Life blog

Molecular Playground: Architectural Scale Interactive Molecules

I just found out that my thesis advisor is working on a cool project.

There's a new science building going up at UMass Amherst (where I got my PhD) and Craig T Martin (my thesis advisor) thought it would be cool to do an art installation where molecules are projected on the walls. He also realized that it would be cool if folks could interact with these molecules.

As he says on the project's site, molecules and chemicals are sort of "inaccessible and uninteresting" to the general public. His vision is to develop a large scale "molecular playground" where folks can actually go and manipulate the molecular projections.

Craig received a grant from the Camille & Henry Dreyfus Foundation to "develop and install in a prominent public space a system for displaying large scale interactive molecules." The molecules will be animated and artistic, so that they can be appreciated even without direct manipulation.

Craig is collaborating with Allen Hanson from the UMass Amherst Computer Science Department.

Cool. I'm looking forward to seeing it.

And check out the video of a demo of the concept (below). The protein is HU, found in the bacterial nucleoid and involved in chromosome compaction. It makes a dramatic kink in DNA, and does some funky things. Check out the tongues going down the grooves on the opposite surface of the DNA. That's a tight grip. There more to it, though. You can manipulate the molecule yourself (with some explanations) on Craig's site.

Video: The Future of Science Publishing

In February, in a Barcelona restaurant, Mark Kramer caught up with me and asked me what I would be speaking about at the 3rd WLE Symposium (notes from the talk are in a preceding post).

He was kind enough to give me the video, so check it out below.

(and, no, I don't lisp like that - it's the audio quality)

Talk: The Future of Science Publishing

I think about the fusion of mobile and Web all the time. And I’ve been talking about and thinking about designing services and software for years. But I also was an academic researcher for about 10 years, with 18 co-authored papers.

All this converged about a year and half ago when I met Matt Cockerill from BioMedCentral, an Open Access publisher of scientific papers.

He had a sort of embarrassment of riches - servers full of papers, videos, info. The problem was how to take all that info and make it work, derive relevance, give value back to the scientists.

That got me thinking. I framed it as a problem - how to make it easy to find-navigate-recombine-share? Suddenly, I saw this as one of the big challenges for the Web.

Now, I see it everywhere in other areas, but science publishing catches my attention, mostly due to my recent focus back on science.

The Rise of the Scientific Paper
Scientific papers arose about 450 years ago as a way to distribute, between scientists, public letters and correspondence on findings and reports. The natural scarcity of publication and distribution made this a necessity.

From this arose lead publishers (for example, Nature and Science) and all that science publishing entails - star editors, reputation, authority, impact factors, and so on.

But that’s so Web 1.0.

Waves of the Web
OK, so I try really hard not to use the Web 1.0, Web 2.0 etc terminology. I view the Web more in waves than labels. Each of these waves take the cycle of create, consume, connect to another level.

For me Wave 1 was the Age of the Hyperlinked Document.  The first wave was characterized by a rush to digitize traditional publishing assets, such as databases, newspapers, encyclopedias. This wave also saw the rise of Web indexes (Yahoo), search (AltaVista), email, and the browser wars. But in the end, the creators were traditional publishers and indexers. Regular folk just "browsed" stuff, without any contribution.

Wave 2 was the Age of the Fragmentation of the Web. This wave saw the coming of micropublishing (blogs, wikis), emergent (crowd-sourced) indexes (wikis, delicious), social networks, and new ways to search (Google, Technorati). And expectations of interactions with people and content was heavily influnced by IM (rapid morsels of conversational text) and rich interfaces (through flash, video, and AJAX). But the biggest change (at least in this story) was that everyone became a publisher

Publishing, therefore, had gone from static monoliths to morsels of info free to socialize. This has caused the collapse of traditional publishing (witness the record and newspaper industries). Furthermore, there has been an explosion of morsels of data on the Web. Everything has become search-able, comment-able, link-able, embed-able, feed-able. Data and people mix in a social, living, Web.

In short, Wave 1 weakened traditional publishing that used to be based on scarcity. Wave 2 made everyone a source of info, everyone an annotator of data, everyone a publisher; it took hyperlinked documents and morselized the web.

How have scientific publishers fared in this Wave 2?
They've basically kept the status quo. Online. Stuck in Wave 1.

As with many other traditional publishers, science publishers replicated their closed subscription-based model on the Web, republishing their content online.

Open Access has been battling the status quo for 10 years (at least in terms of access). Only now are they getting strong recognition, impact factors, authority, and a little respect. But they are predicated mostly on and restricted heavily by the traditional model of science publishing (for example, stuck to impact factors).

Recently science publishers have been experimenting with comments and annotations. But with little traction (and I have a few ideas as to why). And, granted, the non-paper publishing part of traditional publishers have embraced the Web, but I am speaking of the core product here.

So many similarities...
The irony is that Tim Berners-Lee actually envisioned the Web as a way to share science information and publications. Openness and sharing are at the heart of science. And the core cultural structures replicate well online. Wave 2 behaviors are the same as in research: find, navigate, recombine, share.

And the Web also has structures found in traditional publishing, such as ways to deal with authority and primacy.

In short, science publishing as it should be mirrors the Web.

If there is a Wave 1 and Wave 2, is there a Wave 3?
My view is that we are entering the true era of (and need for) the Semantic Web. Context is about relevancy is about meaning is about semantics. I claim that the semantic Web has not advanced in the past many years because the focus has been on what I call "librarian" tasks of formatting data and manually building ontologies and so on.

What we know now (from Wave 2 behavior) is that emergent semantics, created through data-mining, but especially via people just using the Web, will be key in helping us navigate the sea of data. In short, the next wave of the Web will require a mix of data mining, librarian tasks, and people to make sense of it all.

How do I see science publishing taking advantage of the Web?
I mapped out behaviors and how it could be on the Web.

 

Culture vs tech
Risking sounding dramatic, I think more changes are inevitable, despite publishers wishes to hold on to traditional structures. But the sad irony is that the future of science publishing depends on culture not tech. All the tech is here, and it’s evolving, mixing Web, mobile, context, semantics and other wonder, whether the scientific publishers want to or no.

But will scientists lead the way?

This post was written from the notes of my talk at the 3rd WLE Symposium in London back in March (presentation below).

The Future Of Scientific Publishing

View more presentations from Charlie Schick.

Changing the journal impact factor through real-time transparent statistics

I've mentioned Mendeley before. They refer to themselves as a Last.fm for science papers, but I think it'll be much more.

One thing they realize they are changing, as a side effect, is the impact factor (sort of like a Page Rank of science papers, based on incoming links (citations) to the paper and the journal).

Link: Changing the journal impact factor | Mendeley Blog:

At a higher level then, Mendeley’s significance isn’t just about real-time impact factors and article-level metrics. It’s about using technology for the first time to crowd source data and forever change how research is done. That is why I’m crazy enough to move half-way around the world. Mendeley literally isn’t just another “Silicon Valley” start-up.

