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.

What can we learn from Asilomar?

There was a flurry of indignation recently on the DIYbio discussion group over an article in the Wall Street Journal over the safety of bio hackers (with added aggravation from Fox News' dramatic title to the exact same article).

Interestingly, this kind of alarm is not new, especially to biology. In the early days of molecular biology, there was a sudden panic that recombinant DNA was inherently unsafe. There was no basis to understand what was possible, what was ethically permissible, and what was unsafe.

Asilomar
In a landmark event, that went on to change the nature of science policy and public outreach, Maxine Singer and Paul Berg, pioneers in molecular biology, assembled about 140 scientist, lawyers, and politicians to discuss the future of recombinant DNA.

The Asilomar Conference on Recombinant DNA, named after the place it was held at, addressed the principles for safely conducting recombinant DNA experiments, listing potential risks and outlining containment principles. The discussions also involved assessment of organisms, principles for choosing bacterial hosts, and what constituted good microbial practices. And finally, it explored the need for proper education and training of research personnel to carry out the recommendations that came out of the discussions.

There were a few interesting, non-science, aspects to this conference, as well. There was a desire to be transparent in the discussion and involve the public, to allay any fears non-scientists might have. Also, the Asilomar scientists drew up a series of voluntary guidelines rather than a regulatory body.

What can we learn?
Asilomar is part of the culture and history of any molecular biologist (at least it was for me, I learned about it early in my career). Therefore, the precautionary thinking, the openness and public discourse, and the self-organizing regulation is part of molecular biology.

DIY biology is part of all this, and the same culture is part of a community that already is a cautious as it is curious and open. I am not sure if there's a need for an Asilomar for DIYbio, but with calls for licensing and calls from the FBI, clearly something definitive needs to be established.

It's been great to see the discussions around this by the DIYbio enthusiasts. They clearly understand the situation, now it's a matter of getting the message across.

Image from MIT archives.

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

When the Central Dogma is not enough - microbial small RNAs

One thing that has always bugged me was a sort of pendatic repetition of what's called the Central Dogma of molecular biology - that DNA goes to RNA goes to protein.

What bothered me was that it way oversimplified the complexity of information transfer and control in organisms. And for me, the excitement has been in all the exceptions to this Dogma.

For example, I had a sort of Rip van Winkle gap between when I left science to when I re-engaged years later (missed the deep stuff, while keeping up lightly with the superficial stuff). Back in 1999 we were talking about some weird things going on in nematodes, where you could control gene expression simply by adding some small RNAs to cells. Fast forward to 2006 and I find out that these small RNAs have been found everywhere as a control mechanism.

Now mix that with the resurgence of microbiology (or at least it looks like a resurgence to me) and folks are starting to use small RNAs as a way to read gene expression patterns in micro-organisms. The idea is that it's a quick readout before the organism starts responding to the effects of collection and removal from its native environment.

"If we think of marine bacteria and their proteins as tiny factories performing essential biogeochemical activities — such as harvesting sunlight to create oxygen and synthesize sugar from carbon dioxide — then the sRNAs are the internal switches that turn on and off the factories' production line. Their discovery in the ocean samples opens the way to learning even more detailed information in the lab: the researchers can now conduct lab experiments to look at the effects of environmental perturbation on microbial communities. These new sRNAs also expand our general knowledge of the nature and diversity of these recently recognized regulatory switches." [apologies to the person I got the link of, as I have forgotten who it was] 

Cool.

Image from wikipedia

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.

Ginkgoo comes out with BioBrick Kit with New England Biolabs

Gotta say that it's really good when you can start buying kits that make things easier and push down the threshold for someone to do something (especially in science).

BioBricks are standard parts used to make functional pieces of DNA that can be placed into bacteria. The guys behind BioBricks, and their commercial spin-off, have been building and cataloging parts in a Registry of Standard Biological Parts. Making a catalogue and building standard parts are considered a big chunk of getting Synthetic Biology (synthbio, as others call it) off the ground.

Now Ginkgoo, a player in synthbio and a team of folks who are drenched in BioBrick use and knowledge, have released a kit to streamline the assembly of BioBricks into multi-part constructs. And with folks like Mac Cowell of DIYbio working on the manual, there's hope for us outside of acedemia.

A young company with lots of promise, it's great to see them starting to flesh out their products. Looking forward to meeting these folks some day.

Image from the NEB product page.

Pause for station identification

Wow. I haven't done one of these in a long time.

Molecules on the mind
My name is Charlie Schick, I am currently Editor-in-Chief of Nokia Conversations (but not for much longer).

