherever learning takes them.

"But being Web-based is also about access, and because our materials are freely available to everyone, we needed an easy, low-cost way to let people use a book if that's the medium they are most comfortable learning from," said Baraniuk, the Victor C. Cameron Professor in Electrical and Computer Engineering.

QOOP's on-demand service will allow Connexions users to order customized course guides and a variety of fully developed Connexions textbooks. Standard paperbacks will take just 3-5 days to produce and ship, and traditional hardbacks will take about a week to produce. QOOP ships directly to customers.

No other publisher of open-source educational content can match Connexions offerings. This is partly due to Connexions early adoption of Creative Commons open licenses. Because all content on the site is authored under these licenses, there are no copyright conflicts to negotiate.

Open content, open source - sounds like all the right connexions are being made.

Why Hackers Do It

If you've ever wondered what makes hackers (not crackers) tick, you can relax: somebody has now submitted a doctoral thesis on the subject (in German) to give us an academically-rigorous answer.

It has as its title "Fun and software development: on the motivation of open source programmers," and includes, in an appendix, an email from RMS, whom the doctorand unwisely addressed as an "open source developer". To which Stallman inevitably (and rightly) replied:

Thank you, but I do not consider myself an ’open source developer’, and I don’t like my work to be described as ’open source’.

My work is free software (freie Software, logiciel libre).

One result, noted by Heise Online, is particularly striking:

Only about half the programming work is thus undertaken by the developers in their free time; for 42 percent (in temporal terms) of their engagement with open source the programmers are being remunerated -- an astonishingly large percentage. On this point the author of the dissertation Benno Luthiger Stoll remarks that this figure is likely to be even higher when the big picture is taken into account: The developers most likely to be paid are those working for large open-source projects; projects that in many cases have their own project infrastructure, he notes. Those active open-source programmers questioned, however, had come from Sourceforge, Savannah and Berlios, which in general tended to host less elaborate projects, he adds.

Happily, it also seems that

When compared with some 110 developers working for Swiss software companies, those engaged in open-source projects were seen to have more fun.

But maybe Swiss software companies are particularly boring.

PortableApps.com - Open Source on a Stick

One of the many benefits of open source is that it allows people to experiment. In particular, it lets people try out all sorts of whacky ideas that would simply be stifled at birth had they involved closed source. A good example is Portable Firefox, which consists of a slightly-modified version of the free browser such that it can be placed on a USB drive and run from it, without needing any further installation.

I knew that this had spawned things like Portable Thunderbird, which does the same thing for Mozilla's email client, but I hadn't realised that things had gone much further. For there is now a site called PortableApps.com, run by the person behind Portable Firefox, John Haller.

And what a cornucopia of a site it is. In addition to portable versions of Firefox and Thunderbird, you also find "ports" of OpenOffice.org, the IM client GAIM, the Web site editor NVu and the anti-virus program ClamWin. There's even a mini LAMP stack - though this is without the GNU/Linux part. However, the PortableApps site indicates that portable operating systems are on their way.

The software on this site represents quite a significant achievement, because it means that you can literally carry around in your pocket all the main apps that you need on a USB drive. Provided you can find a PC with a USB socket you can start working as if it were your machine.

Some Microsofties See the OSS Light

I don't know whether this is big enough to call a trend yet, but it's striking that several ex-Microsofties are setting up new companies based around open source. The latest one is Ohloh, whose site explains:

We're mapping the open source world by collecting objective information on open source software. Search our site for the most current software metrics and project information on open source software projects.

eWeek has some details on the ex-Microsoft people involved:

Collison and Jason Allen, a former development manager for XML Web Services at Microsoft and now vice president of engineering at Ohloh, co-founded the new company. Other former Microsoft executives involved in the startup include Paul Maritz, who served as a member of the executive committee and manager of the overall Microsoft company from 1986 to 2000. Maritz is an investor in the company, along with Pradeep Singh, who spent nine years at Microsoft in various management positions and left in 1994 to found Aditi Technologies, an Indian outsourcing company, Collison said.

I think one of the reasons for this move from the dark side can be found in another quotation from the same story:

"unlike 1999 one can do a startup on very thin capital, and that is the way we are going about it," Collison said. "One would have to be insane these days to take a traditional Series A round [of venture capital funding] with the open-source software and outsourcing opportunities that are out there."

In other words, it is the open source infrastructure that makes low-cost startups possible; and once you start using open source yourself, you begin to find that it's rather good, and realise that potential customers might think so too....