Spot on. When I heard Victor (one of the founders) talk about this at Next09 I practically jumped out of my seat.

Thompsons was set up in an age when you needed someone to manually go through references and such and report to the community. That's probably part of the reason it takes three years to establish an impact factor. [I pointed this out already a while back.]

PLoS and BMC, who imported the broken authority model from the print world, missed an opportunity in the past 10 years to upturn Thomspons world. So, it's good to hear that PLoS is starting to be transparent in their traffic and links, providing the start of a new way to look at authority.

One thing: being a bit publisher-minded, I, myself, missed the other side effect of opening up stats that could show authority - basically, such transparency might be able to highlight a high-impact paper from an obscure journal. In the traditional world, that paper would have been buried by the journal's own impact factor.

Yeah, we need to open up these stats on a real-time paper level. There's no reason not to do it.

(and go read the rest of the article on Mendeley's site)

Image from wikipedia, on Page Rank

Mendeley, the future of science publishing

I was at Next09 this week, giving a talk with Rudy de Waele on "Mobile 2.0". Next09 was a good conference, a mix of talks in German and English, covering things like social media, Web tech, and mobile. And, of course, I caught up with a ton of interesting folks I know, and met a ton of interesting folks I was pleased to meet.

There were some startups also pitching there. I met Jon Froda and Ezra Goldman who were pitching their companies, working in helping corporations capture processes and manage change processes through more social Web services, respectively. I also met Renato Valdes Olmos who had a cool NFC social gizmo.

Bringing citation software to the Living Web
One particular startup I almost missed (Rudy pointed it out to me) was Mendeley. I had heard about it from some of the folks I follow on Twitter (as @molecularist) and had it on my "must check" list, but had no idea what it really was. Rudy summarized it succinctly as "Think of Last.fm for scientific papers".

That was enough to grab my interest, as it seemed to touch on key aspects of the future of scientific publishing that I have been thinking and thinking and thinking and thinking of over the past 18 months or so.

Mendeley is a combination Web and desktop app service for managing your bibliography of science papers. A desktop client helps you extract metadata, annotate, and share the scientific papers you add to your bibliographic database. You can also backup your database online and fill the database ("one-click") with papers from other publication databases.

One of the key upcoming features is a "recommend" feature that helps you find other papers related to the ones you are collecting.

I suppose one could say it has features from delicious (social bookmarking) and StumbleUpon and Last.fm (social discovery), with a twist of sematics and data-mining.

I got a demo of the desktop app and Website and am really impressed. It seemed simple and useful and all the right elements were there.

Kindred spirit
Victor Henning, who is the Founder and Director of Mendeley was kind enough to sit down and talk to me after his talk. He indulged me in my excitement to share thoughts with him regarding what they were doing.

He told me that the idea for Mendeley arose from his and a friend's general frustration in using citation tools that were basically industry standard. Like all great services, Mendeley was something that they built because they needed something like it.

They've been brewing the service for a few years, and have been in a beta for about 4 months. Already they have thousands of users from some of the top research institutions in the world, and are growing at a great clip. Based on the papers placed in the system (over a million), the largest groups of users are from life sciences and computer sciences.

Another cool story is that they reveal a lot of the usage stats, and saw an emergent version of an impact factor as an article from PLoS rose to the top among the most added paper in their database (I think the Web is so well suited to track emergent authority and such).

Good foundation
I shared some thoughts I had about science publishing, and it seemed that some were issues Victor was thinking about. He's quite excited about the service and feels like he could always do more. We touched upon a ton of cool potential and upcoming features. And like always, ideas are more plentiful than one can implement. But, the core is solid, they have a grate foundation that they can build upon, and their position enables them to offer valuable services that folks would pay for.

Furthermore, he mentioned some designers and developers who are working with him and it seems he has an amazingly strong team to make this happen. What's more, some folks from Last.fm, Warner, and Skype have put in 1.5M Euros into Mendeley. So they are going to be moving along for some time still.

And something tells me I'll be cheering for them all along.

Social networking and health - notes from SXSW

I was at SXSW last week and sat in on some seminars and conversations that I found particularly intersting.

One session was a "conversation," held in a small room where most of the folks sat on the floor. It was packed and the discussion was excellent.

Titled "Social Networking in Health: e-Patients, Data & Privacy," it was a discussion around the use of social networking services by doctors, patients, and the curious. The use of social networks in health raises all sorts of questions of privacy and secutrity and also questions some social assumptions and the like.

I took some notes (by no means comprehensive) and will try to put them in some sort of order below.

Privace and electronic records
The discussion started on some of the dark aspects of social sharing online. The worry was whether services that revolve around health should be a walled garden (though folks knew that the assurance was only so good, leaks happen). The worry is what happens when the discussion of the illness gets caught by employers, say, talking about dealing with depression.

There is a strong regulation called HIPAA, which I was told is all-encompassing, yet based on common sense, to protect patients and their electronic data. And there's no escaping the move to everything related to our health being digital. Having all confidential information digital is not new, as data warehousing of claims clearances already has put our health info in digital format. Also, users are driving electronic records for safety in drug interactions, for ease of managing, for portability. And when patients do participate in social networking services, they are not naïve, they usually know what they are posting and to where and the reputation of the site they are posting on.

The irony, someone mentioned, was that the main theft of records is actually physicaly based. But there is the perception that paper is secure, since usually they are in one place or contained, and it's through electronic records that a lot of celebrity leaks happen.

Health discussions
Fortunately, the discussion veered away from the usual hand-wringing about privacy and started to hone in on the value of social networking for patients and doctors. There were indeed a few people in the audience who were working on such systems, many of them hospitals or doctors.

While so much of medical data is related to Health Records, the feeling is that Social Media is a much smaller area in Health. Using Social Media for discussion is no different than normal life. [Though I think digital forwarding as a huge challenge - who owns what someone can forward?] Sharing online helps ease patients' anxieties around their illness or a procedure, learning from another patient's perspective. And promoting social conversations around illnesses leads to awareness, prevention, and even money savings for the patient.

A lady who runs a discussion site suggests that there has been a change in culture about what can and is being discussed. Also, younger folks are more comfortable sharing online. There was a feeling, too, that with all the churning during this economic crisis, that employers will be more lenient and understanding (though someone did raise the specter of a WalMart "understanding").

There are employment protections for some psychiatric illnesses and genetic information. Folks mused if this legislation could be extended to cover more diseases, to protect against discrimination against diseases. But there are also local cultural issues, as a lady from Brasil mentioned, things like dealing with faith and fatalism with respect to illness and health.

Finally, while folks thought there was good discussion between patients and between patients and doctors, there seemed to be no discussion between pharmaceutical companies and patients, most likely due to perceived liabilities. This was viewed as a bad situation.

