Life blog

Are scientists afraid of blogs and tweets?

Nature has a nice wee article (no subscription required to read this one, FTW!) on the state of what one might call "informal" peer review - the challenges and questions to published works that come from blogs and tweets and the like.

For those of us who have been talking about the changes needed in the whole infrastructure and culture of science discourse (particularly the lock publishers have on research papers), this Nature article holds no surprises. Indeed, it comes off making some scientists seem a bit whiny.

The article points to some recent events where scientists have been skewered online for papers or claims made. This reminds me of the early days of blogging when folks were trying hard to control the message and were freaking out when anyone said anything.

The paper does have some great examples and quotes though. For example, David Goldstein, from Duke's Center for Human Genome Variation, is quoted saying, "if the work is solid, it hold up over time". And the efforts by PLoS with comments on papers, how arXiv.org works, and ratings from F1000 are good to show to those who are probably reading the article to figure out how to survive the blogosphere.

My favorite comment by the author, though, is:

One solution may lie in new ways of capturing, organizing and measuring all these scattered inputs, so that they end up making a coherent contribution to science instead of just fading back into the blogosphere.

I've been harping on this for a while and still think there's an opportunity to create a solution like this. I think there is a lot of good thinking, plenty of examples in other industries, and folks are doing parts of this solution, such as trying to think of other ways to change how we calculate the impact of a paper (à la Technorati or through real-time stats), author ID systems, or ways to turn the science paper into the social object. The article also mentions Jason Priem's work on alternate paper metrics (alt-metrics).

It feels like 2004 all over again as another industry discovers the power of devolving the power back to the masses. And the Web was initially designed by scientists, for scientist - what's there to fear?

UPDATE 28jan11: Related to this topic, Zachary Knight has an incisive commentary on how all this was protrayed.

Image from Mike Babcock

Functional roles for noise in genetic circuits

I have a thing about noise (see my ramblings here). And as folks try to turn elements of biological circuits into well-behaving engineered parts, I’ve been trying to put my finger on why biological noise means so much to me.

A series of articles in Nature back in September covered the cost of feedback control, the fundamental limits on the suppression of molecular fluctuations, the functional roles for noise in genetic circuits (subscription required for all three).

The main review mentions that noise is a nuisance in the design of deterministic (engineered) circuits. But goes on to show that noise in biological systems provides critical functions that are hard to achieve with deterministic circuits.

Noise in biological systems is unavoidable, there are limits to how much a feedback system can reduce noise. And the review goes on to discuss many areas where noise is integral to the stability or responsiveness of a process, such as gene expression coordination, state-switching, positive feedback, differentiation, and in development.

How might we understand this noise and actually engineer it into our deterministic circuits?

One thing, though, that tempers my bias towards keeping noise in biologically engineered circuits is that digital electronics also had their start in a noisy analog world. Will engineering biological circuits be forever mired in the analog noisy world of biology or will these circuits eventually be complex enough to exhibit the precise nature that biological engineers seem to want? Should biological engineers seek to incorporate noise into their calculations or strive to limit stochastic fluctuations?

Really, that’s a bit beyond my ability to understand circuit design and noise and all, so I leave it to smarter folk than I. :-)

Image from BarelyFitz

 

The subtlety of life - clever codon usage

Here’s a paper from September I haven’t had a chance to comment on.

Zhang et al reported in Science (review, paper - subscription required) how two almost identical protein sequences can have different translational modifications. In this case, β-actin and γ-actin are 98% identical, the differences are marginal and don’t explain why one protein is modified with arginine and the other is not.

The difference is actually quite subtle - there is one amino acid in the protein sequence that is lysine in both proteins, but the codons in the RNA are different. That difference is enough to change the relative translation speed of β-actin so that it rapidly folds and gets arginylated but not degraded as happens in the slower translation of γ-actin. In the end, this affects the relative lifetime of each protein in the cell, leading to differential functions.

That’s so cool.

