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July 31, 2008

The Goldilocks processor

If there is one thing that troubles processor architects right now, it's working out how many cores they should stick on a die. The number of transistors they can plant on a chip doubles every two years and there's no sign of that supply running dry in the next five years.

What's the problem? Just take the processor core you have already and then step and repeat it across the die. It's worked for graphics processors.

Unfortunately, only some software parallelises so well that it will spread across many cores. Many times, the overhead of distributing the work outweighs the advantage you get from running the code in parallel. This, in effect, is the modification that Gene Amdahl made to his eponymous law of performance in computers.

In its most basic form, Amdahl's Law says it's only worth speeding up things that you do a lot. Big, nested loops are good targets. Lots of branching straight-line code? Not worth the effort. With parallel processors, if you can spread the work of loops over many of them, you see a speed-up. But there is a limit governed by how much code you need to run on just one processor.

In a paper published in this month's IEEE Computer, a pair of researchers from the University of Winsconsin-Madison - one of whom has now moved to Google - has attempted to extend Amdahl's Law to the world of multicore processors where you do not necessarily make all the processors the same size.

Up to now, most of this kind of spreadsheet-based performance estimation has concentrated on what happens if you make all of the processors the same. Last year at the Design Automation Conference in San Diego, Intel's Shekhar Borkar, looked at the trade-offs facing the company as it looks at the possibility of moving from four to eight and sixteen-core chips to designs in the next decade that could support thousands of on-chip processors.

Borkar cited Pollack's Rule, which says the performance increase of a processor is roughly proportional to the square root of the increase in its complexity. Put another way, if you double the number of transistors in a processor, the chances are that you will only get a speedup of about 40 per cent.

In this environment, having lots of fairly simple cores looks to be the favourite option. But, power becomes a big, big problem. Borkar noted that simply sticking slavishly to this plan would have a devastating impact on power consumption, because all of the energy is used to support the interconnect that feeds all the processors.

Using 100 much more complex, bigger cores would bring the power needed for the mesh down by a factor of ten to just 15W. "What we need is a really careful balance," he said. "Just because we can integrate thousands of cores, don’t get carried away and implement a thousand cores."

Tilera's Anant Agarwal defined his own version of Pollack's Rule: the Kill Rule. This says: "A resource in a core must be increased in area only if the core’s performance improvement is at least proportional to the core’s area increase."

Agarwal reckoned that dual-issue superscalar processors will become the norm as they largely satisfy his Kill rule, although there is a broad spread of those designs. A complex dual-issue architecture might need 15 million transistors, including cache. The simpler designs offered by companies such as ARM and MIPS Technologies, which rely more on the compiler’s ability to schedule instructions effectively, might be squeezed into a 5 million transistor block.

The argument from Mark Hill and Michael Marty from the work at Winsconsin-Madison is that you can do it all. With enough transistors to play with, you can have some brainiac superpipelined, superscalar monster that gets to work on all the straight-line code and have lots of smaller, simpler processors get on with the parallelisable stuff.

They show, for a very large array, the monster-plus-servants approach shows reasonable acceleration for code that is 90 per cent or more parallelisable and certainly performs better than the situation where all cores are equal.

There is a warning here. This assumes that your only constraint is the number of transistors. It doesn't take account of interconnect overhead or power consumption. But it's a result that tends to vindicate the asymmetric design of the modern PC if you start to use the GPU for acceleration.

Where the gains could be greater is in the idea of a reconfigurable array. The idea is that you make a monster processor out of lots of little ones. The speedups on this look great. Then again, given that nobody knows how to make this kind of machine, you would hope so.

The problem is that big processors are not made out of little ones. It's more that, inside every monster processor there is a little one and a chunk of stuff that tries valiantly to keep shoving data through that processor. You can't easily turn processors into prediction and speculation units, at least not with current architectures.

Hill and Marty argue that, despite this, it is a result that is worth closer inspection. What if you could reorganise processors to act as speculation units? Or maybe come up with new architectures that can be split apart and recombined as needed? There is one architecture that looks as though it could be a contender for a separable architecture: this is the TRIPS processor out of the University of Texas. It starts out as an array of processors with an instruction-scheduling scheme that pulls them into virtual machine.

