On the verge of creating synthetic life

Craig Venter made headlines back in 2001 for sequencing the human genome, then he went on to trying to map the oceans biodiversity, and currently he’s working on a project to create the first synthetic lifeforms – micro-organisms that can produce alternative fuels, and according to this presentation … hes very very close to achieving that!

The talk covers the details of creating brand new chromosones using digital technologies. What makes this so amazing is that this technology has the potential to change the world, it would allow humans to create Synthetic Bacteria that are engineered to perform specific reactions: produce fossil fuels, make medicines, combat global warming1 etc.

In a recent interview with New Scientist Venter described how this technology would hopefully reduce our dependency on fossil fuels2:

Over the next 20 years, synthetic genomics is going to become the standard for making anything. The chemical industry will depend on it. Hopefully, a large part of the energy industry will depend on it. We really need to find an alternative to taking carbon out of the ground, burning it, and putting it into the atmosphere. That is the single biggest contribution I could make.

Not everyone seem’s too happy with this, with accusations that Venter is trying to play God. How much you subscribe to that view depends on one’s own religious perspective. I was encouraged to come across a wonderful critique that addresses this question from a Muslim perspective, which is well worth reading3, the author offers a conclusion of sorts:

I approached Dr Venter after the lecture and asked him whether any religious groups had raised objections about his work (I do wonder what he thought of a hijab-clad woman asking him such a question). He replied in the negative, reminding me that his work did not begin until the project had been subjected to a 1.5 year ethical review. He in turn asked me: “Why? Should there be [any objection]?”. After hearing the facts, and mulling it over, the only answer that came to my mind was: “No”, and upon further reflection, I still stand by my answer – and Allah knows best.

If Venter succeeds the implications specifically for the Pharmaceutical and Chemical Industries as well as the world at large are profound.

  1. http://www.telegraph.co.uk/news/main.jhtml?xml=/news/2007/06/08/nbiofuel108.xml[back]
  2. New Scientist, Issue 2626 page 57[back]
  3. MuslimMatters.org, Craig Venter Playing God[back]

The Web’s secret stories

Here’s another wonderful ted talk, this time by Jonathan Harris

Jonathan wants to make sense of the infinite world on the Web — so he builds dazzling graphic interfaces that help us visualize the data floating around out there. He presents “We Feel Fine,” which uses a technique called passive observation by scouring blogs to collect the planet’s emoti(c)ons. It’s an amazing social tool. Jonathan also presents and the “Yahoo! Time Capsule,” which preserves images, quotes and thoughts snapped up in 2006. And he premieres “Universe,” which presents current events as constellations of words — a tag cloud of our collective consciousness

The visualisations they have implemented across these applications are absolutely amazing . I’m very very impressed.

Google doesn’t seem to like the idea of Microsoft merging with Yahoo!

Unless you’ve been hiding beneath a rock then you are probably aware of the news that Microsoft has offered $46 Billion to buy Yahoo! When I first heard this news I thought I couldn’t help but feel that in many ways it was an admission that as things stand it really cant compete with Google. Yahoo has certainly been struggling lately and current trends seem to suggest that this situation doesn’t look like it’s going to improve any time soon, particularly since Yahoo! revenue, like Google, is advertising driven and it’s pretty obvious who is winning that contest.

Since the announcement of the offer was made on the 1st of February many people have been waiting to see how Google would react. Well today David Drummond, Senior Vice President, Corporate Development and Chief Legal Officer responded on the Official Google Blog, in a post interestingly entitled “Yahoo! and the future of the internet“. The post is full of some unusually aggressive statements (by Google’ standards) about this potential acquisition:

…This is about more than simply a financial transaction, one company taking over another … It’s about preserving the underlying principles of the Internet: openness and innovation. Could Microsoft now attempt to exert the same sort of inappropriate and illegal influence over the Internet that it did with the PC? While the Internet rewards competitive innovation, Microsoft has frequently sought to establish proprietary monopolies — and then leverage its dominance into new, adjacent markets…Microsoft plus Yahoo! equals an overwhelming share of instant messaging and web email accounts. And between them, the two companies operate the two most heavily trafficked portals on the Internet. Could a combination of the two take advantage of a PC software monopoly to unfairly limit the ability of consumers to freely access competitors’ email, IM, and web-based services?