What's out there
Lots of services were mentioned through the course of the discussion, so I'll list the ones I captured.

- Google Health
- Microsoft HealthVault
- Facebook causes
- Patients like me
- Hello Health - This sevice provides for doctor-doctor and doctor-patient discussion. With the service the doctor shares videos and bookmarks with patients. Interesting thing is that to register, ou first need to have a face to face meeting with the doctor.  
- Truesera - Billed as "connecting patients to enlightened doctors and facilitating doctors to get involvedself." The service became self--correcting (in terms of the facts of the discussions) after passing critical mass. That suggests that one could create a useful resource with factual information (much like Wikipedia, which leads me to wonder if there is a Wikipedia for Health)

Talk about real-time search

There's been some buzz around the next phase of search being "real-time". Read Write Web wrote two articles on instances where Google Search failed to connected to the sought-after info, such as "Gmail down" or the river landing in NYC. While I have been telling folks that 2009 is the year we have a serious Google competitor in search, Jonathan Borthwick lays out the reasoning and fingers real-time search as the challenge for Google.

Gerry Cambell has a nice chart that puts it more prosaically. I like his axes of expressed vs considered and delayed vs instantaneous content. That lays out a spread of types of content out there that one may look for or follow. He sees real-time search of expressed and instantaneous content more in line with how we live our lives and navigate a sea of information.

Yes, I think this is one aspect of where search needs to go, but I am not sure it's the only piece. Trending and sentiment analysis, for sure, are much better when using expressed and instantaneous info, indeed, I am constantly looking for a tool that can help me with that.

But I feel there are other aspects that need to be fed in. For example, I think there will be a touch of semantic mining to add value to this real-time search. And I think, at some level, the search needs to know who is searching and fold in relevance that way.

Current search seems to miss the semantics and context and personal aspects of the query, aspects that will increase the value of the results.

Furthermore, I do think that while the linear nature of search, and I expect, real-time search, is not ideal, it will still dominate, since it's easier to build upon an expected mode of interaction and data scanning than to build some fancy (and theoretically more useful) interface to the query results (or at least, that's one area that I am cautious of pushing for innovation).

As a parting thought, this push for real-time search, I feel, has come from the regular use of live streams of info, live streams that are now overwhelming us and for which we need, you guessed it, new filters. So, I do think, at some level, we'll have better real-time search tools, if only to allow us to get a good sense of what's happening in our many incoming lifestreams.

Image from Gerry Cambell

Itching to mutagenize

I've been thinking back to my bio-tinkering days. I used to work on protease inhibitors called serpins, serine protease inhibitors. Serine proteases are enzymes that cut up other proteins and have a serine (an amino acid) as the key component of the calalytic chemistry. The two main serpins I studied were practically identical except for the region that acted as bait for the serine protease in the inhibition process. And it turned out, one of the serpins actually inhibited cystein proteases, proteases of a different class, but which use a cystein as the key amino acid in a catalytic process almost identical to serine proteases (see figure to right).

Biochemists will find that cool, in a geeky way.

Site-directed mutagenesis
Furthermore, I showed that changing a few amino acids was enough to change a serine protease inhibitor into a cystein protease inhibitor, and vice versa. I did this by mutagenizing (a fancy word for changing) one amino acid of the protein at a time.

It was a fun process and what really appealed to me was being able to change the function of a protein at the atomic level.

As a grad student, I did similar work with DNA, effectively changing a few atoms to change the function of the DNA with respect to an enzyme that recognized it.

Taking that thought farther, yes, one could change all sorts of DNA and proteins molecules and create new functions. But that's hard. Small changes, when you're lucky, are not so hard. But, really crafting whole new types of enzymes or protein functions is the real alchemy of the 21st century as synthetic biology takes off.

Nature trumps all
Fun, though it is to create new functions for molecules, I do think nature has probably experimented with every chemistry possible and created a whole slew of useful enzymes. Will it be necessary to make new types of enzymes? I'm not sure. Nature is interested in a sub-set of chemistries that might be useful for us. We might be able to find an enzyme that suits our needs most of the time, but I think at some point we might need to modify, or even create, an enzyme with a new function.

And it's already happening on the DNA level (making sequences better at binding proteins or promoting activity). But I haven't really heard about folks messing with the proteins themselves.

It's the filtering, stupid

I've been struggling for a while around a very big concept - how to bring scientific publishing to the modern web world of social, collaborative creation. Yes, the current science publishing system is indeed a social, collaborative effort, but I think it quite weak when using current online tools. So I've been spending a lot of time thinking of all the places the current system could be helped by all the tools I use daily in the social, living, collaborative Web.

Ugh. Big Gulp, indeed. So, the best I can do is break it down into smaller chunks. Partly because different parts of the find-navigate-recombine-contribute cycle of scientific publishing are at different Web-savviness. Partly because it's easier to digest for me. And partly because some parts are more likely to change sooner than other parts.

Finding and navigating
If you take the progression of content being generated on the Web, it just seems to be getting easier to publish and more fine-grained. We went from big publishing houses, putting out digital representations of physical units, such as The Article, or The Paper, or The Book. Search and index sites like Google and Yahoo stepped in to help us find and navigate all the Stuff. And the letter to the Webmaster became the feedback channel.

Things quickly got pared down to the blog post size and a democratization of tools causing an explosion of all sorts of info on the Web. RSS feed readers and personal home pages stepped in to help us manage these morsels of information. Comments and new posts became the feedback channel.

The latest push in data generation has been nano-sized grains of info, flooding us through Facebook, Twitter, and all sorts of status update services. Used to keeping up with things by reading everything, we have become stuck just keeping up with what others might be saying. And our tools to follow this are just not keeping up.

I was banging my head trying to summarize what this was. At Le Web, I found myself hearing things related to "filtering". I realize now that this thought might have been triggered by a good talk by Clay Shirky (which I only discovered recently through my tweeps) on filter breakdown - if you can't keep up with the stream then your filter is broken.

That gave me the word I was missing to describe the first and what I see largest issue with the future of science publishing. Indeed, I see filtering as a problem that is relevant to personal social Web use and even to business use of the social Web.

Linearity
The current filter tools we use, such as Google or Technorati, are too linear (an earlier rant of mine on this topic). You need to go through each item in turn, and the hierarchy is linear. There is very little by way of discovering new things or understanding the conceptual relationships between items other than order in a list. While I am at it, blogs are linear too. When there are more than five comments, the conversation breaks down and it's between the poster and the commenter. What's more, after more than five comments per post, a blog becomes less a conversation with the poster, since keeping up with all that can be difficult.

Personal home pages, such as NetVibes are not the solution, since they are still set up by the user and still require the user to read things. No help from the tool except managing the multiple streams. Even sites like Alltop seem to be curated pages for mulitple feeds. No help from the tool, once more.