SAP's Success is Being Sapped

SAP is a strange company. Largely unknown to the general public (at least outside its native Germany), it is large, and until now, hugely successful in its chosen field of Enterprise Resource Management. It is also a dinosaur and doomed. Indicative of this is its very ambivalent attitude to open source, which some of its executives show little sign of understanding.

This story from the Reg confirms my suspicions: that its power is being sapped by rival closed-source companies. Just wait until the up-and-coming open source ERP companies start hitting their stride....

Open Source Evolution

Carl Zimmer is one of the best science writers around today. He manages to combine technical accuracy with a writing style that never gets in the way of his argument. So I was delighted to see this piece on his blog, entitled: "In the Beginning Was Linux?", which includes the following section:

Biologists have long recognized some striking parallels between genes and software. Genes stored information in a language of DNA, with the four nucleotides serving as its alphabet. A genetic code allowed cells to translate the information in genes into the separate language of proteins, which used an alphabet of twenty amino acids. From one generation to the next, mutations introduced slight tweaks to the software. Sex combined different versions of subroutines. If the software performed better--in the sense that an organism had more reproductive success--the changes might become incorporated into the genome across an entire species.

Now, this is amusingly close to the opening chapter (and central idea) of Digital Code of Life, but Zimmer goes further by drawing on the theories of Carl Woese, one of the most original thinkers about how life might have evolved in the earliest stages. It would take too long to explain the details to non-biologists, so I won't attempt it here - not least because Zimmer has already done with customary clarity in his post. Do read it.

EU Software Patents Battle 2.0

Florian Mueller, who did more than most to rally people against the software patents directive in the European Parliament, has flagged up the next - and potentially even more serious - threat from software patents.

This time, though, it's couched in rather obscure terms. The battle is not about allowing software patents "as such" - since they are explicitly forbidden in Europe - but about how litigation over patents should proceed. The point is, if the current proposal for something called the European Patent Litigation Agreement (EPLA) goes through, the European patent offices, many of which are happily handing out software patents, would have enormous influence over the litigation of such questionable patents, which is hardly right, methinks. As Mueller explains:

The legal status of software patents in Europe is contradictory. While the existing written rules, which go back to the year 1973, disallow patents on computer programs “as such”, the European Patent Office (EPO) and various national patent offices have granted tens of thousands of software patents. However, European patents, even if granted by the EPO, can only be enforced country by country as of now, and national courts declare many EPO software patents invalid when their holders try to use them against alleged infringers. Critics argue that the EPLA would create a new court system that would be under the control of the same group of government officials who already govern the EPO, and that the judges appointed by those people would support the EPO’s granting practice and its broad scope of patentable subject-matter with respect to software and business methods.

It's still very early days for the EPLA, but fore-warned is fore-armed.

Moroccan Fisheries Escapes Proprietary Net

Not my title, I hasten to add (though I wish it had been), but the one used by this article. The latter does what it says on the tin - a sardine tin, I presume, since Essaouira is a major centre for fishing said species.

Croats Have a Go at...OSS Policy

It seems that Croatia has joined the Euro-club of OSS enthusiasts. At least that's what I'm told. I really must get around to learning Serbo-Croat....

Update: More details in English here (with thanks to James Tyrrell.)

Towards a Wikipedia Done Properly

Larry Sanger's name has cropped up several times on this blog, so I was delighted to interview him recently for The Guardian. You can read the finished result here. Larry rightly takes me to task for the misleading headline and sub-head, but in my own defence I have to point out that I didn't write them.

A Study in Official Openness

It is probably hard for those outside the UK to appreciate the extent of the secrecy that has pervaded public life here for centuries. The clearest manifestation of this is the pernicious Official Secrets Act, which makes pretty much anything a secret if the Government says it is.

Against this presumption that the public has no right to know anything, the passage of the Freedom of Information Act in 2000 was a major milestone, and credit must be given to the current Government for finally making it a reality. This is especially the case since it is clear that the information released by Act is proving a major embarrassment at times, thanks to both an increasingly demanding public and a commendably independent commissioner, Richard Thomas.