TRIPS calls for a change to software compilation. You also have the work on speculative compilers such as Codeplay's Sieve-C, which runs on regular combinations of PC processors and GPUs. This is designed to work on parallelisable code - it expands the amount of software that can be run in parallel by allowing it to make mistakes and then fixing them afterwards. This kind of strategy might be used to have all the speculation work performed in today's monster processors done in software on a bunch of simple processors.

There are no ready answers, but Hill and Marty have indicated some areas where it might be worth computer architects looking, just as long as the performance predictions aren't completely knackered the minute you invoke power consumption or interconnect overhead.

Posted by Chris at 12:53 PM | Comments (2) | TrackBack

"We only send the releases out, we don't actually do anything"

Yesterday, yet another in the wave of "press release distribution companies" sent me by email a release for femtocell-maker Ip.access. So far, so good. "Femtocells," thinks I. "I'm writing something on femtocells, better have a look."

It's nothing more than saying the company has a white paper on how funky femtocells will be. But, there is a chance there could be something useful in it and I was just beginning to line up interviews. So, I first went to the link to download the file...and found out I need to fill in a form to get it. I'm not over-fussed about filling in a form but, as this is likely to go into some form of CRM system, I figure it's just as easy to save a salesperson a call and get it from the PR. Who, of course, will be named at the bottom of the release and set up the interview at the same time.

I hit Reply and start banging out the email only to notice an odd bit of text in the introduction "...please do not hesitate to contact them via the details below". Then I realise that Neondrum, who sent the release is only distributing the release, with all the usual disclaimers: "[We] cannot accept any liability whatsoever for the inaccuracy or otherwise of any information contained in this news release" etc. All they're going to do is tell me to contact the client. OK fine.

But there are no other contact details.

I asked Neondrum to send them over. Ten hours later (in the meantime, I'd found that CompanyCare had been looking after Ip.access and contacted them directly) I got a reply:

"Sorry, the introductory message was badly worded - ip.access haven't provided a specific contact for this media advisory, if you want to find out more you need to download the paper."

Thanks. That's so helpful. And from a company that publishes a booklet that it claims contains ten top tips for online PR. I wonder if "always provide a contact number" is in there. I'd find out, but you have to register as a client at Neondrum to stand a chance of getting it. If someone has a copy, send it over, I could do with a laugh.

Posted by Chris at 10:33 AM | Comments (2) | TrackBack

Did Cuil get its launch wrong?

The hype cycle works quickly these days. At about 9pm US Pacific time, Techcrunch published its first story on the search engine startup Cuil. It was far from being the only site with the story around that time: the company had told a bunch of bloggers and journalists about its plans the week before with the aim of seeing it all come out in a big splurge on Monday, 28 July, 12am US Eastern.

A few hours later, the Cuil site died. Oops. But, no mind, just the effect of thousands of people hitting the site to see how it performed versus Google. "Flatlining right after your launch is more of a rite of passage than an embarrassment."

A day later and the euphoria had gone. "The story quickly turned from Google killer to Google's lunch."

Getting a backlash so quickly? "This was entirely the company's own fault. It pre-briefed every blogger and tech journalist on the planet, but didn't allow anyone to actually the test the search engine before the launch," complained Erick Schonfeld.

And you're surprised? Who says the old promotional tricks don't work?

I can't imagine that Cuil's management didn't know the search results would be terrible. So, what are you going to do? Let people play with it before the big unveiling and see a bunch of posts say: "Move along folks, nothing to see here"? Or are you going to pile on the statistics and the big claims and hope nobody notices there is a problem? With this kind of product, people are going to notice pretty quickly but there is the question of whether it matters.

Cuil got the backlash in early. In the old days, this kind of backlash would take weeks. It took just one fishwrap cycle for Cuil. But, this arguably gives the company the chance to recover or to simply fade away. Whatever they do next, there are a lot of people who will remember who they are. Can you say the same for Hakia or any of the other Google wannabes? (For what it's worth, I don't think any the putative Google replacements are going to get anywhere - the technology cycle doesn't work like that. Like rarely gets replaced with like unless the leader stumbles really badly. It's generally a different concept that shoves the old guard out of the way.)

A similar thing happened with the 'Ginger/Segway' launch, although this one played out in a different way. There was a lengthy "Ginger is coming. It will change the world" phase, helped along because the company concentrated on Dean Kamen versus the product. Then the Segway launched and everybody laughed. I still think it's a joke machine but they keep making them. And you don't find that many people who haven't heard of a Segway.