It seems like every so often, things we view as well understood turn out to have another layer of subtlety built in. For example, differential codon usage is usually considered a synonymous change, nothing momentous. Sure, there’s been studies of codon usage relative to the abundance of corresponding tRNAs and how that might be used to modulate abundance of a protein (a quick Google search revealed some interesting codon-usage papers). But I think this case is novel, differential codon usage actually affecting the post-translational modification of a protein simply by tweaking the speed of translation.

How might we create a codon usage table that takes into account tRNA abundance, contribution to translational speed of different codons, and speed of post-translational processes to be able to model and predict things like the differences between the functions of β-actin and γ-actin.

Also, how prevalent is this subtle effect on post-translational modification and how susceptible is it to breaking and causing trouble in a cell?

image from Science review (found via Google images, mind you)

The new germ theory

Lizzie Buchen from Nature (link below) wrote a great article on some cool work folks are doing to change the way we view bacteria.

For example, one group (like a joke, it’s a microbiologist of extremophiles, a neonatologist, and a human microbial geneticist) is studying the effect of bacteria on a devastating intestinal disease in premature babies. They want to know if there’s a role or not for bacteria in this disease.

What’s interesting is that up to now, most understanding of bacteria in humans has been stuff that is pathogenic and can be cultured easily. Bringing in someone who is skilled at finding and characterizing microbes from extremely inhospitable places might help discover new things about our own microbiota.

I don’t know if it’s because I’m all interested now in human microbial ecology or if indeed there has been a resurgence in the study of human microbiology, all I know is that not a week goes by without a new paper or review in this area.

Quite exciting, isn’t it?

Here’s the article: Microbiology: The new germ theory in Nature (no subscription required FTW!).

The Short Lifespan of a Tweet: Retweets Only Happen Within the First Hour

For some, Twitter is a social network and for others it is just a broadcast medium. Judging from the latest data from social media analytics and monitoring service Sysomos, for the majority of users, Twitter is indeed mostly a broadcast medium. After analyzing over 1.2 billion tweets, the Sysomos team found that only 29% of tweets actually produce a reaction - that is, a reply or a retweet. According to Sysomos, just 6% of all tweets are retweeted and these retweets have a very short lifespan. Virtually all retweets happen within the first hour after the original tweet.

via @alexdc via www.readwriteweb.com

Hm, Tweet lifetime of attention around an hour.

Methinks it's due to the way people follow. For example, we've noticed that Facebook posts peter out after about two days. But I bet the power curve is more like 24 hours.

And knowing the Facebook pattern, I never thought of what the pattern would be in other channels. With this new piece of data, it clear (d'oh, and so obvious) that the way once follows a stream affects the lifetime of a "quanta" withing a stream.

Thinking of YouTube, you have a high degree of promotion of videos and also folks searching for videos, which might explain why a video I made two years ago is still gaining tens of thousands of views a month - it feeds itself and grows.

Now I'll be looking at stream design in a new light.

Do we need a DIYbio academy?

Among my many ideas I have lying around is some form of institute to support the DIYbio community. This is different from the meet-ups happening in places like Somerville, San Francisco, Houston, and New York. And this is a bit more than what DIYbio.org is providing (sharing of ideas within the community).

This idea adds some pieces that seem to me to be missing (please correct me, of course). I’ve been turning over these thoughts for some time, and since nothing has really materialized (remember, I have a high idea-execution quotient), here are my thoughts.

In my notes, I call it the Molecularist Academy (why? check out the URL above). But the name is inconsequential, what’s important is the mission - Funding, Education, and Outreach.

The mission supports seeding of money - to jump-start activities; legitimacy - practitioner education and safety (certification?); and advocacy - promotion and community education to communicate what DIYbio is about and what folks are up to.

Funding
There are a few interesting funding models out there, such as Kickstarter, Biocurious, and Awesome Foundation. My thought is to create a traditional funding system backed by large sponsors and donors to provide DIYbio-specific grants for exploration, seeding ideas, and to support activities. This funding system would have someone actually reaching out to sources such as biotech industry associations (around here, the Mass Biotech Council), leading biotech businesses (around here, Biogen, Genzyme, NEB, among others), the NIH and NSF, institutes like the Wyss and Venter Institutes, universities, and community organizations.