I have been watching as various multi-dimensional search engines for various particular streams have appeared. Since I use Twitter a lot, I have been more keen to see a new tool to follow Twitter (and was happy that Twitter bought Summize). Indeed, for work, I find Twitter useless due to the volume of of the data stream and my desire to follow and participate in that stream. There are no tools that do this. The tools I have seen are simple word counters (Twitstat, twitt(url)y, Twitscoop, twitrratr) and can have serious failures (for example in this pic, see how a negative reaction was misconstrued)

Semantics anyone?
Folks have been talking a long time about a semantic web, where "meaning" added to information makes that information in some way richer. There are a ton of tools out there based on semantics and folks thinking and working on it. And there are some interesting search engines for the sciences, such as DeepDyve, NextBio, and Knewco, all of which layer some form of multi-dimensional interface on top of search data.

In the social Web space, there is one company that I have been talking with a bit, Crimson Hexagon (hopefully, more on them later). They semantically analyze feeds of data for sentiment analysis.

But, many of these seem like librarian jobs, where much of the semantics is hard-coded in the data as it is classified and created or by data-mining static sets of data. I'd like to see semantics arising out of the use and creation of the data, much like people tagging their photos have added a layer of semantics in Flickr, rather than some librarian in the company data-mining all the time.

The closes analogy I get to explain user-generated semantics versus librarian-style categorization is the difference between Yahoo 1996, with its cadres of employees manually cataloguing the Web, versus Delicious, where the users do it as part of their regular, personal, use of the service. Another analogy I like to use is how paths on a commons can be designed: don't put down paths at first and then observe where the grass is worn down, indicating optimal user paths.

Water water everywhere
I think it's great that there are so many folks working on this. But, the Semantic Web has been expected for a long time, but we've been too busy being geeky rather than applying it for something useful. The services above are all going in a good direction, though, and all of them are trying to get all that stuff on the web and filter it.

I feel that this year someone will come out with a wizz-bang search tool that throws in some form of semantics (part librarian, a priori, and part user-generated) and simple but powerful visualization and navigation of relationships between results. I think there's still a hole for a tool to allow individuals or corporations navigate streams of data. The companies above are all trying it in their own particular way.

Is there a winner in any of them? Or will one arise that takes the most useful features of each of these?

At least I like some of the predictions RWW made for 2009

Yup. Yup. And yup.

"One word son: filters."

2009 Web Predictions - ReadWriteWeb.

- Apps that do filtering, inferring and recommendation have a great year; several will release plug-ins for Google Reader, Twitter, Facebook and other 'sipping from the firehose' apps.

...

- New real-time web app launches that integrates Twitter, FriendFeed & more in ways we never could have imagined.

...

- More contextual browsing technologies will hit the market powered by improved top-down semantic recognition engines.

A wander through personal genomics

So, I've been talking about trends in biology that I think are significant (maybe because I've only started following biology again in the past year). In any case, I've said the trends were synthetic biology, the future of scientific publishing, and personal genomics.

Personal genomics is where individuals have detailed access to their genomic information (your genotype). To put us all on the same page, your genome is the totality of all your DNA - your nuclear DNA and your mitochondrial DNA. I claim that it also needs to include your micro-organismal biota DNA, as well. But, what the genomic information gives you is the programmatic basis for who you are, where you've come from, and what you might pass on.

Genetics 101
To be frank, you already have a clue as to what your genotype is, through observation of your phenotype (how your genotype is expressed in an observable attribute). For example, if you have blue eyes and only one of your parents do, you know that the non-blue eye parent is carrying a blue-eye gene (in normal cases, of course, but you get the idea). Indeed, the long list of questions of parental and family history that doctors ask are a sort of genetic profiling to give an idea of your own hereditary susceptibility to diseases.

Knowing all your DNA code at this time (through sequencing) is unlikely, mostly due to cost (unless you are on this list, or this program, or are this guy). Sure, it will come (and on the way, someone will win a prize). But for now, you need to be satisfied with just the direct sequencing of known stretches of DNA.

Another way is to look for indicative SNPs (pronounced 'snips', small nucleotide polymorhphisms, basically differences in code at a certain position of the genome). These SNPs are used as markers associated with a gene or phenotype. Hence, knowing SNPs, which are easier to scan for than sequencing the whole genome, are the state of the art in whole genome understanding.

Booming area?
While the dream of personal genomics is to drive more targeted pharmaceutical treatments, I think where it will really boom is in giving people their information to do what they want to.

I have seen a few companies pop up that offer various forms of DNA tests for regular folks, for curiosity or what. It definitely sits in a general self-knowledge, self-measurement trend that new sensors and tools have begun to provide.

One company I have been following is 23andMe (a play on humans having 23 pairs of chromosomes). In a nice twist, the genetic testing (they scan one million SNPs) is really just a conversations piece, a social object that customers discuss on 23anMe's socially-driven service. Yep. Social sharing meets biological diagnostics.

How much can it cost? 23andMe used to charge about $1000 per test (and I think that was for 500k SNPs). Recently they lowered the price to $400 and cover over one million SNPs. I suppose, at some point, the price will level off to ensure business profitability. Well, so long as profitability is based on selling tests. Which I probably suppose it won't be, since these are smart folks running the company.

Thoughts on this
While I am still trying to get a feel for how 23andMe is positioning itself, I do think that the drive in personal genomics will come from people wanting to know more about themselves, to help them make lifestyle decisions, and to feel more secure about their potential health future and of their children. And having the information before knowing what it means is fine, since companies like 23andMe keep combing the literature to add meaning to the data.

Also, pulling on the self-quanitification thread, one might want to marry this with other whole-organism tests. Metabolomics, the sum total of your metabolites, gives a great understanding of your current physiological make up. Marry a string of metabolic analyses with the understanding of your genome, and you have a powerful whole-body understanding. And metabolomics is a mature field with a good technological and informatics underpinning. And it is not expensive.

And and and, what's more. If you think of the genomic data 23andMe are sitting on, they stand a lot to gain from adding further info to the genomic set. They are already doing surveys that they can match to customer genomic profiles. Imagine if they had detailed metabolic information? Then they have a powerful repository of information to mine about health and genetics. Ripe enough to make oodles of money on, without violating anyone's privacy.

Hm.

Image by Image Editor

Hm. Just noticed changes in Google Search

Hm. Just noticed changes in Google Search
Originally uploaded by schickr

When was the last time Google messed with their search page? Seems like in this past week's big push (they killed Lively and made changes to Gmail) they seemed to have added some controls to their search results (or at least, as suggested below, I finally got to see it).

There are promote and remove buttons and a comment button. Has the GOOG finally realized that robots can't do it all?

This feature has been getting rolled out for a while (a report from Read Write Web). And it seems to me that it actually is something personal, rather than publicly shared. Though it's probably one more, "use it privately and we aggregate and data mine it" (like Gmail).