Sounds like interesting times ahead. I personally struggle with the notion of Yahoo! selling up to Microsoft. Yahoo! has far more in common with Google than it does with Microsoft. On the internet Microsoft has never really succeeded even after acquiring successful properties like hotmail, because they could never really figure out what to do with them. I think it’s partly because Microsoft doesn’t really come across as a consumer oriented entity, it’s more of an enterprise oriented company. I still think they are very much entrenched in the “how much can I charge you for a license to use X” world and never really sought to look beyond that for other options until it was too late and the barbarian( Google) wasn’t just at the gate it had plowed right through it.

I personally dread to think of what might happen if Microsoft got their hands on a service like flickr and here’s why …

I remember when Yahoo! first acquired flickr 2005, the user base complained fearing Yahoo! would somehow destroy their beloved flickr. We know that didn’t happen and Yahoo! invested in not only improving the service but also succeeded in growing it into one of the most popular social sites on the internet. So if that worked out ok why wouldn’t the same thing happen again if Microsoft was at the helms. I’m going to go out on a limb here and suggest it’s because Yahoo! gets the internet. If there’s one thing Microsoft has proven over the last few years it’s that it definitely doesn’t get the internet. Or another way of looking at it is this … if Microsoft bought Yahoo! would it allow flickr to continue to run under the same ethos and principles it was founded on?

Maybe Drummond is right? maybe this isn’t just about a transaction, maybe it is about preserving the underlying principles of the Internet: openness and innovation.

But then again how truly open is Google?

SWIG-Uk Special Event: Alberto Reggiori & Andrea Marchesini – The BBC Content Aggregator for the Memoryshare Service

Alberto and Andrea presented some of the work they have been at Asemantics. Most notably they showed how they are using Semantic Web technologies on a developing a new generation of feed aggregators for the BBC’ MemoryShare service which is described as an archive of memories and events from around 1900 to today.

One of the key messages that Alberto tried to convey was around the adoption of RDF and the difficulties around trying to use it solve the various problems that are faced by the SemWeb community. In his opinion  RDF is …

  • Complex, because it tries to solve too many problems at once
  • Search is hard
  • Granularity management, Read/Write is hard
  • We currently have a poor software tool chain

He argues that the solution is to combine existing Web 2.0 technologies with RDF, and actually hide RDF, and instead present data in formats that are more widely accepted and entrenched, because customers don’t get The Semantic Web or RDF. I think Alberto got the biggest laugh of the day when he likened the adoption of RDF to the Resurrection and summarily pronounced on one slide that “RDF is Dead” only to have it resurrected three days later!

One of the things that Alberto and Andrea presented was some current work they are doing on an specifying and developing SPARQL to Objects (S2O) which a SPARQL Extension that maps RDF Graphs to JSON Objects. Whilst the output format seems pretty friendly I’m not convinced I like how it binds the semantic of the output to the semantics of the query – but guess there are some advantages to this approach.

I enjoyed Alberto’s talk and was able to spend a bit of time chatting to him during one of the breaks, he’s a passionate researcher with some interesting ideas. He recently did a podcast with my colleague Paul Miller as part of our Talking with Talis series, which you can listen to here.

SWIG-UK Special Event: Leigh Dodds, Facet Building Web Pages with SPARQL

You can view the slides from Leigh’s presentation here.

Leigh is CTO at Ingenta. They have built a web framework, called Facet,  for building web applications on top of RDF. In their opinion there was no good system for integrating RDF repositories with an existing web framework  in Java . Although the framework does have some limitations it seems to me that it is quite simple and perhaps even elegant.

It appears that by embracing some limitations in RDF Modelling Leigh has succeeded in building a framework that, on the face of it, provided a fairly flexible means of building web pages from an RDF Repository, and because of way it’s designed and built it lends itself to being integrated very easily into existing templating environments ( JSP, Velocity etc. ).

Leigh was asked several questions by the audience and his answers provided further insight

Question: how do you use this for searching when you get a list of results back?

Answer: Not using this for searching.