Tom at Tom's Tech Blog points to Sarah Lacy's criticism of the rush to publish that made so many writers publicly change their minds in less than a day. Her argument is that people should hang back, think a bit, then publish. That's a lovely thought. It is one I shall treasure. Because, although she's right on that score, in principle. Unfortunately, it doesn't work.

The current ad-driven business model for Internet publishing does not reward delay, no matter how good the analysis is. The initial burst of interest is the one publishers want to catch: waiting does not often get you a big audience. And, although the marketing consultants bang on about 'conversation' and 'engagement', the sites making money off of publishing need audience to sell ads. PRs also know this and exploit it: that is what they are paid to do. It's very easy to forget while doing interviews, especially under embargo - I know that I forget it all the time - but you always have to be thinking: "What have you kept hidden and why?"

For every piece of placebo-tech in the briefing - "it's got relativity powered indexing for improved relevancy scoring" - there's a caveat. Spotting the caveats is, however, more than half the fun.

Posted by Chris at 9:15 AM | Comments (0) | TrackBack

July 30, 2008

ARM's latest architectural licence: sold to its first ever customer?

ARM hinted about this deal in an analyst meeting last week, but the company this morning confirmed that it has sold an architectural licence for its processor architecture to "a leading handset OEM...to develop a roadmap of mobile computing devices". The company is not saying who the customer is but a lot of the signs point to Apple.

Nokia decided to outsource much of its silicon design and the company has traditionally bought the off-the-shelf ARM cores anyway, which Texas Instruments then put into system-on-chip (SoC) parts. Motorola already has an architectural licence. Samsung would be a possibility as the world's second largest chipmaker, but signed a big deal with ARM earlier this year to get early access to ARM's own designs.

Following Apple's purchase of chip design firm PA Semiconductor, ARM people have been particularly jumpy of late whenever Apple gets mentioned. And questions asking whether Apple already has an architectural licence (the computer maker was the driving force behind the creation of ARM and one of the original investors) were met with a "you'll have to ask Apple", rather than a "yes", a "no" or a "no comment".

PA's designers have a lot of experience with ARM, although their most recent offering, which is getting dropped like a stone, was based on the PowerPC. ARM's investor meeting is about to start. But, realistically, if the company was going to say that Apple is the new architectural licensee, it would have done so already.

ARM CEO Warrren East just warned that it will take time for the company to see royalties from any products sold that use the processors licensed under the new arrangement (9:20): "It is an architectural licence with a leading OEM for both current and future technology. Don't get too excited on any revenue on this: it will take some time. The revenue [from this deal] will be recognised over several years."

ARM's emphasis on this deal is that it is all about the future. Tim Score, CFO, said (9:38): "When ARM signs architectural licences, they are typically for an architecture that is already in play. So you tend to get a big revenue bump. This one is also for future architectures, so the revenue has to be spread over a number of years."

Posted by Chris at 9:07 AM | Comments (0) | TrackBack

July 29, 2008

A couple of quick thoughts on Google in the Knol age

Although Seth Finkelstein has debunked the idea that Knol is being promoted too heavily in Google's search listings, a lot of people reckon that the number-one search engine is rapidly losing its way. That Knol is a big mistake that results from policies that favour Google's ad business over its search service.

Knol is a magnet for the get-rich-quick brigade who reckon they can siphon off a load of money through ads for dodgy health supplements. It might work as a competitor to Squidoo, Mahalo and even Wikipedia. But, a lot will depend on the image that Knol attracts in the short term. It's got a good chance of becoming the .info of information and quick reference sites, where the only people who show up are spammers with slightly more original content.

But does that matter to Google? Regarding Google's business as being in search is a mistake. It's an advertising business. And one of the unfortunate drivers of the online classified ad business that the company now effectively dominates is that a bunch of people are only too happy to click on ads for the 'health supplements', teeth whiteners and other kind of products being actively promoted on Knol pages. They may well be the most active ad-clickers around.

There's a good chance that Google will make more cash out of the dodgier Knol pages than the ones designed to look more like entries in an encyclopedia.

People are misreading Google's slogan, "Don't be evil". It's not a slogan. It's an admonishment to those sucking on the Adsense teat: "Don't be evil...or we'll kick you off the search results pages. You can be a bit naughty, mind."