I think this is a big thing for Google.

“Taste good, sequence it” and “Look cute, sequence it.”

When I first started working in science, sequencing was just beginning to be a 'kit' science, where anyone could buy a kit and sequence. It was long ago enough for us to wonder at it, knowing that in the early days it took experienced scientists a long time to sequence anything through elaborate chemical means. Back then, any sequence was a big science paper.

Then Sanger worked his magic and things started to take off. Soon it became possible for a grad student to sequence a gene during their thesis work. Sequencing no longer became special but was required to publish a genetics paper.

In my time...
When I was a grad student, I had my own DNA synthesizer on my bench (well, it was the labs, but I used it a lot). The machine was able to make short stretches of single stranded DNA (10-30 based pairs). While we used it for studying the very DNA we made, others started using such machines to make DNA synthesis primers for sequencing.

Now a tech could sequence a gene in a few weeks.

Then automated sequencing machines appeared that allowed you to easily read long stretches of sequence, straight into a digital format. These machines were expensive, so either there was core facility or company with a bunch of tech managing the machines.

By the time I was a post-doc, you just had mix sample and DNA primer (also ordered over the Web), send it off, and get an email with all your sequences. It was fast and easy for what I was doing and I was able to sequence my clones in one go. Such sequence by mail was instrumental in me being able to focus on my core protein biochemistry work.

Shotgun wedding
While many of us were 'walking' down the chromosomes (current sequence suggesting primers for the next run), a clever man, Craig Venter, just started blasting the genomes apart, randomly sequencing it all, and letting the computers stitching it all together (called 'shotgun sequnecing'). He started with small viral genomes and just kept going for bigger and bigger genomes such that in the end it took him some 3 years (if I recall) to do the entire human genome.

Of course, the Human Genome Project guys who were toiling away for 15 years or more, were upset at the risk of being scooped. So, they had a sit-down with Venter (a REAL maverick) and agreed to reveal the sequences at the same time. BTW, this is the 2nd thing Venter should get the Nobel for.

And we're off!
Now in the post-genomic world, we're sequencing whatever we can get our hands on (see funny quote bellow). Genotyping is now a $400 service (it's not full genome sequencing, but powerful nonetheless). And Venter, for his 3rd Nobel, sailed off on his yacht, sucking up sea-water and sequencing all the microorganisms in it.

The writer below expresses her wonder at how things have changed in such a short period of time.

I have to agree.

Link: The Spittoon » My Mind Has Been Blown By Genome Sequencing

“Taste good, sequence it” and “Look cute, sequence it.”

Obviously there are good scientific reasons for both of these projects. But can you believe we live in a time where you literally could just sequence something’s genome because it was tasty or cuddly?!

Image from wikipedia

Random walks through synthetic biology

Synthetic biology is the design and building of novel organisms or biological systems. Sounds amazing, but we have been doing it to some degree for millenia, through husbandry of plants and animals, evolving them over time to drop the traits we didn't want (say, poison, aggression, horns) and promote the traits we did want (say, domestication, wool, meat, seeds).

With the advent of recombinant biology (where genes from one organism are added to another organism), we've been able to modify all sorts of creatures in important or bizarre ways. And, of course, genetically modified crops scare the Jeebus out of some fokls.

Microorganisms are commonly used to grow recombinant proteins, say, human proteins in E coli. But the current spirit of synthetic biology is to rebuild or build (micro)organisms to do some specific tasks or work.

I've spoken about Craig Venter many times. The work he's doing now, that should win him his 4th Nobel, is to specify a microbe that makes biodiesel. Indeed, we already use microorganisms to create biodiesel from various feed-stocks. But Venter takes it up a notch, to the point of specifying the _whole_ microorganism to do exactly the biochemical pathways he wants, rather than mutating or adding or subtracting a gene here or there.

Another person I'm watching is Drew Endy*, from MIT. He and a bunch of other adventurous bioengineers are creating a catalogue of genes that can be used as parts to easily build specific functions in microorganisms. Along with his cohorts, he's been running the iGEM competitions and creating a foundation called BioBricks. There's already a spinoff from these iGEM folks, called ginkgobioworks.

While many of the things I see coming out of this bioengineering seems like trying to shoe-horn a digital thinking onto analogue structures, the breath and depth of the creations, many of them just brilliant in their ingenuity or play, makes me overlook such a anti-digital peeve of mine.

Really, things are just beginning in this new age of synthetic biology. And it'll be really exciting for folks entering it at this stage. I'm looking forward to see how these bioengineering companies flourish.

BTW, the Boston Globe has a good write up of this new breed of bio-hackers.

Image from lofaesofa

*Endy is giving a Long Now seminar on 17 Nov 02008.

Eye opening: Opera's latest State of the Mobile Web report

When I see stuff like this I feel ashamed for ever thinking Africa's use of mobile was any 'less' sophisticated than Europe or Asia.

I keep reminding myself of the rise of photo sharing in Brasil, the use of mobile sites like MOSH and Winksite in India, and the number of hits nokia.mobi gets from China.

Forget the ringtone-wallpaper part of the mobile services cycle. These folksk are leapfrogging right to browsing and more interactive internet-connected apps.

Link: Eyes on Africa: Mobile Web use surges in Africa according to Opera's latest State of the Mobile Web report

Fast facts

• The use of Opera Mini in Africa increased by 180 percent from January 2008 - September 2008
• Globally, Opera Mini was used by 19 million people in September 2008, a 341 percent increase from September 2007
• Opera Mini users accessed 4.5 billion pages in September 2008, a 420 percent increase from September 2007
• In September, Opera Mini’s 19 million users generated more than 65.2 million MB of data for operators worldwide
• Egypt is now the tenth largest user of Opera Mini in the world

Gah. Why are folks trying to be digital in an analog world?

Call me old-fashioned, but I want some analog-computing being done with biological systems. I'm never comfortable with digital thinking with biological macromolecules. On-off systems built on chemical concentrations and macromolecular binding just don't seem to make sense to me.

Eh, there are folks doing this who are smarter than me, so I suppose I need to see more systems built to teach the point to me.*

Link: RNA-based logic gates compute inside cells

Detecting tetracycline isn't especially interesting, but RNA that binds to specific small molecules is actually relatively easy to make; repeated rounds of amplification and selection for binding can evolve these RNAs in a couple of days. This means that, in a matter of days, researchers can grow yeast colonies that glow in response to a variety of chemicals, or even to combinations of chemicals.

*Really bummed out that I will be missing _another_ Long Now talk (I'm in SFO two weeks prior). Especially this one with Drew Endy, bio-engineer extraordinaire. I was so looking forward to meeting him. Oh, well. Thank goodness for the video feed.

Swimming the sea of knowledge (the Concept Web?)

