Nathan Torkington at OSCON: What's Coming up on the Radar

By James Turner
July 23, 2008

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O'Reilly blogger Nathan Torkington spent some time with James Turner of O'Reilly News at OSCON 2008 in Portland. He shares some of the trends and technologies that he thinks will play a big role in the near future, including open source biology and the rise of mobile computing.

Radar is O'Reilly's more futuristic forward-looking blog as opposed to current events. What are some of the things that are really on the radar right now?

We're looking at things like Open Source Biology for example; if you look at synthetic biologists like Christina [Smolke] you will see people who are turning the techniques of molecular biology into a toolkit that is kind of like an Open Source Programming toolkit. It's a project to create an Open Source set of genetic building blocks for building your own organisms. And it's somewhat scary; yes.

I was going to say.

But the potential for damage is a lot greater than you know.

Yeah; I was going to say the core dump in the biological world could be a lot worse.

Yes; exactly--spawning and forking for example--yes. Regardless of the wisdom or folly of it and the potential for danger it's actually happening, so we feel obliged to have a look at it and make sure that you know we know what's going on. They're learning from Open Source and coming up with licensing models and repositories and taking those sorts of ideas and hoping to create the same kind of collaboration on biological building blocks as Open Source has produced on software building blocks.

In fact we've seen science in general going to more Open Source models. I'm thinking primarily of the Public Library of Science which has been a real change from the traditional Science Journal background.

Yes; significant. The idea there of open access to knowledge [in] the same way that free software advocates are in favor of open access to source code is a widely drawn parallel and you can almost look at Open Source as borrowing from that academic scientific tradition of publish your results and make sure that you're working and your data sets are available so that others can check what you've done.

I find it personally interesting because I've always had an interest in genetics and genomics and things like that--that it really is becoming more of a hack-your-own endeavor now.

It is.

I'm in fact right now doing an article for a publication on the new personal genomics where you can for $1,000 get back a couple hundred thousand or a million of your single nucleotide polymorphism results, which is a real difference.

Yeah; that's companies like 23 and Me where you spit in a jar and send it off to them, they do the sequencing, find the bits that are different--they encode variations in your particular DNA and then connect you through like a social network with people who have the same thing. You can say oh, I didn't realize that you were also reacting in this way to caffeine.

I didn't know you had wet ear wax--that's one of the ones--

Very useful; very useful.

You wouldn't want to get married to someone who had a different ear wax type than you though.

That would be disgusting--not going to happen. If you look at personal genomics, that's just the current popularization of it. But the potential for let's say we take a drug now that you go out and you test it out on 5,000 people and you decide from that 5,000-person sample which is supposed to be representative of the people that will buy the product when it's for sale whether it works or not. In the future you'll be able to say which genetic markers indicate that this will work for you, which is completely different from the idea of a drug working or not working. Suddenly, you've got personal targeting of medications.

Right; and in fact they're already doing things now with genomic-pharmacology, where for certain drugs like Lipitor and some of the other ones, they can determine if you're an over-metabolizer or an under-metabolizer and know we have to give you more or less because you're going to get an adverse reaction or not enough of it.

It's amazing because in you know five years or so we've seen the technology for sequencing DNA go from being something only professionals can get access to because it costs tens of thousands--hundreds of thousands of dollars or you know didn't exist 10-years ago, down to the amazing stories. There's by a guy called Hugh [Rienhoff-00:04:44], and his daughter was not quite diagnosed with a condition and he couldn't get a precise diagnosis out of anybody. He was fortunate in that he happened to be a molecular biologist and comfortable with the equipment. He went and bought on eBay a sequencer for $1,000 and stitched up his daughter's DNA and figured out exactly what she had and was able from there to go to the medical literature and figure out well if that particular pathway is being interfered with how could we restart it? What operates on that? And then to a GP to get permission for a test of the substance that he had found against his daughter's condition and she's doing a heap better. That's an amazing uplifting tale, but it's because you've got this equipment going from professionals to the people like him, Pro-Ams, right just like digital cameras went from being incredibly expensive and only the pros could have them to now--it's not so bad. A hobbyist, a serious hobbyist can have one.