I do think there’s a bit of a local focus needed, as I feel the biggest contributions DIYbio can make is actually in the local communities the different groups have sprung up in.

And by creating a formalized fundraising and granting structure, the hope is to build an endowment that lasts as the DIYbio community grows. (and I've wondered about alternate ways to fund and legitimize practitioners, in an HHMI-sort of way - more in another post)

Which leads to the next mission focus.

Education
I carry a lot of baggage from my institutional science days, so I am always stuck between letting a thousand flowers bloom and hoping folks don't kill themselves or others while futzing with biotech tools.

The education part of the Academy would set up courses and seminars to teach techniques, science culture, and, most importantly, safety certification. The Academy would be vetted by existing safety organizations and provide legitimacy to the practitioners. And, there would be a structure of re-certification and continuing credits sort of education.

Safety is a big deal and my brief foray into how to communicate it made me realize that it’s much more than just putting up a bunch of pages of regulations and recommendations. Folks like the FBI and the local regulatory bodies likely want more structure.

As part of this Education mission, I’ve also been trying to gauge the need for a patent clearing system, to make sure DIYbiologists are working with the appropriate product licenses, which suggests the Academy should work with tools providers to create special DIYbio tinkering licenses.

And that leads to the third and final part of the mission.

Outreach
This is public outreach, outside the community.

I’ve spent less time thinking of this part as the folks from DIYbio.org already seem to be doing a good job of reaching out to the public and news groups to explain what DIYbio is and can do, and reaching out to agencies who should consider the implications of DIYbio.

And I know there’s been talk of extending this outreach to courses and seminars to engage schools, local communities, and influencers to make DIYbio part of public thinking.

Outreach should also include working with regulatory and policy agencies to take DIYbio into consideration when revising or creating regulations and policies. DIYbio.org has been very good here too.

And, finally, as part of outreach, would we need to have an Asilomar-type event, bringing stakeholders together to hash out the future of Natural Philosophy in the 21st Century, particularly as it pertains to Biology and non-institutional biologists?


There it is
So there’s my Academy, supporting funding, education, and outreach to promote DIYbio. Of course, this could be built upon the existing DIYbio.org structure. I just wanted to get these ideas out there.

What do you think?

Image from tiseb

As an aside, I was looking more into Biocurious and see they are thinking the same things, though still with a crowd-funded model.

Take back the graph! Facebook, The Cloud, and a return to the basics of social networking

"Take back the graph!" was @mattmiz's reply to my rant that The Cloud was shite, Facebook was poison, and that the future will be peer-to-peer social networking.*

Head in the clouds
How did I come about to that, since not long ago, I was Mr Cloud, harping about a time when all would be in the Cloud, with a dashboard (or a "door") to all our lifestreams, connecting to everyone, sharing, loving, communicating?

At least, that was the original vision of Ovi I first pitched at the end of 2005 (to the wrong crowd, though). I thought that the killer service would be Cloud-based and full of lifestreams. The last flourishes on these thoughts in the past years revolved around visualization and filtering of all these streams.

But I believe this no more.

Here is where I rain on everyone's parade
Facebook is the best example of how Cloud living can go wrong. Folks who are first discovering social networking are getting so mired in Facebook without understanding how Facebook is so twisted with respect to the users.**

And nothing is really in the Cloud. Is anything ever really in the Cloud? No, everything has always been on someone's servers. Their servers. Your data, their servers. [Despite this, there have been efforts to take back the graph, great standards work to democratize social networking - see here a suggested alternative.]

So, I say, The Cloud is a fantasy.

The past is future
Back in my father's day, data resided on someone else's machine. When I started with computers, it was the dawn of PCs, where the data resided on my machine. Then we hooked up all those PCs to communicate until some of those PCs got huge and ended up shouldering the work, serving up data stored out there somewhere.

And now The Cloud dream is to return to a time where the "terminal" is an appendix on the network, and that the network would store everything and do all the work. Terminals are to be just windows onto the Cloud, Just as our terminals were getting interesting and wide-spread - smartphones, tablets, amazing laptops.