I've been spending a lot of time thinking about how to find, navigate, recombine, and contribute to ... what's out there, though mostly focused on science and the next generation of science 'publishing' (in quotes, since it'll be quite different from traditional publishing, more back in the hands of the scientists like in the old days).

A friend pointed me to this cool site called WikiProfessional, where they have these cool info navigators. A quick perusal suggests that they focus on the 'find' and 'navigate', though I think they also have a wee bit of 'contribute' through the addition of semantics as you navigate and annotate.

There are a ton of collaborators working on this and I dug a bit deeper into the main one, Knewco, It was on their pages that I stumbled upon the image to the right, about the Knowlet, trademarked, but spot on representing what knowledge really is: a concept with a cloud of facts, co-occurring items, with a few predicted concepts thrown in.

I like.

UPDATE: And here's a paper that goes into the details.

I like. A lot.

The Electric Knife Syndrome

I'm at the Mobile 2.0 conference in Barcelona. I was talking with Mark Kramer, and Bryan and Stepanie Rieger about the things we usually talk about. I had mentioned how I was at a conference where the enthusiasm for the 'technology' made folks forget to use simpler and better solutions. That led Mark to tell us about his stay in Albania where he saw someone using an electric knife to cut bread at a shop. There was no reason to use the electric knife, a regular knife would have sufficed. Mark suggested that it was using the ultimate tech to be cutting edge.

Another example of this came up later in the discussion. I then realized that we were discussing what could be called the 'Electric Knife Syndrome', where the tech used is subtly inappropriate in relation to existing solutions. This is slightly different from Post-Optimal Objects, where the solution itself is useless. But I think the Electric Knife Syndrome occurs more frequently and we forget a simpler solution is available.

Image from tizzle

Twitter is the queen of micro-down

My design for Twitter's "over capacity" screen
Originally uploaded by Mykl Roventine

Twitter has been so popular that it finally reached a stage where it was down more  and more frequently (Down is the new Black). But, after a total melt-down, they got their act together and sailed through Apple's WWDC without a hitch.

Or so they want us to think.

One of their clever solutions is to throttle down various features as things get heavy, features such as pagination, IM, mobile page.

I was wondering how that might work in practice, but now I know.

Instead of all of us suffering with a massive down time, the down time is spread across all of us, micro-down moments, one at a time. And because the micro-down time shows up once in a while to an individual (it goes away to micro-down someone else as you reload), _individual_ perceptions are improved.

So, the Queen of Micro-blogging is also the Queen of Micro-down.

At least this is what it feels like. Is this the case? Does anyone know?

Does Anyone Use Phone Booths Anymore?

A long forgotten phonebooth
Originally uploaded by schickr

PhoneBoy asks this question (link below). Indeed, I think the folks who have been ramping down their phonebooth assets were so narrow-minded (as in 'phone booth are for folks who need a to place a call and do not have a phone') that they blew a golden opportunity.

In telecomms, one perennial battle is for locations to put stuff - poles and pipes for wires, plots of land for towers and dishes, rights-of-way for repair trucks, and little squares of sidewalk for phone booths.

About two years ago I came up with some (IMHO) great ideas on how to use phone booth. For starters, there is still a place for them everywhere for quiet space for the talker or for peace for those around the talker. Indeed, on some Finnish trains there are phone booth for folks to use with their mobile so as not to disturb the passenger. I use it all the time for privacy.

It take no genius to realize what one can do with a booth if someone is sitting there for 3 minutes or more (and PhoneBoy is asking the right questions). It can also be a booth for offering other services, such as booth-only WiFi (to make the person come into the booth), or directory information.

The hard part of setting up a service like that today is securing the little plot of sidewalk. But the phone booth guys already had all that: location, a wire coming in, electricity.

And the telcos and their partners blew it all thinking that we don't need phone booths anymore.

Link: Does Anyone Use Phone Booths Anymore?

Maybe instead of ripping out the hardwired phones from these phone booths, maybe they can leave them there as a reminder of days gone by or for those times when you need a little bit of piece and quiet when you’re trying to make a call? Or better yet, turn them into pico cells for the mobile network operators?

Awesome Clay Shirky interview (with a side-comment that cuts too close)

Glenn Fleishman did a great interview (back in March) of Clay Shirky on the topics in Clay's new book 'Here Comes Everybody'.

Clay, as always, has some great stories to tell. Glenn is pretty good too. Yeah, you should go and download the interview from Glenn's pages (link below).

The whole interview is great, but it was the very end that made me reel. Glenn asked Clay what business could do to take advantage of the participative nature of the Web. I overly simplify, but Clay, among other comments, mentioned that instead of proclaiming the next great thing in a press release and putting all the money into one pot, that companies spread the money across many endeavors and see what sticks (and do it without fanfare). Basically, have many experiments, put it out there, and see if folks like it rather than gab about it (Show vs Tell?). He uses the example of Wikitorial.

Gosh. I have lots to add to that and a few more examples. (My tongue is bleeding, I am biting it so hard. Though a beer can loosen it, in case you are interesting in a tale of enlightenment, abandonment, discovery, creativity, stealing, cluelessness, and dissapointment.)

While I hope that some companies hear what he has to say and take the learning to heart, I fear that most, as Clay points out, will end up focusing on the wrong thing. Or, as Glenn says, miss the elephant parade passing in front of them.

Sigh.

Hey, I'm just road-kill on the info superhighway. Go listen to some smart people (the link is below, in case you forgot).

Link: TidBITS Blog Post: The Internet Organizes Itself: Here Comes Everybody

I sat down with Clay on 14-Mar-08 to talk about the book for a short article that appeared in the Seattle Times, focused on the business side of his book. However, the Seattle Times allowed me to publish a podcast of our roughly 40-minute conversation.

As an aside: Clay does validate some thoughts I've been having. It's always nice to inadvertently come to the same conclusions as others smarter than me.

Image from Joi Ito

Plaxo is acquired by Comcast, Zyb by Vodafone

Ok. This is last week's news.

But, I am not seeing much discussion about this. Why?

Mashable picked it up right away. But not one person commented on Plaxo's own site (link below).

Is this significant? Does it matter? Does this remind you of 1999 when Telcos bought Web-heads and did nothing with them?

FWIW, I just deleted my Plaxo account. Never really got anything out of it. BUT, with Pulse, they had an uncanny way of adding things I was thinking of. I think Pulse could have been like FriendFeed (and was about much earlier), but it happened to be attached to a company that made its name in corporate contact management. Eh. Brand dissonance.

Also FWIW, Zyb announced it was picked up by Voda two days later. Their post got a bunch of comments. Zyb was on a similar trajectory as Plaxo. Both were considered the leaders in this area, but we always felt Zyb a better mobile offering. (and I did not delete my Zyb account just yet)

We followed both closely since synch is a part of the (ever) upcoming Ovi.com that I was a part of (and Nokia also has the My Nokia Back Up service). Yeah, both companies had set out to mix PIM back up with social networks. And, yes, the company who can solve this issue will do well.