Right; and in fact Wired had a thing that was like do your own gel [inaudible-00:05:57] you know. Yeah; you have to have a centrifuge around and a couple other things that probably you know your Oster blender is not going to handle but--.

Every well-equipped lab has a centrifuge.

Yeah; but probably not everybody--well maybe every mad scientist would have it.

There we go.

Of course I've got one in my basement.

The Wired subscription list of mad scientists or--.

Yeah; right [Laughs]. The other thing is--that fascinates me is you give $3 to to generate 100 pair sequence protein now; it's like send us your--.

Oh right the manufacturing, the cheap manufacturing; yes. That's the other side of it. I feel like we're up in the Web. That's my model for all of this kind of change and so if you look at the growth of the Web it--a lot of it was driven by that personal computer revolution and the fact that not just Commodore 64(s) but the IBM PC in particular. There were a lot of these machines laying around that you could put to other uses and that drop in hardware from many computers down to PC was sort of--it was roughly comparable to the drop in hardware costs between the sequencers of years ago and of today. I'm sorry; I've completely forgotten where we were--sorry.

Generating--I mean and someone said these guys are like doing the PLA(s), the Programmable Logic Arrays of Biology. You know give us what you want for a sequence and we'll do it for you, which again can be very scary if you think about it--do this thing which is kind of like smallpox but it really isn't smallpox.

Not to mention you don't necessarily want them competing only on the basis of price. You know quality would like to be in there somewhere.

Yeah; that's probably true.

When you're one pair away from smallpox.

Right; so beyond Biology what else are you tracking right now?

We're looking heavily at mobile; obviously everybody is at the moment and things like the iPhone have just shaken--the mobile phone really needed something like that where people could--everyday people could access the power of the Web through their phone. We've had it for years but it's been so appalling painful to use that it was aversion therapy for people. Now we're finally getting to the point where people love to use the Web and the power of the Web on their phone. It's got a GPS built into it. Lots of lucrative services are now possible.

I was amazed that I was one of those people who stood in line a couple weeks ago. I was just out taking pictures and Northwest, -near Mount Hood and one of the services that I got for free was uploading to [Twitter] not only where I took the photo but what the weather forecast had been that day where I took it.

[Laughs] Yes.

That's what I find really brilliant about what the iPhone is doing right now is on a Windows Mobile Device you can have lots of applications and lots of services but it's almost like there are these walls to protect anything from using anything else. There's a GPS but you can't use it, and the iPhone seems to have really gone the other way of let's make mash-ups out of everything that's on the phone.

They've definitely gone a lot further than anybody else has. It's not the great open platform that everybody has been hoping for, but it's certainly a wonderful step in that direction and it's something you can hold up to other manufacturers and say look; this is really what we need--more like this and less like this crappy device you were trying to sell.

Do you think Android is going to live up to that--?

I think so; yeah, yeah I think it is. It's going to be hard because it won't have the sex-appeal of the iPhone behind it but in terms of functionality and the applications available for it--yeah I think it's going to do exactly the same sort of thing.

That's the traditional problem we've had is that you can say Linux is great; it's capable; it does all those things but then you go look at Mac OS X and you say yeah but this is sexy and usable and I think that's the challenge that Android is going to have.

Sexy and usable are two different things. The biggest problem I think that Open Source and Linux for example have had has been the usability for the common person that it's unless you live in that stuff it hasn't been that easy to use, and that's changing. They're making great strides there and that's what the big challenge for the Android phones will be is making sure that the user experience is seamless and beautiful and polished.

Right; I mean if the answer is well how do you compete? Just go down to the command line, you know.