For the past few years I have used this site mostly to philosophize on the fusion of Internet and mobile devices. But I've seemed to have made a definite shift back towards my first life - biology, science, and such similar geekery. Hence the name change of the site and its new de facto direction (or is that a meander).

My bio says that I have thoughts and actions ranging from biomedicine, molecular manipulations, indiscriminate writing, the long now and a post-electronic age, various forms of performances thespian and corporate, and philosophizing on the fusion of Internet and mobile devices. I am not sure what will transpire over the next 6 months and after, but my thoughts will be still roughly in those areas, just with a different emphasis and priority than before.

And a word from our sponsors ... you.
As I've said before, thanks for reading my stuff. I am not sure how things have changed between us, what with long breaks between writing and a total topic shift from what originally brought us together. That so many keep coming back to this site, suggest that I do have something of value to you all. View me as one of those sites that is outside your usual comfort zone and that will stretch your mind.

Heh.

Standard Disclaimer (riffing off of Cringley)
Everything I write here on this site is an expression of my own opinions, NOT of my employer, Nokia. If these were the opinions of Nokia, the site would be called 'Nokia something' and, for sure, the writing and design would be much more professional. Likewise, I am an intensely trained professional writer (heh), so don't expect to find any confidential secret corporate mumbo-jumbo being revealed here. Everything I write here is public info or readily found via any decent search engine or easily deduced by someone who has an understanding of the industry. On the flip side, this is my personal site. Please don’t flood me with ideas that you think Nokia might be interested in. There are other channels for such biz dev, and this site is not part of them.

Funky bioelectronics

I'd been meaning to look into this more ever since reading about it in the quarterly tech review in The Economist, back in Dec.

There are folks who are creating nanoscale structures of pores and particles, combining them with extremely sensitive detection tools, and creating new breeds of macromolecule detectors.

A hard drive for GMR
One of them uses the same tech as in hard drives, used to detect magnetic particles. They are called called Giant Magnetoresistive Sensors (a gnarly review for you hard-core geeks).

As Shan Wang from Stanford says,

"Magnetic nanotags (MNTs) are a promising alternative to fluorescent labels in biomolecular detection assays, because minute quantities of MNTs can be detected with inexpensive giant magnetoresistive (GMR) sensors, such as spin valve (SV) sensors."

Wicked.

And Wang has an example of how this can be used, in this case, in the detection of Human Papiloma Virus.

Pores and beads
The other methond is the sequencing of DNA by passing it through a nanopore. Because, like beads on a string, as DNA passes through a pore each base has a slightly different (and detectable) electrostatic effect and one can read out the sequence as the strand goes through the pore. The only person I found actually playing with this was Aleksei Aksimentiev from whom I took the image above.

Surface issues
When I was doing biochemistry, I used a ton of specialized equipment to measure enzymatic activity. But one that I never got a chance to use was a gizmo from Pharmacia that took advantage of a funky effect called "surface plasmon resonance." The only way I can describe it is an effect by which mass on one side of a surface affects the refraction of light on the other side of the surface (Wikipedia is not any clearer). In that way, you can have something binding on one side of a chip that is then detected spectroscopically on the other side of the chip, with great sensitivity and in real time. From that, you can calculate the on and off rates for molecules binding, which is what a lot of the biochemistry I did was about.

In any case, it's always interesting when hard-core physics meets biology. While I start getting glazed eyes when getting too close to physics, the best parts of my training were when physics and physical chemistry helped explain a phenomenon we were studying. I would say the strength of my training was the mix of physics, chemistry, and biology that made me see systems at many interacting levels, each contributing to the model and experiments.

And, as in most multi-disciplinary endeavors, these folks, above, mixing hard-core physics and biochemistry are also adding to a richness that either disciplines on their own could not.

Exciting.

Hackspaces on the mind

I don't know why, but ever since returning from SXSW09 I've been wondering about hackspaces. As you might know, hackspaces are like a nerd collective, where there is equipment to use, friendly folks to show you how to use them, and a rich environment for play and exploration.

While writing this post, a quick search for hackspaces led me to a recent article from Wired about folks flocking to hackspaces, so I guess I am feeling a vibe that's going around. The article provides a good overview of hackspaces. Despite what the article says, hackspaces are not new. And hack spaces are not just focused on electronics, either.