Do you think Zyb and Plaxo have done well with this fusion?

Link: Plaxo's Personal Card: Comcast to Acquire Plaxo; Pulse to Become Central to Creating Unified “Social Media” Experience Across the Web, the TV (and more)

Joining forces with Comcast is a real win for our customers, our investors, and our employees. Comcast has an exciting vision to bring the social media experience to mainstream consumers. Together, we will be able to help users connect with all the people they care about, across all of the devices they use, with all the media they love to consume, create, and share. This is also great news for the Internet industry at large, where Plaxo has been – and will continue to be – a strong advocate for opening up the Social Web.

From my sideline seat, Thompson Reuters seems awfully archaic

Can someone please explain to me how and why Thompson Reuters Scientific has such a grip on scientific journal Impact Factors?

If you look at the list of various indexing services, you can see that they are all brushed aside for Thompson Reuters. It seems to me that unless a journal is indexed by Thompson Retuers, then it really is not considered to have any relevant impact on the scientific literature.

OK, so maybe these guys were anointed by the community to stand in as the über-authority index. I can deal with that. But, I think also there is an opportunity for an independent authority index, à la Technorati.

I think it just might be my natural inclination to suspect a single source of authority ranking. But I think it's more likely because I see so many tools available to measure impact that could be more responsive and maybe more granular than what the current system seems like to me.

I've started looking into this. People are coming up with alternatives. It also seems like Thompson Reuters realizes that they might lose a hold on their position.

Yeah, my brain has been munging on this lately.

Link to article that set off this brainwave: BioMed Central Blog : Orphanet Journal of Rare Diseases tracked by Thomson Reuters and set to receive first impact factor in June 2008

Orphanet Journal of Rare Diseases was recently accepted for tracking by Thomson Reuters. It is included in the ISI Web of Knowledge database and will receive its first impact factor this summer. We are delighted with this achievement, which confirms the prominence and reputation which Orphanet Journal of Rare Diseases  has achieved in its field.

Link to recent journal article: Effectiveness of Journal Ranking Schemes as a Tool for Locating Information

As de Solla Price observed [3], the number of scientific journals and the number of papers published in those journals is increasing at an approximately exponential rate. The size and growth of the research literature places a tremendous burden on researchers—how are they to select what to browse, what to read, and what to cite from a large and quickly growing body of literature?

Mechstreams - when machines start lifestreaming with us

Ok, so lifestreaming is the rage of '08, what with SocialThing! and Friendfeed and all similar services hogging all the attention.

But I also see something that's been bubbling under the surface that I call 'mechstreams'. I see machines edging in as equals in our lifestreaming services, sending out streams of data indicating what they are up to or thinking or what. And I don't mean info alerts like weather or news, but info about what is going on.

This is not new, really, but I think the time is right for these things to mix with real lifestreams.

Examples:

• Tom Armitage hooked up the Tower Bridge to Twitter so that it can say 'What am I doing?' every time it goes up or down.
• I heard yesterday from Jan Chipchase of a teapot that says when it's boiling water. In this case, it's an unobtrusive tool to keep an eye on elderly folks - if the teapot is being used, then the old folks are doing fine.

I think this is fine and dandy in this day and age of the re-birth (again) of ubicomp and semweb (both of which I have been waiting to bloom for a very very long time).

So, where do you see this going? Tom Armitage gushed about this about a year ago. Have things really developed further?

[PS: In the course of actually slowing down to write this post, I keep finding more discussion of this topic. The inestimable Julian Bleecker used the term 'blogject' for objects that blog. He wrote up a minifesto 2 years ago. Krap, I need to get out more. Some days I feel like Rip van Winkle waking up and missing a huge chunk of the discussion.]

SwitchAbit as the great data switchboard in the cloud

Just stumbled upon this (no longer remember how):

Link: At SwitchAbit, Twittergram Shares a Common Future - GigaOM

So what is a SwitchAbit? Think of it as a web services switchboard that allows you to plug any type of content from one service (say Flickr) to another (say Twitter) — or even between multiple services. The dashboard is likely to be released later this summer.

Last year I had a few Ramblings on noise that focus on the internet as a noisy environment with data emanating from apps all over the place and how can we find, navigate, recombine, and contribute to that noise in a human way.

I've read a few recent posts that revolve around this topic and that I am still trying to digest. But, these thoughts tie three key trends I see unfolding before us: lifestreams (human streams of data), mechstreams (streams of data from machines), and the semantic web (meaning attached to everything).

Mowser and dotMobi: Ouch, the cognitive dissonance is huge here for me

What do I get when I mix a top level domain I really do not like, with a concept (transcoding) that I have been grappling with for years, and two really smart guys I highly respect (Russ Beattie and Mike Rowehl)? Severe cognitive dissonance.

I don't know what to think.

DotMobi
Ok, I am not of the 'one Internet' crowd that believes that mobile devices need to be able to view the Web same as any PC. I think that there is and should be many ways to mobilize Websites or use Web services on mobiles. But, I am not of the camp that thinks we should have a top-level-domain specifically for mobile sites.* To me, that's a ghetto, a return to the bad parts of WAP. So, dotMobi has never sit well with me (this is NOT my employer's view, mind you).

Transcoding
There is a place for transcoding, depsite what some very very good friends, who know better than I, advise me. Yet, Mowser, which was recently acquired by dotMobi (see link below), is a transcoder. I like it. Some folks (even dotMobi, it seems) are not into transcoders (such as Google's proxy) that munge all the hard work the Web developer has done. Mowser does a good job trying to stick to that work, and also provides options to go to the full page.

Miker and RussB
Gosh, these are two very smart guys who truly understand the fusion of mobile and Web. And they have the tech chops to put their ideas in practice (magdat and Mowser are examples). Russ and Miker took the ultimate gamble to get Mowser off the ground. Unfortunately, they need to recharge their batteries now before putting in another crack at their ideas, with the learnings from Mowser strengthening them. I am looking forward to them coming back in a few months or a year, reinvigorated and ready to shake the tree some more.

So, yeah, it stinks that Mowser didn't catch. But, is it good that a top-level-domain company is getting into transcoders? Eh, could be, at least for dotMobi. They already offer a tool from mobileSiteGalore to help folks make .mobi websites (I use Winksite for my personal site and Nokia Conversations, I also use Mippin for Nokia Conversations). Mowser can be well integrated into that.

What do you think?

So, yeah, 1) good for Mowser, 2) good for Miker and RussB, 3) good for dotMobi. It's just the dotMobi part that must be grating on me. Eh, my problem, not theirs.

Congrats Miker and RussB!