As the foreword to his first Annual Report makes clear, he is acutely aware of the central position that his department occupies in today's world, where there is an inevitable tension between his two main tasks: promoting openness and protecting privacy:

Never before has the threat of intrusion to people’s privacy been such a risk. It is no wonder that the public now ranks protecting personal information as the third most important social concern. As technology develops in a globalised 24/7 culture, power increases to build comprehensive insights into daily lives. As internet shopping, smart card technology and joined-up e-government initiatives reduce costs, respond to customers’ demands and improve public services, more and more information is accumulated about us. According to one estimate, information about the average working adult is stored on some 700 databases. New information is added every day. Much of this will be confidential material which we do not want others to see or use unless we say so. There are obvious risks that information is matched with the wrong person or security is breached. The risks increase substantially as information is shared from one database to another, or access granted to another group of users. Real damage can arise when things go wrong – careers and personal relationships can be jeopardised by inaccurate information. Identity theft can involve substantial financial loss and loss of personal autonomy.

The vast majority of information that is held on adults, and increasingly on children, serves a useful purpose and is well intentioned. But everyone recognises that there must be limits. Data protection provides the framework. It raises questions about where lines should be drawn. What is acceptable and what is unacceptable? What safeguards are needed? What is the right balance between public protection and private life? How long, for example, should phone and internet traffic records be retained for access by police and intelligence services fighting terrorism? Whose DNA should be held, and for how long, to help solve crime? What safeguards are needed for commercial internet-based tracking services which leave no hiding place?

All power to Mr Thomas' elbow.

Of FAQs and NAQs

FAQs - Frequently Asked Questions - are one of the characteristic concepts of the online world, born, presumably, of a cheery belief that it is possible for experts to distill any given area into a few pithy questions and answers for the benefit of newbies.

But things are moving on. The Guardian has pioneered what it calls "Newly Asked Questions", and now we have a new kind of FAQ: "Frequently Awkward Questions", aimed at the entertainment industry. I imagine that others will follow in due course.

Why Microsoft Got Thwacked

If you were wondering what exactly the sticking point was that led to Microsoft getting thumped by the European Union, here's a helpful press release from the Free Software Foundation Europe. The central problem is the company's refusal to make documentation available that would allow GNU/Linux to interoperate perfectly with Windows, thanks to the Samba free software project:

"Microsoft is still as far from allowing competition as it was on the day of the original Commission ruling in 2004. All proposals made by Microsoft were deliberately exclusive of Samba, the major remaining competitor. In that light, the fines do not seem to come early, and they do not seem high," comments Carlo Piana, Milano based lawyer of the Free Software Foundation Europe (FSFE) regarding the decision of the European Commission to fine Microsoft 1.5 million Euro per day retroactively from 16. December 2005, totalling 280.5 million Euro. Should Microsoft not come into compliance until the end of July 2006, the daily fines could be doubled.

These fines are a reaction to Microsofts continued lack of compliance with the European Commission decision to make interoperability information available to competitors as a necessary precondition to allow fair competition.

Microsoft's refusal to comply - and its willingness to incur fines amounting to hundreds of millions of Euros - is a measure of just how worried it is about Samba in particular, and open source in general.

The release also points out how risible are Microsoft's claims that it cannot easily supply the requested information:

"If we are to believe Microsofts numbers, it appears that 120.000 person days are not enough to document its own software. This is a task that good software developers do during the development of software, and a hallmark of bad engineering," comments Georg Greve, president of the FSFE. "For users, this should be a shock: Microsoft apparently does not know the software that controls 95% of all desktop computers on this planet. Imagine General Motors releasing a press statement to the extent that even though they had 300 of their best engineers work on this for two years, they cannot provide specifications for the cars they built."

Open Access...to Search Spam

Open access is usually about being able to read high-value texts that are normally only available for a correspondingly high fee. But, in reality, it's about access for free to stuff. For example, as Open Access News points out, you can have open access to "value-added" search spam data (and note the scrupulously precise use of the CC licence at the bottom).

OpenDocument Fellowship Rings the Changes

ODF just goes from strength to strength, as many posts on this blog attest. One of the main organisations pushing the standard is the splendidly-named OpenDocument Fellowship, even if it tends to keep a low profile (maybe it's just because I'm a member).

It has recently redesigned its Web site, and it's well worth taking a look for the useful ODF resources to be found there. These include introductions to the whole ODF idea, a handy list of applications that support ODF, the latest news and members' blogs with postings on related matters.

Of Sakai and Moodle

Sakai may not be a name that is known to many in the world of free software, but it's one of the leading open source projects in the field of education. IBM has certainly heard of it, having just donated a goodly lump of code to the project. And if Sakai proves of interest, you probably ought to check out Moodle, too.