How did we let that happen again? Bad move.

Peer to peer social networking
I claim that we need to move data and communication back to the edge of the network, residing in your machines, sitting in your hands, your laps, your tables.

I used to say that the ultimate social networking device was the mobile phone - your buddy list in your address book, billions and billions of text messages exchanged, a direct 1-1 link through a phone call.

Can that model be extended? Can we create a world where there is no Cloud, just a bunch of network bots pushing packets, be they IP or SMS or whatever communication packet we need to route? What will a peer-to-peer email-blogging-website-social network be like?

Do you want to have full control over your data, your social graph, your communications, just like you do now with your mobile phone?

So do I.

How will we do it?

*I've not really written these thoughts down before, since I've sort of stopped worrying (or at least tried to), or hoped to do something myself. They are peppered in the bookmarks and comments I have made in the past years, though. And since I have a high idea to execution ratio, here's the thought for anyone to build upon.

**I deleted my first Facebook account in 2008. I only got another one last year because of work. But, yeah, it'll be gone as soon as I can ditch it.

Fed up with platic bags

One thing I've noticed here in the US is that there is trash everywhere, collecting in the "unspace", places where there is no movement or wind or people to brush them away.

A few things stick out - styrofoam cups, plastic drink covers, and plastic bags.

My proposal: Plastic is to be prohibited for uses where the lifetime of use is less than a day.

Can we start with that?

Starbucks and Dunkin Donuts could start by no longer using those plastic cup covers that have a very short usage life but a very long trash life. Next, all fast food places could stop using any sort of plastic for drinks, utensils, plates, covers,and wrapping.

I think the cost of whatever alternative we come up with to match the convenience and public health features of plastic will be significantly outweighed by the reduced cost to our environment and reduced pollution.

What do you think?

Check out the great promotion by the Body Shop (image inset).

StatusNet - can this lead to P2P social networking?

StatusNet is the open source microblogging platform that helps you share and connect in real-time within your own domain.

via status.net

I keep coming back to the thought a life not mediated by the cloud. One manifestation of this would be a peer-peer social networking, some internet-plumbed service that does not require a central server.

Back to the future: Mag+, BERG, and hypercard

If 2009 was the Year of the Netbook, it's getting to be pretty clear that 2010 is the Year of the Digital Book Reader.

The Kindle and Nook are simple readers with whole bookstores inside them. Indeed, the Kindle has hit on a formula that I think everyone will riff off of (as opposed to exploring other potential biz models).

Now we hear of big magazine publishers exploring layouts that are digital reader friendly. And the amazing BERG worked on a project called Mag+ (video below), showing the future of digital magazines.

It's been really interesting to see the traditional publishing industry drooling at a way out of their downward spiral (being drawn down by their 20th Century biz models). Equally interesting is to see that what was old is new again.

I'm reminded that the early days of the Web was about converting traditional print publications into digital facsimiles. And stretching my memory pre-Web, all this digital book reader talk reminds me of Alan Kay's Dynabook, Jack Scully's Knowledge Navigator, and, my favorite, Hypercard.

So, we're back to creating digital facsimiles of print pubs (albeit better than before). But, when viewing Mag+, I think we could go a wee bit further.

Nah, I don't think we need to turn digital book readers into full-fledged, 'net-connected, hyper-linked information devices (can you say "tablet"?). I'd like to see traditional publishers extend into a third hyper-linked dimension to take advantage of digital formats, rather than just a flat, though pretty, book or magazine. Mag+ does show that, but I am left wanting a tad more.

Yeah, print pubs are mostly flat, but let's not reproduce that flatness in a digital world.

What do you think?

Mag+ from Bonnier on Vimeo.

Image from TheCreativePenn

UPDATE 29jan10: Here we go again. The iPad was announced on 27jan. And Venture Beat writes about a company, inkling, that is taking the textbook into the 21st century. Very exciting.

Institutional science needs to change

I was having lunch with some old ex-lab friends. Unlike me, who left the lab at the end of the 90s, all three of them have kept on doing research and medicine and have their own labs with students, post-docs, and techs. The good news is that their research is progressing, the bad news is that funding is tighter than ever.