Being a bit of a bike tinkerer, the hackspaces I think of are more like the LA Bicycle Kitchen and the Broadway Bicycle School. Back in the 80s, I was inspired by the Broadway Bicycle School, and after reading about the LA Bicycle Kitchen a few years back, toyed with the idea of starting up a similar sort of thing.

There are also ample examples of shared work spaces. My buddies at Republic Publishing hang out a lot at The Hospital in Covent Garden. Todd Bida pointed me to the Cambridge Incubation Center. But these are shared facilities for small businesses and independent workers. And, there are tons of examples of youth centers that provide a hangout-homework-chilllax atmosphere for teens (yes, scoped out a plan for one of these, as well).

Indeed, hackspaces take the shared workspace, add a dash of cooperative thinking, with a healthy dose of tools to create something special for folks to just make something in a supportive environment. Shared spaces, as described above, are usually "co-existence" places, where folks work in parallel, with little cross-fertilization (and that's OK, too). In my mind, I would like a more interactive and social environment (for example, I asked my buddies from Republic how much they interact with others from The Hospital).

With my latest urge to get back into science, I wonder if there might be a market for a, say, DIY biology hackspace. The capital costs for hacking biology are huge, what with incubators, autoclaves, shakers, pipettes, disposables, and the like. In labs I worked in, the burn rate was something like $1500 per person per month (full-time hard-core research, of course). And start-up costs usually were in the hundreds of thousands of dollars.

But that speaks for the benefits of shared equipment that comes with a hackspace. And the rise of synthbio and DIYbio suggests that there might be a need for some sort of bio hack space. 

Of course, a whole ton of barriers crop up in my head: regulation, training, disposal, licenses, and so on. But just a matter of detail, right?

Image: mine

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)

Changing names

As you can tell, I've been writing more and more about science, biochemistry, medicine, and the like. I've moved most of my mobile industry writing to Nokia Conversations, the corporate blog I run for Nokia (for now; more on that later).

Suspecting that I will be writing less things related to what I've been writing about in the past 5 years, I decided to change the name of this site to Molecularist, a name I came up with to describe a person who fiddles with molecules, such as proteins and nucleic acids, much as I did before I jumped into the world of wireless, and much like I've been hanckering to do for the past year or so (and more on that later, too, I hope).

So update your bookmarks and feeds. If you want to. I would hope you'd keep reading me, just to stretch your mind (or to get it off the usual mobile stuff you have normaly read hear).

BTW, there will still be talk of Web services, since lots of the science I've been thinking of intersects with the future of the Web and social networking and other interesting stuff. Also, by finally getting my own domain name, if I ever get tired of TypePad (upon which this site runs) it'll be easier to move (but, after a persuasive talk with Sippey, I'm sticking for another year at least).

Ta.

Image from EraPhernaliaVintage

(of course, I'll be changing other things around here to reflect all this)

MIT makes all its new scholarly research publications Open Access

This is amazing. I know folks battling for Open Access in science for over 10 years. Even with heavy hitters, such as Harold Varmus, PubMed, and others supporting Open Access, status quo still dominates the science publishing industry.

Now, Peter Suber reports that the MIT faculty has voted unanimously to give the university nonexclusive, irrevocable, paid-up, worldwide license for all scholarly articles, which the university will then make available through an Open Access directory.

Might this be the tipping point for Open Access? As I see newspapers sinking while holding onto their 20th century biz models, might the big science paper publishers wake up to this change in their world (ten years coming, mind you).*

I'll be giving a talk next week about the future of publishing. Let's see what folks say.

[via @perryhewitt] Peter Suber, Open Access News:

Hal Abelson's [MIT faculty member] 'comments:

I chaired the committee that drafted the resolution and led faculty discussions on it throughout the fall. So I’m particularly gratified that the vote was unanimously in favor. In the words of MIT Faculty Chair Bish Sanyal, the vote is “a signal to the world that we speak in a unified voice; that what we value is the free flow of ideas.”

*BioMedCentral showed that even the old model could work in Open Access, such that they got bought out by Springer.

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?

Redefining the concept of organism

A while back, I stumbled upon an article by Freeman Dyson on Carl Woese. Carl Woese is a long time scientist studying the origins of life and revolutionized thinking around early life, microbiology, and phylogeny.

Freeman Dyson's article is a great overview of the discussions around pre- and post-Darwinian evolution*. Darwinian evolution is what we are used to, a standard "fight for survival" of non-interbreeding species that slowly evolve their fitness to the challenges in the environment.