While things are good for Google, nobody will really care:

"You show them you have in you something that is really profitable, and then there will be no limits to the recognition of your ability. Of course you must take care of the motives - right motives - always." - Mr Kurtz, Heart of Darkness

Posted by Chris at 9:43 AM | Comments (2) | TrackBack

Policy of the day

Valleywag has picked up on Google-wannabe Cuil's policy of not collecting personal data on the surfers who use its search engine and asks:

Why isn't this their marketing slogan?

I don't know. Because the policy won't last?

Posted by Chris at 7:37 AM | Comments (1) | TrackBack

July 24, 2008

A note to Giles Coren: the subs are always right, even when they're wrong

In the case of Giles Coren's purple-tinged prose, the Times subs were right anyway. He complains that by interfering with the onanistic euphuism of his final paragraph, the subs ruined the money shot. Removing an indefinite article led to a premature conclusion. There was no firm climax for Coren, but the whimper of an unstressed syllable.

In the letter, Coren lets the Times, and now us, know that Soho is associated with sex. So the whole thing about "wondering where to go for a nosh" was very important. Should they ever resurrect Round the Horne, I'll be sure to point them in your direction.

The first commenter at Guido Fawkes (and no doubt commenters at other places, I didn't look that hard) pointed out that if dear sensitive Giles wants his glorious copy to never feel the cold caress of a sub-editor, he should give up writing for the Thunderer and just post reviews to a blog. He can be secure in the knowledge that no-one will ever cause him to be seen finishing a review with the indignity of an unstressed syllable.

I can just imagine the subs now doing all they can to ensure that Coren's promise is never broken. He will always go out with a bang. In the meantime, maybe the Guardian's Media Monkey can expect a spanking from the pishkeh of epistles.

Posted by Chris at 4:52 PM | Comments (0) | TrackBack

July 22, 2008

Let's all crowdsource a product nobody really wants

Techcrunch's Michael Arrington wants a web tablet and, not only that, he believes it will only happen if the design is crowdsourced, claiming that the machine doesn't exist. Oh really? I've seen loads of them. It's just that they tend to be prototypes in places like the Philips HomeLab.

If you look at the Philips Research site and poke around a little, you will find pictures of a device not a million miles from the Techcrunch mock-up being used as an oversized remote control. You can see an example below. Philips Electronics has a heavily stripped-down screen-based remote that you can buy in the shops as a kind of souped-up OneForAll.

The problem is not making a web tablet. I don't think it's even a case of getting the price down. It's working out whether you have a big enough market for the device to ship in high enough volumes to justify the wafer-thin margins needed to justify a $200 price on a product that has something like a 10in colour screen, processor, WiFi and a few gigs of storage.

Crowdsourcing can absolutely get the design done: hardware and software. Open-source hardware design exists. People have already worked out the licensing for that and mechanisms to make it work. The problem comes when you get to volume. Openmoko's Neo FreeRunner is a niche product - a mobile phone for Linux hackers - but in incredibly short supply. Distributors reckon they might - just might - get some by the end of July.

To get a product like this off the ground, you have to attract the attention of someone who has the money to get thousands slapped together and shipped over from China. And this is where you come face-to-face with the demand for a product like this. Or the lack of it.

If this thing has a regular LCD screen, it doesn't matter how little power you want from the processor, it will eat batteries for lunch, then sit plugged into the wall until it's ready for dinner. The only way to avoid that problem is to use a screen that does not depend on a backlight, which is what Amazon did with the Kindle, which is not all that far from the Techcrunch spec. Unfortunately, Firefox won't look that snazzy on the muddy greyscale screens of today's e-ink technology. But at least the batteries last.

OK. Let's take on the usage model. To be more than an iPhone, you need to work on it. So, Arrington postulates a virtual keyboard. That pushes the size of the screen up to around 12in and still leaves you with a problem. The optimum angles for viewing and typing are quite different, even if you can somehow touch type on a surface with no tactile feedback.

I get worried when the mock-ups from OLPC look feasible but, if you are going to have a screen-based keyboard, the XO-2 is likely to be more usable than the Firefox tablet that Arrington proposes. At least you can tilt the screen you use as a display to a decent angle without bending your wrists at unnatural angles. But, by the time you get that far, you are back at the good-old subnotebook, simply having replaced the keyboard with a second screen. And that, of course, is the product that Palm killed off last year, following several other attempts into obscurity.