I had asked them who was writing a grant (of course, knowing that one always is writing some grant). There was an awkward pause as all three of them seemed to be lost in their thoughts, then they gave me an update of where things were at, since last I was in science, listing some stats to show how things were getting tighter.

When I left research, I had the naïve idea that I would no longer need to hustle for money. But, we all know, the biz world is just the same. Yet, for sure, the biz world seems to have a multitude of revenue and funding options that don't seem to be available to institutional scientists.

I feel that the whole endeavor of Science (I come from a biology background, so my thoughts are around that area, really) has been stuck in the 60s - the way we fund science, the expectations of the apprenticeship (PhD and Postdoc), the publishing and reputation cycle, the job progression - all seem to have been built in a model that came into being in the science boom of the 50s and 60s and really hasn't changed.

Am I missing something? I've been out 10 years, but it seems like nothing has improved. Funding is tighter, people still can't get academic jobs, and publishing is getting more onerous.

How do I envision the future of institutional science?

I'm not sure.

I've mentioned how science publishing could change, taking cues from the current way we use the Social Web. I think DIYBio points to how science could change how we explore the natural world and who does it. And, brilliant folks, like at Biocurious and Pink Army Coop, are looking at ways to diversify how we fund and participate in funding the future of science.

In summary, the business of institutional science is sclerotic and the clues to how we move forward are right in front of us. And, as usual, institutional culture is in the way of this change.

Do you think the way we do science should change? Can it? Will it in our lifetime? How do you envision the future of science or are we fine the way we are?

Image by caterina

Building a Minimal Airplane?

At the iGEM Jamboree there was a lot of discussion of Minimal Cells, cells that have the fewest number of components to function as a laboratory organism. One of the key benefits is that it's a defined organism that does only what it needs to do and gets out of the way of the main things someone wants to use them for, say, to create an engineered machine.*

From the discussions, a few said that the route to a Minimal Cell was to subtract components from a current cell and see which ones were essential for operation.

That didn't sit well with me. And it took a while for me to develop an analogy to explain why.

To me, removing components from an existing cell to create a Minimal Cell is like removing components from a Boeing Dreamliner to see what's essential for an airplane (a Minimal Airplane could be like a Wright Flyer).

The mistake is forgetting that even bacteria are highly complex and evolved organisms with complex multi-subunit enzymes and structures. That complexity causes a limit to what can be removed, simply due to the complexity-overhead the bacteria has accumulated over billions of years.

In the plane analogy, the Dreamliner has a ton of essential components, say fly-by-wire, that really were added in evolution, replacing a simpler version, such as manual flying. The function, "controlling the flaps," is what's important, not the component. And the fly-by-wire system makes a whole load of other systems essential (complexity overhead), but which could be dispensed with in a manual system.

Makes sense?

I suppose I am of the school of bottom-up rather than top-down construction of Minimal Cells. And I suppose these discussions have already happened. [Indeed, Foster and Church's 2006 paper "Towards synthesis of a minimal cell" is a good foundation paper.]

I'm not trying to knock on all those working on Minimal Cells. here is a benefit to top-down reductionism, teaching us which pathways and functions are essential, even if we are not finding out the ideal components.

I'm just trying to develop a metaphor for myself to help me think of how to build a Minimal Cell.

That's all.

Image from Boeing

*Heh, one interesting thing I noticed at the iGEM Jamboree was a vocabulary developing around synthbio - machine, quorum sensing, chassis - words I've never used before in biology and that come from engineer-speak. I like it. :-)

Report on iGEM 09, from a newbie

This iGEM was my first. I'd read about it, talked about it, but this is the first time I've been immersed in it.

OK, so I wasn't part of a team, so I told folks I was a "lurker." That was out of the ordinary, since most folks were either staff, team members, or volunteers (which is what I should have done to save the registration fees - maybe).

Clever little undergrads
I'm not going to go into details as to how the teams got to the Jamboree. Suffice it to say that anyone who wanted to come, came; also, the teams were undergraduates who thought long and hard on what they would build and then built everything over the summer.