What really flipped me was Dyson discussing pre-Darwinian evolution, an idea postulated by Carl Woese back in 2004 in an article titled "A New Biology for a New Century." The thought is that early life was a time of promiscuous gene swapping. That, as I see it, an organism was a sack of molecules and genes that worked together to propagate a collection of "features." Then, at some point (Woese suggests at least three) an organism stopped, found a good set of genes, and brought this lateral gene transfer down to a trickle. And there you have a "species."

The three times Woese mentions were the times that gave rise to Archaebacteria, Bacteria, and everyone else. This free mix and match with a sudden stop makes sense of why there are three large groups of cell structures, yet that they are related in some way.

This idea really hit home for me when listening to Penny Chisholm, a microbiologist, talking about Prochlorococcus on Science Friday. This small cyanobacteria might be the most abundant photosynthetic organism, but Chisholm and colleagues only discovered it in the 80s.

What was interesting was her answer about different species of Prochlorococcus: she called them "genomic variants."

This ties back to what Woese was implying about lateral gene transfer and pre-Darwinian evolution and sacks of organisms with a collection of genes. If all organisms are in the possibility-space of all arrangements of genetic elements, then a particular strain of organism would be a peak of variation in that particular area of arrangement of genetic elements (but still part of a continuum of possibility-space).

Micro-organisms still do a lot of gene transfer (witness the spread of antibiotic resistance across species). But I suppose at some level they mix up everything and can have a large amount of variation across a single species. Hence, Chisholm's observation that Prochlorococcus species are best viewed as variants than distinct species. Promiscuous lateral gene transfer across Prochlorococcus "species" deflates the definition of species as non-interbreeding organisms.

As microbial biology has a renaissance due to the rise of synthetic biology (humans effecting lateral gene transfer in micro-organisms at a scale we haven't done before), understanding "speciation" in terms of "genetic variants" will go a long way in understanding how and what genes are to be used.

*Dyson also compares the way cultures laterally transfer as the post-Darwinian era.

Image from If you dream it...

Phylostratigraphy: Genetic Archeology

The Economist reports on some scientists that did some phylogenetic comparisons to see when certain genes arose. The scientists noticed that genes that appeared earlier in evolution are more likely to be disease genes than genes that arose later in evolution.

For some reason, the writer for the Economist suggests that older genes would have had more time to evolve any disease away. But, on the contrary, I suggest that older genes are more fundamental and therefore more prone to be involved in diseases. Though I am not sure sure why the scientist found that "genes specific to mammals, by contrast, barely ever carry diseases." Surely there are genetic diseases that revolve around brain genes foud in humans. But it could be even those genes go far back in time.

Nonehteless, the word "phylostratigraphy" is damn cool.

Link [via @preoccupations]: Genes, disease and evolution | Bad old genes | The Economist

As they reveal in a paper in Molecular Biology and Evolution, the researchers found that the majority of disease-causing genes were present in single-celled organisms and that most of the rest arose when multicellular creatures began to evolve. Genes specific to mammals, by contrast, barely ever carry diseases.

Image by Stephen Witherden

Presidential DNA tested for 2012 election?

Wow. This is a deep topic. While I think the discussions around DNA testing will start raging in the next 12 months, for sure there will be a question of whether presidential candidates should have a DNA test as part of the public health report.

Ho-boy, this is getting interesting.

Link: Presidential DNA: Don't Ask, Don't Tell? : The Personal Genome

The next presidential candidates will face an electorate that is radically more conversant in and curious about DNA than ever before. We should reasonably expect that the presidential election of 2012 will include, for the first time, requests for candidates to make their genetic information part of the public record.

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

Potential of immune system reboot?

This is cool (below). Gene therapy combined with a re-install of the immune system.

I am writing a story where the main character basically gets an immune system reboot. Due to the longevity of the people in the story, they are more susceptible to auto-immune diseases as the immune system breaks down or goes awry. Therefore, folks get regular immune system resets and required re-immunizations.

I know someone who is over 80 and is healthy except for an auto-immune disease that he got in the past 5 years. A reboot would cure him. Right?

Link: The Spittoon » Very Personalized Medicine: Genetically Customized Bone Marrow Transplant May Have Eradicated Patient's HIV

The doctors reasoned that if they could find a donor who was not only immune compatible with their patient, but also had two copies of the Delta32 mutation in the CCR5 gene, perhaps they could simultaneously eradicate his leukemia and his HIV infection.

Remarkably, such a donor existed. And 600 days after his bone marrow transplant, the patient is both leukemia- and HIV-free.

A good warning for writers, by Joel

Another great article by Joel Spolsky on, basically, literary laziness.