Link [via Tweeps @twhume and @mtrends]: dotMobi Acquires Mowser Assets

dotMobi's acquisition of Mowser's technology, developed by Bay Area mobile pioneers Russell Beattie and Michael Rowehl, is another way for dotMobi to provide a complete range of mobile content creation solutions for businesses of all sizes.

...

"At its heart, Mowser is a PC website-to-mobile website content adaptation engine," said Trey Harvin, CEO of dotMobi. "dotMobi has been vocal against 'blind' content adaptation because it doesn't allow site owners to have control over their content. dotMobi believes that brands and businesses should always have the final say over how their material is presented, and that the content should uniquely take advantage of the capabilities of a mobile device. This has been one of our core philosophies all along, and something dotMobi is looking forward to addressing with the integration of the Mowser assets into the dotMobi product line."

*I do think .sex would make a great top-level domain. It can be typed with just the left hand, and might cause a flurry of left handed domain names to be registered. Heh.

Plug: Design event coverage on Nokia Conversations

Just wanted to say that, even though I could not attend, Nokia Conversations is covering the Open Studio event in London today (29apr).

We have two writers there, posting things as the day progresses. We're also hoping to get some cool photos and footage to share with everyone.

So, if you're into Design, come check us out.

Blood from stone: Don't focus on ad revenue from social networking services

Ok, so it's not a revelation when I say that you don't need to make money off your core service. Your core service drives the interaction with the customer, but the money can come from some other area.

But, be careful where you _think_ you can get the money.

I've never been a fan of ads as a mean to make money. At least not for someone who is just displaying the ads. The real money maker is the one who _sells_ the ads.

But, for most services, it's the best we got.

Bollocks.

I've never been satisfied with folks trying to build services that generate 'eyeballs' just to 'monetize' that traffic with ads. I've been even less enthused by social networking services that try to convert what is a personal interaction between the users of the service into a chance to score advertising views.

Online social networking services thrive because they are a form of social lubrication. They are a means to an end, but not the end. We're social grooming to _do_ things together - learn, invent, trade, strengthen trust.

Then make money by promoting the activity, not by having folks mill about. Yes, social network is the concentrator, but what the folks end up doing is where the money's at.

One good example is O'Reilly. Is it a social networking service? Sure is. Where do they make money? Selling info to the network, the info the network trades in when within the O'Reilly social network. For O'Reilly, it is the social network that differentiates them from just another publisher.

So, now I'm wondering about social networks overlaid on top of interest domains.

Social networks, such as Facebook, which do not have a focus for the _why_ people come together, might never gain the proper traction to make money beyond a few anemic ad clicks, or, like Facebook, will have to contrive sleazy ways to get money off the social network.

Someone like Facebook should optimize the service around the key reason folks use the service, rather than crate gimmicks to just keep folks around.

MySpace is at least trying to capitalize on Music and LinkedIn on business services. And there are a ton of examples, I am sure.

Just thinking out loud. These thoughts arose from noting that Google and Facebook are seemingly slowing down, and observing the interactions happening in my Twitstream. For some of you, I am sure this line of thinking is nothing new.

Comments?

Loïc muses - Global Or Die: Is There A Future For Local Startups?

Loïc wrote a great article (with video) on global thinking for start-ups, with a ton of great tips (link below).

But, I think he's being a bit narrow-minded about the death of local internet services.

In many ways he is right that being a copy-cat who makes a localized version of a global service is not an easy task anymore. Nonetheless, I do think there's a future for local startups. Indeed, I think hyper-locality is the where a lot Web growth is. Much like social media is breaking down the power of Mass Media, I think we need to realize that in some segments, it pays to be local.

For example, a yellow pages or classified service, really does best with a local presence. A media service that is local would do better than some global service.

Just as mass media no longer is for everyone, not every service is at its best if global. Yet, it's just hard to scale globally with a local business. Web-heads like to add servers, not people, to grow the company.

I know some people who are creating great local services that are not copy-cats and will do well specifically because they are local. Do you know of any?

Link: Global Or Die: Is There A Future For Local Startups?

My friend Loic Le Meur wants to convince startups to avoid the lure of focusing only on local markets. He asked to write the guest post below, which I think is worthy of debate.

*Also, Loïc's a great example of someone who realizes the tyranny of Silicon Valley, that the Valley really is the only place in the world to run a tech business. I've railed against that tyranny, me not being from the West Coast. But, the past few years has shown some growth in cities like New York and Boston in the mobile and Web space. Also, I don't know if it's just because I have so many tweeps from there, but lately a lot seems to be happening in London, too. That's good.

Biology is messy! Synthetic biology will be synthetically messy, too! (plus BONUS)

I've been reading about iGEM and the Registry of Standard Biological Parts. It's a component view of biology - that there are parts in biology that can be used much like electronic parts.

Eh, I know they don't think it's that simple, but it sure can be misleading what they are trying to do.

These folks are characterizing biological parts and creating a catalogue from which to plug and play and mix and match to create circuits that do something. They are looking to establish standards, construction tools, and some abstraction to make it easier to build synthetic systems. And that's all fine and good. It's like the early days of electronics. And they have done some amazing things, light replicating photography with bacteria, some cool circuits, and more.

But, in my biomedical-scientist eyes, I just wished they would think more than just creating digital circuits on analogue systems. Also, I feel that biology doesn't gate well, I mean, it's very non-linear and hard to do on-off 'mathematics' with biological components. And by trying to build digital stuff, they lose the value of analogue.

In short, I think the questions they are asking are not the right ones for the system.

And thinking back to Craig Venter, moving forward, synthetic biologists are going to have to think of analogue, of biological answers to questions. We are so accustomed to neat and clean binary fixes to things, but seem to forget that in biology, so much is probability, fuzziness, and selection, and failure is so much more nuanced.

I've designed many macromolecules and expression systems, grew all sorts of micro and macro organisms, and dealt with all sorts of biological systems. In so many ways, we were not far from the brewers of Mesopotamia, coaxing and praying for a healthy growth and production of the right enzymes.

Yet, we have had in the past 30 years, and even more so in the past 5, a deeper understanding of the mechanisms. But, we mustn't just translate that all into our digital minds, we need to think of these organisms and molecules on their terms.

When I was a grad student, my advisor was a physical chemist doing biochemistry. To him, DNA wasn't just A T C and G, but a chemical entity. I came out of there seeing proteins and DNA in a way that my molecular biologist colleagues did not, and a deeper understanding of the complex interactions in biological systems.

In the same way, synthetic biology is going to have to go beyond linear circuit building, but take advantage of the strength of these marvelous billion-year evolved systems.

Here's a video of Drew Endy, a leader in this field, putting synthetic biology in perspective:

BONUS: If you really get a kick out of visualizations, the Machinery of Life, by David Goodsell, is a really neat peek into the molecular world at the scale of proteins and bacteria.