The Firefox tablet looks great in principle - up to the point where you start thinking about whether you want to cough up the money needed to pay for one.

Posted by Chris at 1:37 PM | Comments (0) | TrackBack

July 21, 2008

How neutral is neutral?

Last week, Tom Watson, UK minister for transformational government – a title that makes you wonder if there will soon be a minister for leveraged e-government solutions – claimed Whitehall computers would be carbon neutral within four years. Apparently it would be achieved by switching them off more often. This must be some use of term 'carbon neutral' I haven't previously encountered.

Unless the plan is to run all of Whitehall's machines off solar panels, nuclear or wind energy alone, it's hard to see this plan being achievable without some serious massaging of the numbers. It's no bad thing that Watson wants to cuts the energy usage of government computers but does touting the target as being carbon neutral do anyone any favours. Because, all the Cabinet Office has to do in 2012 is buy enough offsets to make it happen no matter what the actual outcome is. All that happens in that case is that the public ends up forking out for a plan that it did not really want for the sake of a slogan.

It's easy to understand the attraction of saying "carbon neutral by 2012" but the whole project is potentially meaningless without some idea of the kind of energy savings the UK government aims to make. They are not even sure of the definition of carbon neutral. From page 2 of the plan entitled "Greening Government ICT":

"Works is ongoing with Defra to define Carbon Neutrality and how this can be delivered...These targets will be reviewed in light of the ongoing work in the definition of carbon neutrality."

OK. So we don't know what the target is because we have no definition for the conceptual target. Excellent. And if the definition isn't what was expected, we alter the target. Or buy some more tree-planting vouchers, although that is, at least, not a popular option:

"Off-setting to be seen as a last resort and only through an accredited scheme in line with Defra's code of best practice."

Given that it's impossible to make a computer entirely carbon neutral – at least given the current energy-supply mix – would it not have more sense, if not as attractive-sounding, to come up with some hard targets on how many kilowatt hours per machine central Government was aiming to cut? An idea of how much is possible if you put your mind to it is going to be a lot more useful to business than a lesson in how much you can get away with by purchasing greenwash tokens and messing with definitions.

There are some good things that can come out of the exercise.

It would be good to at least get a guide of the realistic savings that turning off personal computers at night and consolidating servers will really have. One big problem with modern computers is working out when they are actually off. Hitting the switch on the front does not necessarily do a great deal if you have an electronic switch inside tide to a 200W power supply. The only way to be sure is to pull the plug on it – will civil servants do that?

When it comes to servers, will this be the point that outsourcing and the use of public-private partnership contracts come home to roost? It is fine consolidating servers in principle but buying in a few licences of VMWare may be the easy bit. Who will guarantee the latency figures on servers that are run at very high peak utilisation rates?

The plan is bad news for PC makers and Microsoft because it puts a brake on how often hardware gets upgraded. If the only reason to upgrade a machine is so it can run Vista, that does not put Microsoft in a good position. However, if it focuses attention on fixing existing business software rather than forcing everyone into a constant upgrade spiral, that's likely to be better long-term.

Posted by Chris at 6:04 PM | Comments (0) | TrackBack

July 18, 2008

Progressive exaggeration

If you read the paper by Masahiko Inouye and colleagues at the University of Toyama on their production of the first lengthy chains of double-stranded artificial DNA you wonder how analyst Ruchi Mallya managed to come up with the idea that this stuff might be the future of green IT.

Mallya postulated "a biochip that will make standard computers faster and more energy efficient".

If you read the press release from the American Chemical Society, the publisher of Inouye et al's paper, you begin to see where that idea came from. However, there is a subtle difference in meaning:

"The finding could lead to improvements in gene therapy, futuristic nano-sized computers, and other high-tech advances, [the researchers] say."

The claim on the release is slightly more believable - we're not talking about trying to reinvent conventional computing here. But even that is a stretch from what the researchers themselves claim in the actual paper:

"The artificial DNA might be applied to a future extracellular genetic system with information storage and amplifiable abilities...This type of research is primarily motivated by pure scientific exploration and eventually directed toward biomedical applications."

And in the conclusion:

"...the present molecular framework has a potential for storing genetic information and for application to enzymatic replication directed toward engineered genetics. Furthermore, the artificial DNA may be a superior building scaffold for constructing nanostructures of materials interest because of the stable C-nucleosides against ubiquitous naturally occurring enzymes such as DNase."