Which to me makes perfect sense each of the queries that are configured returns a sub graph, or lens that is effectively a view of data that you can pass to a templating engine for rendering.

Question: Is the schema annotation mechanism for a known data set rather than in general?

Answer: yes its application specific and configurable at application level.

Again I thought Leigh had made this clear during the presentation and therefore should have been obvious. Whilst some might consider this to a limitation, I wouldn’t necessarily view it as such.

Question: have you considered how your framework might work with Rich Clients, Ajax etc?

Answer: That’s why they support JSON output. Only currently doing basic AJAX lookups at the moment.

This is one of the features of the framework that does pique my interest, as we move more and more towards building richer client interfaces on the web there is an expectation that web frameworks and web services should support outputting data in JSON. At the moment our Platform doesn’t formally support this, but it is something we are definitely intending to do.

It makes sense to provide data back to the client in the format they need it rather than a fixed format that the application then has to process and convert. I’ve seen the problem when building desktop widgets, whilst XML is great and portable, most widget frameworks are based on ecmascript and understand JSON natively so wouldn’t it be nicer if web services would return JSON.

Anyway ldodds++ 🙂

Question: Will you open source it?

Answer: Hopefully, it will be, need to be dis-entangled but wanted to share the ideas here today so people can get a sense of the value.

I’m hoping that they do, I’d like to have a play around with the framework and possibly even extend it.

All in all I was actually pretty impressed with Leigh’s talk, I’ll be keeping an eye out for Facet.

Microsoft brings Windows Live services out of beta

Microsoft has finally released out of beta it’s suite of Windows Live Services, offering users half a dozen downloads and web apps.Among the offerings are IMAP-enabled Windows Live Mail, Windows Live Writer (one of my favourite tools!) for offline editing and uploading blogs, A Picture Gallery application and a parental controls application for web browsing.

This offering by Microsoft does echo Google’s Google Pack, which was also an online/offline software bundle. The difference between the two is that Google’s offering includes products from other vendors whilst Microsoft’s offering does attempt to tie you more to Microsoft’s own Platform.

I’m not complaining though I like variety …

Mp3 to iPod Audio Book Converter

Since I’ve been listening to a few Audio Books lately, I’ve noticed rather quickly that many of the places you download Audio Books from allow you to only download in .mp3 format. The problem with this is that when you add these .mp3 files to your iPod it doesn’t know that they are Audio Books, so it wont remember where you listened up to the last time, and it wont neatly categorise the .mp3 in the Audio Books menu, and wont let you alter the playback speed.

I found this free Mp3 to iPod Audio Book Converter, which will convert any .mp3 file into Apple’s .m4b audio book format, and so far the results are pretty impressive. Unfortunately it currently only works on Windows, and isn’t available on any other platform.

Google Research Talk: Semantic Web

Google have recently launched http://research.google.com that will provide information on research activities at Google. There’s a series of video talks that are associated with these research activities.

This is a talk by Eyal Oran, Sebastian Kruk and Stefan Decker entitled “Semantic Web”.

Our development group has been doing a lot of semantic web related work here at Talis, in fact we have built a semantic web platform that we have built several applications upon, so the entire research area is something we are all very passionate about.

The talk covers some of the basic principles of the Semantic Web but also takes about FOAF, RDF and introduces ActiveRDF:

an object-oriented API for managing RDF data. ActiveRDF can be used with different RDF stores and integrates with Ruby on Rails. An addition to ActiveRDF is BrowseRDF, a faceted metadata browsing library. Faceted browsing is a natural technique for navigating that graph. We developed an expressive faceted interface that allows navigating arbitrary semi-structured data and formally show the improvement over existing interfaces.

I found the talk quite interesting, and it’s given me a fair bit to think about.

PhotoSynth at TED

PhotoSynth is a Microsoft technology that I have talked about before, it’s certainly one of the most impressive visual technologies I have seen.  Here’s a video of Blaise Aguera y Arcas at TED this March presenting PhotoShop to the conference attendees and getting a standing ovation … quite deservedly in my opinion. The video is also a great introduction to the technology and what its capable of doing.

I agree with Blaise when he says Simply put, it could utterly transform the way we experience digital images.