No; I was a Judge in the Android Developer Contest and I got to see a lot of the early apps that were being built and already you know there was a mixture of sort of [Inaudible] concept that were very much in the rough unpolished state. There were also a couple of amazingly detailed, very nice apps that showed off the features of the phone and were completely usable by people. I could give it to my parents and they would love to use it and be happy with it, so I think it's not impossible. It's just a matter of directing the developers. The great thing that Google has done is bootstrap the developers enormously; I mean Google--Apple [4] Developers initially and it was the people who broke into the iPhone that proved to Apple that you can do much better things when you have access to the technology than you can through the Web applications that Apple were trying to sell initially. Google didn't have that problem. They've got access to a wide base of developers who are doing good things with it. I'm really looking forward to the launch; it's going to be fun.

What's the date--what's it like for it now?

I've heard that there will be phones the last quarter of this year I think is what they're saying.

Do we know yet who is going to be available for providers?

No; I don't know. I don't know.

That's going to be the other challenge. Verizon has said they're going to let people on their network but--.

We ran a phone conference, Emerging Telephony a year or two ago, and when I was involved in it I remember the thing that everybody came up with again and again and again, the biggest problem on the mobile phone is the fact that you can't have access to the device and when you have access to the device you can't have access to the network. The operators make it very difficult to get applications onto the phone or they make it very difficult for the phone to access the features of the device. There's all sorts of problems, and slowly bit-by-bit we're seeing them disappear. As something like the iPhone shows, you can give people access and be rewarded by much more money.

Right; the equation for them has always been that why should we let you for instance have access to the bluetooth profiles or let you move photos off the phone when we can charge you 20 cents to move a photo off the phone?

Right; and it's interesting that the iPhone bluetooth isn't [unfitted]. That's one of the--I think and I remember hearing someone say that's one of the bugs that they had. The--the business model of the carriers has always been, make ourselves as far from a pipe as a possible; whereas if you--the success of the Internet has been the pipes are dumb and the smart-set at the end. [Phone Rings]

So what--iPhone pipes--?

Yeah; they just want it to be as far from a dumb pipe as possible.

We've got mobile, we've got bio; what else are you looking at?

What else are we looking at? There's something I call Open Beyond Source that encompasses a lot of that where people are looking at the lessons of Open Source and saying well what can we apply it to and there's the open democracy folks who are saying, let's shed a bit of light on government and there was that great what if the changes to a piece of legislation were made in a repository like Subversion, so you could see who authored that change; who added that bit in; who took the good bits out? Adding that kind of transparency and you look at somebody like Larry Lessig and he's working for the transparency funding. Learning a lot from the way that the quality of a project goes up when the work that happens on it is done in the open, so we're--there's Open Source hardware for example. I think last year we had Phil Torrone at OSCON talking about that, the company selling Open Source hardware projects and it was one of the few making money out of it and sort of showing the way to everybody else. There's all sorts of projects, like [Inaudible] which are Open Source hardware and sprouting up a lot of Open Source projects around them.

I was fascinated by--I'm not sure, I'm not going to remember the name of it but was it Rep Rap?

Rep Rap.

Rep Rap, right.

It makes you sound like Scooby Doo when you say it. [Laughs]

Yeah; but the idea--it's not quite doing what it says it does because there's still significant components that it doesn't build itself but it's getting on the way toward being the thing we've always feared, which is a machine that builds itself.


You wake up one morning up to your ears in them.

Yeah; and the--okay so far from that--it's not funny at the moment. It's wonderful, the fact that it runs on ingredients that you know it's got a limited supply of. You know you're going to wake up to your eyeballs behind them.

Right; that's where we need the Nano-technology to get in to take your dog and make a toaster out of it.

Right, right; and then we can wake up in [Inaudible]. There's an infinite number of bad possibilities for this but the good ones are also nice, and it's also wonderful to see that Rep Rap is one of the few Open Source projects in this area. You know well it may well be the only 3D printer in the area and the things that you can do with those are just mind-boggling.