There is no mention of computing in the paper, just the application to information storage and in the widest sense possible. I've covered some of the potential applications mentioned by the Toyama team in the earlier blog post. But it's worth noting that the paper does not go into the applications in any detail: it's all about the artificial DNA, how they made it and how it behaves in vitro.

The research is so new, they have barely had time to explore the possibilities of replacing the standard bases in DNA with unnatural variants. They were also careful not to move too far away from structures found in conventional DNA to ensure that it would behave normally. Future work by them and others is likely to see how far you can diverge from the structure that nature evolved.

From the perspective of the ACS, maybe this progressive exaggeration doesn't matter. The paper has received a lot more attention because of the claims made for it rather than the claims made in it. But it's a clear case of how using tiny snippets in information without recourse to the original material can lead to crazy conclusions being drawn.

Posted by Chris at 10:58 PM | Comments (0) | TrackBack

GATC: in computing, it spells slow

Datamonitor analyst Ruchi Mallya has taken a quick look at the production of the world's first strands of DNA of reasonable length that use artificial molecular groups in place of the guanine, adenine, thymine and cytosine groups found in the natural stuff. The piece asks: is artificial DNA the future of computers? Jack Schofield at the Guardian asks, naturally, is it going to be the case?

I have a short and simple answer. No. Not even close.

You can use DNA for computation but you wouldn't use it to replace any existing form of computer. It's just too darn slow. And there does not seem to be a realistic way of making logic circuits using DNA that even approach the complexity of today's silicon-based machines, let alone computers in 20 years' time.

The group that has arguably done the most work on DNA computing is at Caltech. I've seen Georg Seelig talk a couple of times on the topic and he is realistic about the potential uses for the technology.

"What is realistic is a few thousand components. We won't get to having millions of components in the same test tube," said Seelig at a recent meeting at the Royal Society.

The processes involved in coercing DNA to compute things are orders of magnitude slower than those in modern computers. If you look at Seelig's 2006 Science paper, you will notice that the graphs are marked in hours. It takes at least an hour for the DNA equivalent of one logic gate to fully switch from one state to another.

People tend to look at DNA as being just a code in which the only important aspect of the double helix is the order in which the four bases appear. And so, it's an easy leap from the concept of code to that of a computer. There is a growing body of evidence that the shapes that DNA adopts play a major role in the polymer's behaviour. This should not be a surprise: shape plays a vital role in reactions mediated by enzymes.

In chromosomes, DNA sequences that are rich in AT pairs are often the sites of 'promoters' – lengths of DNA that unzip more readily than others. This gives the enzymes that transcribe DNA a toehold from which they can crawl along the DNA that makes up each gene.

AT-rich sequences do not just unzip easily. They are bent in a way that makes it easier for the transcription enzyme to stick in some cases but prevent this process in others. Sometimes, the DNA is bent to prevent transcription taking place and it is only when other enzymes attach and alter the shape of the DNA that transcription can get under way. It is these subtle changes that seem to give DNA its versatility.

Seelig has found that by tuning the DNA sequences, it is possible to warp the DNA into complex shapes that react faster. But you are still talking about processes that are at least one thousand times slower than those in silicon.

So, if it's slow and nowhere near as scalable as the silicon transistor, what is DNA computing good for? Doing stuff in living cells. This is why people are investigating artificial DNA. They want something that won't poison a cell but which won't be treated by the cell in the same way as regular DNA. You don't want your smart drug becoming a kind of virus.

The idea is that you could introduce the artificial DNA into cells and have it work out what type of cell it is in. The DNA that forms the 'computer' might latch onto part of a gene or a piece of RNA - which can form double-stranded helices with matching DNA. That process might prevent a DNA logic gate from closing, or activate one and ultimately release a drug or a marker attached to another piece of the DNA computer.

Another reason for using artificial DNA is that it might stand a better chance of escaping destruction inside the cell. Every cell has enzymes designed to break down DNA – it's a good defence mechanism against viruses. They look for certain sequences of bases and then break the DNA at those points. Cells protect their own DNA by tacking on chemical groups to the vulnerable links.

If you want to put the DNA for a smart drug into a cell, you either need to protect the DNA in the same way, which complicates production of the artificial DNA. Or you can use DNA that the restriction enzymes do not recognise. That's why artificial DNA may turn out to be better.