The (Firefox) Fur Begins to Fly

As Firefox teeters on the brink of the first 2.0 beta, things are starting to get serious. No longer are we talking about a flash in the pan: Firefox is now a real, established rival to Internet Explorer, as these numbers from OneStat.com indicate.

Of course, there's a lot of variation in the degree to which Firefox has been adopted, from highs like Germany, with a stunning 39% using Firefox against 56% sticking with IE, to the snivelling Brits, of whom barely 11.5% use the Fox, while 86% cling to Uncle Bill.

The arrival of IE 7 will have an impact, but there's no doubt that Microsoft has left it far too late to roll back these kind of gains (even in the UK).

Wiki in the City

If you've ever wondered what might befall an innocent little wiki in hands of a serious investment bank, take a look at this. It's detailed, and the case studies are particularly interesting.

Open Access... as Haiku

If you don't have time to read through Peter Suber's full explanation of open access, you could always try his haiku version (this isn't new, but I've only just come across it). A sample:

I love print, paper.
But I love searching, linking,
using, sharing more.

...

They don't pay authors,
editors or referees.
Then they want the rights.

...

Sure, change copyright
and peer review. But OA
doesn't have to wait.

Apache Starts to Patch the Holes

The latest Netcraft survey shows that Apache has pulled back some of the ground it lost to Microsoft's Web server last month. There have been some pretty massive swings recently, as the oscillations in the graph show: these are largely due to switches in the hosting sector, which can often involve millions of Internet names at a stroke. For example, Go Daddy moved over 1.6 million hostnames from Apache to Microsoft's IIS platform in June.

These new gains for Apache are important, because it suggests that Microsoft's relentless campaign to "convince" hosting companies to switch to its products (and who wouldn't love to be a fly on the wall for those conversations?) may finally have run out of steam. It will be interesting to see what happens next month.

How the Stacks Stack Up

The ever-interesting Steven Vaughan-Nichols, who goes back a long way in the free software world, has a fascinating article about a comparison of two application stacks, one open source, the other from Microsoft. The results were surprising:

The tests showed that such vanilla LAMP (Linux, Apache, MySQL, PHP/Python/PERL) stacks as SLES (SUSE Enterprise Linux Server) 9, Zope, ZODB, and PHP and a pure LAMP based on SLES, produced "C" results. They weren't bad, but they weren't anywhere near as good as an out of the box .NET stack based on Windows Server 2003, IIS (Internet Information Server), SQL Server 2005, ASP (Active Server Pages), and SharePoint Portal Server 2003.

The results mirror those of the Mindcraft tests back in the late 1990s, when GNU/Linux found itself whupped by Microsoft. But the consequence was a range of improvements that soon took free software past Windows. However disappointing the current outcome for the stack tests may be, I'm sure that the same will happen here.

Remember: every bug report makes open source stronger, and the same goes for adverse benchmarks.

DejaVu All Over Again: Open Source Fonts

Last month I commended Hakon Wium Lie's call for open source typefaces to replace the de facto standard based on Microsoft's fonts. And here's an interesting article about a project called DejaVu that might just do that. The piece has some interesting background information on both DejaVu and its predecessor, Vera.

Microsoft ODF Plugin Story Gets...Richer

When I wrote about Microsoft's announcement that it would be sponsoring a project to create an ODF plugin for its Office product, I said the story was big. But I was wrong: it's actually really big, because of a deeply ironic twist to the story, detailed on Groklaw:

It seems that when Microsoft was looking to build its new ODF plugin, it took a short cut. It seems to have grabbed some code from the OpenDocument Fellowship's program that converts ODF to HTML, written by J. David Eisenberg. His code is released under a dual license, the LGPL and the Apache 2.0 license. Microsoft has put it into its ODF plugin, which is licensed under the BSD license.

Is that allowed? It's nice Microsoft endorses the value of the ODF Fellowship code, since they are forever telling us their own code is better. But we're trying to parse out which license Microsoft thinks it is complying with. Not the LGPL, I trust. My question, and I'm no Apache guru, is what about Apache sections 4.1, 4.2, 4.3, and maybe 4.4, plus the required form of notice in the Appendix? It's certainly possible I'm missing something. But it seems it may be Microsoft that neglected to notice some requirements.

A Straw in the Californian Wind?