Right; the main thing I look at for that is the, you know I have a pair of headphones and gee, the bracket broke, and you know traditionally what I would have to do is hope that the manufacturer had a replacement. Now you could start to think if you had the CAD or if you had a 3D scanner that you could like just put it together enough to scan and then scan it and then have it create a new one for you--.

If you look at the way we're moving in the world towards--maybe we shouldn't be pouring oil into plastic, into all of these strange shapes, which break immediately and then are thrown into landfills. Maybe repair is actually something that we should be doing more of; these close personal 3D printers have a lot going for them.

Right; the real promise would be if things were made out of something we could be easily decomposed back into the source materials.

Sure; that's the promise--you're not getting there at the moment. Decomposing plastic is [laughs] painful at best.

Then the idea, you throw your laptop into the device and then six hours later a new laptop would be very Star Trek(ky) actually.

It's a wonderful dream.

Anything else before we wrap up?

Anything else on the Radar agenda? Oh let me think; I'm sorry--my brain is not kicking in here. That's what I wanted to [mention] first. Oh yeah; yeah, so anything else on the Radar agenda? We're looking at ubiquitous computing, which has got a bit of a bad rap over the years because it started an academia and so it--like artificial intelligence, it's become associated with things that never happened.


We talked about the mobile devices; the world of ubiquitous computing really split into two; there were the Americans who went off to do sensor networks and the big dream there is the real world will be heavily instrumented and you'll be able to get tons of the data that exists about the real world but which isn't captured or transmitted--.

Right; that's like RFID where you're going to be able to know where everything and everyone is.

Exactly; exactly and right down to the smart dust where you scatter these particles throughout a room and they all have little networks and can communicate with one another. While the Americans were working on that, the Europeans have just been going gangbusters on their mobile phones and saying we don't need to put computers everywhere if you take your computer with you everywhere. It leads to a different type of application and a different type of information and a different sensibility but it's pretty obvious that neither one is true--that neither one is the way the world will be. The mobile phone is not going to disappear and we'll just have computers everywhere, and it's not going to be that we won't have computers anywhere but in your hand or on your desk.

Looking at it, you see things like the mobile phone is a great UI compared to Smart Dust for example which in theory can't be seen. At the same time what makes the mobile phone really useful is when it knows about the real world. It can tell you what the traffic conditions are; it can tell you that the event that you're going to is going to be filled with your friends and so maybe you should you know where a tee-shirt instead of a suit and tie--whatever. The more it knows about the real world the more useful it can be and so you're ending up now with people starting to instrument the real world slowly and make use of it through the Web and through the device that they carry around with them all the time. We're tracking ubiquitous computing and that extends the whole ubiquitous computing stuff extends into architecture, urban planning, medicine, lots of fields where knowing about the physical objects in the real world or having the physical objects in the real world be connected to the internet and responsive to it where that's a useful thing. We're watching all of that stuff at the moment.

Connected to that idea of greater knowledge there's going to be concerns these days especially given the increased desire of governments to track information about that leading to even more of a lack of privacy.

Absolutely; and I think if you look at the march of technology through time you'd be hard-pressed to find a point in time at which privacy went up with a technological invention. You might--

Encryption might.

Encryption is pretty much where I was going with that and I think that would have to be the only one and it certainly didn't last long because it was always the controls such that if there was something encrypted the government was able to have a CP to break it. You weren't allowed to use keys long enough to thwart the government.

All right; well no one except the people who would actually be the ones who the government didn't--wanted to look at, who don't care if they're doing something illegal anyway.

Sure; I can't say that ubiquitous computing will be a fantastic advance for your privacy, so I put great hope in ubiquitous encryption and peer-to-peer networking that you can at least make it bloody hard--you don't have to make it easy.

You're never going to be able to keep out the professional thieves, but maybe you can keep out the door rattlers.

Exactly; exactly.

Transcript provided by Shelley Chance t/a Pro.Docs

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