Masahiko Inouye of the University of Toyama said the artificial DNA they have produced should resist attack by restriction enzymes but they have yet to test this. So far, what they have done is design bases analogous to the natural versions that have similar shapes and properties to see how sensitive DNA structure is to these kind of changes. The artificial DNA behaves very similarly to the normal stuff, which suggests that the sensitivity is quite low.

In the UK, Philipp Holliger at the Medical Research Council in Cambridge has made fluorescent green DNA using fluorophores tacked onto the natural bases. These molecular groups are pretty big but even with a fairly high ratio of modified bases to the normal ones, the DNA still formed a double helix, albeit a lot fatter than the one that Watson, Crick and Franklin uncovered.

Holliger wants to go further. "The hope is that we will not be limited to four nucleic acids in our alphabet in the near future," he said.

Artificial DNA has one potential use that is at the border between computation and materials science. Because it is possible to coax DNA into interesting shapes, it could be used to design new materials with complex internal structures. You might use unnatural bases in this structuring DNA to bind to the core material – naked DNA is surprisingly brittle.

Posted by Chris at 9:27 PM | Comments (0) | TrackBack

When memes attack

If you've seen a blog in the last week or so, you've probably noticed people going through a list of 100 books supposedly put together by the US National Endowment for the Arts' Big Read programme. I first came across it at the Diary of a Wordsmith, who has spotted two versions. One is the "US version" and one is the "UK version". But, there is no US version.

The blog meme has become the social networking equivalent of the chain letter and, often, contains about as much truth. The claim behind this top 100 list is that the NEA has put out this list to publicise a reading programme, claiming that the average American has read only six of the hundred titles the "NEA has printed".

I was about to comment at Diary of a Wordsmith about the strange collection of books the NEA has listed and, in full anorak mode, point out that it's odd that Joseph Conrad's "Heart of Darkness" is on there and it's not really a book. OK, just about every English-language edition appears in a volume called Heart of Darkness, but the story itself is a novella. You also have the "Complete Works of Shakespeare" at number six accompanied by "Hamlet" at number 98.

There is also a little bit of weirdness in that number 51 is missing. I can tell you that the missing book is "Life of Pi" by Yann Martell. How do I know? Because the list is not at the NEA's Big Read site but taken from a March 2007 story from the Daily Telegraph. The list was the result of a poll taken for World Book Day intended to find a shortlist of ten.

What seems to have happened is that someone found the list and posted it at the DigitalSpy forum at the start of June, asking people to fill in what they had read. By 25 June, the list had wandered into LiveJournal, kicking off with a bunch of Doctor Who and Torchwood fans. I can't find a direct link but the large presence of Russell T Davies fans on DigitalSpy is probably a clue. By that time, the list was now linked to the ideas of the NEA Big Read and the six out of one hundred claim, which seems to have its roots in the UK's Six Book Challenge, although it's hard to be sure as so many different elements have been conflated.

In between June and now, the list crossed over into the world of blogs and number 51 mysteriously disappeared. I haven't worked out when but Google probably has an answer. I'm just trying to work out a search query that will find it quickly. And how the "UK version" of the list came about given that the original list originated from the same country. Yes, I am beginning to wonder whether I've taken this a bit far.

But, I'm fascinated by the ease with which these memes take over on the flakiest of facts. It says a lot about the web of trust that links people together. These factoids get passed on because people want to believe that people they know tell them the truth. And it leads to awful misconceptions.

Last year, I received a chain-letter email supposedly about those evil Iranians crippling a child criminal by driving a car over his arm. This one had gone right round the houses with, naturally, howls of outrage.

There was only one problem. The pictures were of a street magician and his son doing a trick that Penn and Teller do with a 18-wheeler. Basically, you bung a load of weights on one side of the vehicle so that most of the pressure is on only one set of wheels. You then drive over the 'victim' so that the wheels of the opposite, and much lighter side go over them.

In the case of the top-100 books meme, it's a case of no bones broken. If it makes people read more books, that's all to the good.

But the Internet now helps the crap travels so much faster that the truth doesn't get past wondering where it left its boots.