Newspapers tend to keep their constituencies firmly in mind when they are writing. So you might expect the Los Angeles Times to be beating the drum for Hollywood fairly unthinkingly. And then up pops this editorial on various US proposals to give entertainment industries even more of a stranglehold over content, which concludes:

As they weigh the entertainment industry's pleas, lawmakers shouldn't assume all consumers are bootleggers and every digital device is a hand grenade aimed at Hollywood.

Very interesting: if Hollywood's local newspaper is daring to write this, maybe a few other people in the vicinity are starting to think this way too. (Via TechDirt.)

It's a Dog's Life

One of the fascinating things that I learned when I was writing Digital Code of Life is that many diseases - such as obesity, heart disease, diabetes, certain kinds of cancers and neurodegenerative disorders - are not commonly found in the great apes. As I put it then:

In a sense, the human genome has evolved certain advantageous characteristics so quickly that it has not been debugged properly. The major diseases afflicting humans are the outstanding faulty modules in genomic software that Nature was unable to fix in the time since humans evolved as a species.

Another extraordinary fact is that dogs are even more susceptible to these same diseases than humans are, and for the same reason: the domestic breeds have arisen so recently, and from limited populations through inbreeding. But if dogs are like us, only more so, then they also hold out the hope that by investigating the root causes of their afflictions we might be able to understand our own better.

I see that further steps in this direction are now being taken:

Melbourne researchers are examining the DNA of dogs in a research project aiming at determining the genetic causes of common pet diseases – and to provide a model for combating diseases such as diabetes and multiple sclerosis in humans.

Malodorous Acacia

I've written about what promises to become the patent troll extraordinaire, but here's another, er, specimen. C|net introduces us to the head of Acacia Technologies Group, but don't be fooled by the name. Its patent-based business is anything but fragrant, despite what the interviewee might have you think:

It's the patent system that enabled people like Thomas Edison who actually developed the new technologies, which these companies then want to use to make money without paying for. The invention process is critical to the growth of the US economy and it's the smaller companies that usually come up with the new innovations and disruptive technologies that then the larger companies want to adopt. There's no one forcing them to add these features to their products. Obviously, they're doing it because they can make more money using the new features that were patented by someone else.

For a thoroughgoing refutation of this and other widespread misconceptions about patents and copyright, do read the brilliant Against Intellectual Monopoly by Michele Boldrin and David K. Levine, freely available from here. (Via TechDirt.)

The Smiley's Sad Tale

The smiley is a defining icon of the online generation. But as this article points out, it is also likely to go down as yet another enclosure of the virtual commons, a victim of insensate corporate greed, as companies battle it out for the "right" to claim this symbol as their "own".

The Other WWW: World-Wide Wikipedia

Wikipedia is deservedly famous, but there is a tendency to conflate Wikipedia with the english version of it. One of Wikipedia's many great achievements - alongside its huge size and the innovative partipation of large numbers of people - is that it is energising communities all around the world to create local versions in languages other than English. There is a list of the main languages at the foot of the main English Wikipedia page.

As Wikipedia explains:

Language editions operate independently of one another. Editions are not bound to the content of other language editions, nor are articles on the same subject required to be translations of each other. Automated translation of articles is explicitly disallowed, though multilingual editors of sufficient fluency are encouraged to manually translate articles. The various language editions are held to global policies such as "neutral point of view", though they may diverge on subtler points of policy and practice. Articles and images are shared between Wikipedia editions, the former through "InterWiki" links and pages to request translations, and the latter through the Wikimedia Commons repository. Translated articles represent only a small portion of articles in most editions.

Given this global diversity, and the lack of appreciation of efforts outside the Anglophone world, it's good to see that this three-way interview with leading Wikipedians includes voices from Germany and Japan as well as the obvious English one.

Microsoft's Open Source Windows

It looks like at least one person at Microsoft gets it:

One of the things that I’d like to see us do as a company is release a free, Open-Source, stripped-down version of Windows. There are so many benefits, IMO. We could cut out much of the “integration and innovation” and ship a bare-bones, essentials-only operating system with source that would allow the Open Source community to take a look at our code and really build on it. As SaaS (Software as a Service) and Web 2.0 apps take center stage, there is less and less motivation for customers to plunk down their dollars for a completely proprietary OS, and I see Linux gaining steam in that environment unless we are able to do something significant.

Now, the interesting question is whether this is an officially-sanctioned bit of kite-flying or not. I don't think it is; but I do think we will see an open source Windows one day.... (Via Digg.)