Link: Anecdotes - Joel on Software

This is not the way to move science forward. On Sunday Dave Winer [partially] defined "great blogging" as "people talking about things they know about, not just expressing opinions about things they are not experts in (nothing wrong with that, of course)." Can we get some more of that, please? Thanks.

“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.

Three trends for the future of biology

A chance encounter, about a year ago, with some interesting minds in the field of biomedical publishing had me going back to my roots: biology. I've been fascinated by science from a young age, particularly biology, which I studied and practiced for many years before a wormhole whisked me away and plopped me in the middle of the mobile phone industry.

The consequence of this chance encounter with biologists was for me to reconnect and catch up with what was happening in biology. I really don't know if my fresh eyes are actually seeing something new or if my absence has made me susceptible to an incomplete model of where biology is going. In any case, what I do see are some exciting developments.

To get to the point, I see three major biology trends that present enormous opportunities:
1) Synthetic biology - from crafting whole genomes to messing with computational biology, we are seeing a renaissance of microbiology and microbial genetics.
2) Personal genomics - as genomic analysis tools like sequencing machines and micro-arrays get cheaper, the ability to rapidly analyze ones own genome at some level becomes a reality.
3) Biological publishing - the sheer volume of scientific publications and data, and their increasing availability in open access digital formats, is straining the way scientists explore, syncretize, and contribute to knowledge. [I need to find a better term for this, as it's not about publishing but the whole cycle of the info.]

These three areas have been consuming a lot of my brain cycles, with resultant decrease in posting the thoughts down here. I suppose I needed to mull these things over before starting to haver about them.

I thought I was ready to knock these off but have been having a fun time following the cognections radiating off from these topics. I have a lot of bookmarks with partially read stories. So, further posts on these topics will come slowly as I continue to digest.

Wow. It's nice to use one's brain.

Image from ynse

Cool animation by 23andMe on Human Prehistory

For various reason I've been lurking around 23andMe, a personal genetics social service thingy out of SFO (I follow them on Twitter, of course). One big part of what they do is basic education on genetics, what it means, how its done, and its place in our understanding of who we are.

They've made a really cool animation of human prehistory, from chimps to homo sapiens (link below).

Looking forward to the next chapter.

Link: 23andMe - Human Prehistory: Prologue

Image from the animation

Does paying off the creditors undermine social trust?

Via a few people I went and read Margaret Atwood's Op-Ed in the NYT (link below) about debt and its role in society. Nice read. For me the most interesting thing is the word for 'debt' and 'sin' are the same in Aramaic (see quote below). That turns 'sin', something to be ashamed of and a violation of something beyond society, to 'debt', something you owe the people around you - much more accountable.

Leads me to thoughts about different shame and guilt mechanisms some societies have, say Catholic vs Lutheran.

Hm.

In a related topic, did you know that even monkeys understand fairness (the basis for debt and credit)?

There was an experiment where they gave two (rhesus?) monkeys cucumber slices. No problem. But, then they started giving one of them a grape (much tastier). The one with the cucumber slice threw it back in apparent anger for being treated unfairly.

In another story, this guy got mauled by some chimps who were jealous of the attention (and cake) he had been giving another chimp (the guy was the chimps previously adoptive human parent). The angry chimps just thought it was plainly unfair not to share the cake.

Yeah. I think so much of our massive brain is geared to keeping (up to 150?) various combinations of relationships and debt-credit arrangements. Indeed, the whole human social system is based on tit for tat and retribution for those who violate this necessary social flow.

What do you think?

Link: Op-Ed Contributor - A Matter of Life and Debt - NYTimes.com

Once you start looking at life through these spectacles, debtor-creditor relationships play out in fascinating ways. In many religions, for instance. The version of the Lord’s Prayer I memorized as a child included the line, “Forgive us our debts as we forgive our debtors.” In Aramaic, the language that Jesus himself spoke, the word for “debt” and the word for “sin” are the same. And although many people assume that “debts” in these contexts refer to spiritual debts or trespasses, debts are also considered sins. If you don’t pay back what’s owed, you cause harm to others.

Image from Chrys Omori

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.

Tracing paths in woods nearby

I've moved to a new neighborhood and there's a forest nearby. Today, to get a better idea of all the trails, the dog and I wandered every trail we could find. I also has Sports Tracker on to see what a trace of the ramble might reveal.

The resolution of the GPS kept some paths that I walked over more than once from being overlaid, showing two parallel paths.

But, for me, it gives me an idea of all the paths I can walk there.

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.