Posted by Chris at 6:38 PM | Comments (1) | TrackBack

Oh no, not the DNA computer again

Ruchi Mallya, an analyst at Datamonitor has pored over a paper on the creation of the first long chains of DNA made using artificial bases in place of good old guanine, adenine, thymine and cytosine. And come to the conclusion that it might be the future of computing.

The answer is no, it isn't. While writing the long answer, I felt I just had to point to this paragraph:

"In addition, unlike today's personal computers, DNA computers require minimal or no external power sources, as they run on internal energy produced during cellular reactions."

Yes, processes involving DNA don't involve a lot of energy. But cells don't produce energy, they only convert energy they have managed to store. If they did produce energy, who needs oil? We could run the world on adenosine triphosphate. It's good stuff, you get through kilos of it every day. But it just happens to be a good way of delivering energy, not creating it.

Posted by Chris at 4:27 PM | Comments (0) | TrackBack

July 15, 2008

Welcome to the world of yesterday tomorrow

Cisco decided to hold an open day at its recently refurbished demonstration centre in Bedfont Lakes, one of those anonymous business parks almost unknown to public transport lying halfway between Heathrow Terminal 4 and the Feltham Young Offenders' Centre. No, really, it's lovely.

Apparently, we were supposed to be able to see and play with demos of a "self-learning artificial intelligence", "a high-street shop of the future", "technology being deployed to support disaster relief", "the future of healthcare" and "experience a Cisco TelePrescence meeting".

"We hope to demonstrate some cutting edge and future concept applications of Cisco's technology - which use the power of the Internet to deliver some very powerful applications," gushed the invitation.

The reality? Let's step back, back in time to about, ooh, 1998. The self-learning AI turned out to be a flashback to the agent technology of the late 1990s, tricked out with a slightly more realistic avatar that did weird things like lean into the screen until you could only see its eyes. I am still mystified as to where the self-learning came in as the natural language processing seemed to come entirely from off-the-shelf Microsoft software and the agent was apparently programmed to obey 'business rules'.

The future of healthcare was our old friend telemedicine. This time around the video looks better. You'd hope so as it was chewing up about 5Mbit/s in each direction and on modern codecs versus the 2Mbit/s-max with MPEG2 of last decade's telemedicine trials. According to Cisco, telemedicine is all better now because it uses networks rather than point-to-point links.

What could follow that? Why, yes. Video on demand. By this time, I'm looking around for a blue Police box. Yes, the bandwidths we are dealing with now mean it's HD video-on-demand and it's delivered over IP. Yet, so little else seems to have changed.

The shop of the future was arguably the scariest demo. Picture this. You have in your hands an iPod Touch or iPhone that lets you log in when you enter the store just so it can show you some special offers and plot a path through the emporium using WiFi routers that track your handheld. And we were definitely dealing with a pre-Cluetrain shop of the future as the idea was to "cross-sell and up-sell" the customer. I am absolutely going to log into a store with my pocket computer so I can get up-sold. Oh yes.

Disaster relief was MIA. Instead, it was about tracking hoodies via CCTV with image recognition. Stop me if you've heard this before, won't you?

And so we were in for the finalé. A videoconference telepresence demo. I could see the point of this as, having visited the Computer Laboratory at the University of Cambridge on Friday, where the videoconference suite does not get a whole lot of use, this was one demo that actually made you think that, only 40 years on, the world might just be ready for videoconferencing. Then again, with three gigantic plasma screens and a two-way link crunching through some 15Mb/s of bandwidth, you'd hope it would look good.

If anything, the telepresence demo was a testament to the way that bandwidth prices – if not costs – have plummeted in the last ten years. It may be the one thing that pushes telepresence into mainstream business. But, let's face it, we hear about telepresence and videoconferencing whenever a recession threatens a clampdown on business travel. And, up to now, the technology has slunk away into the corner as people realise they can get just as much done on the phone and, if they're feeling adventurous, a WebEx session (admittedly now a part of Cisco).

I wonder we'll go through another ten years before seeing this collection of technologies get together for a reunion or whether, this time, maybe, just maybe...

Posted by Chris at 6:56 PM | Comments (0) | TrackBack

July 1, 2008

Google thinks you know what you mean, just not what you think you mean

OK, I'm going to lay off the "big bucket of bits is all you need" theory of science, computing and the future in a minute.

But not before this example of where simply using the relative frequency of words to perform spelling correction breaks down.

Posted by Chris at 4:47 PM | Comments (0) | TrackBack