I was impressed with the creativity the teams showed. There was light-induced vanillin production (for the aroma), electrically-induced light production (creating pixels - see video below), various detectors (for toxic metals and mines), and inducible pigment production (to free us of the boring tyranny of all the usual fluorescent reporter proteins).

While some might call for something applied to come out of all this, I am content to see the participant's enthusiasm; their learning of how to solve problems, think, and communicate results; the multi-disciplinary nature of teams, mixing engineers, biologist, sociologist, designers, mathematicians, physicists, artists, and programmers; and the gathering of like spirits to exchange information and dream up even more exciting things.

Keeping up with the E colis
For me, it was heaven. I had not been immersed in this field in so long. It was good to try to figure things out, talk about how decisions were made, and learn all the clever techniques and solutions folks came up with.

Of course, at the end, I started dreaming up some of my own "machines." Who knows if I might be able to build one someday.

E. chromi
I was particularly pleased with the winning team - Cambridge - for their creation of inducible pigmentation in bacteria. Through a network of connections, I had met the irrepressible Daisy Ginsberg, a designer from London who has been exploring the future world where synthetically engineered biological organisms are established and integrated into society. Daisy coined the term Kingdom Synthetica to add to the Eucarya-Bacteria-Archaea Kingdoms that we already have.

Daisy, and her partner in design-crime, James King, worked with the Cambridge team to help them explore the sociological and design aspects of what the team was building.* They got the team to think of a future that had colored bacteria and what that would mean. For example, one team talked about color-poachers killing rare wild-life for color genes; or, global battles over patenting of colors (for example, the Dutch if China were to patent Orange).

The best example of the future was colored poop, formed by these color producing bacteria detecting metabolic states and reporting it through color production, say green for an ulcer or red for vitamin deficiency (see picture). This colored poop was the sensation of the Jamboree. James and Daisy walked around with a silver valise, telling their whole story and ending with opening the valise, much to the surprise of their audience.

It was very fun.

Naming gaming
Daisy christened the Cambridge bacteria as E chromi (@echromi on Twitter). And they presented their colored poop to the MOMA in NYC, so don't be surprised if the valise ends up there.

Other teams also named their bugs, as in Essencia coli (Team KU Leuven) and GlueColi (Team ULB-Brussels).

Once again, these names just point out that this Jamboree is more than a bunch of geeks building gadgets, but a whole way of thinking and mixing and creating. This is all so embryonic and what will come out of it no one really knows. But what is sure is that mixing folks from different background in a fertile playground with no dominant player is a sure way to come up with lots of interesting things.

Now I'll go off and start building my E coliroid (hm, what might that be?).

Here are some images and video that I took at iGEM:

*One nice feature of the competition was a thorough list of judging criteria, nudging the team to do more than just building something. Most interestingly, teams were encouraged to do a sociological survey around ethics, society, and synthbio. This added non-scientists to the teams. One of the most interesting findings (as these we mostly qualitative, due to experimental design constraints) was that folks were against genetically modified organisms (GMO) in general, but were fine with GMO use in humanitarian work, such as toxic waste or mine detection.

Vestiges of the past in our tools: Fruit fly culture bottles

In a previous post, I discussed how we've forgotten techniques and instruments of the past. These techniques and instruments could come in handy as garage scientists try to build their labs.

In that post, I mentioned that folks keep fruit flies in plastic bottles that look like milk bottles (well, only if you know what a milk bottle looks like, otherwise, it's just another oddly-shaped bottle). In case you're wondering, the use of milk bottles goes back to the days of Thomas Hunt Morgan, the genetics genius who chose the fruit fly as a model organism. Somehow, he and his contemporaries did a ton of great science without the kits and super equipment we have today.

What do you think?

I think these vestiges are really cool and I like seeing them wherever I can (and I have a ton of stories about these vestiges). 

Do you know of any more?

Image from wikipedia.

Oh, what we've forgotten...

In this new era of natural philosophers (neo-natural philosophers?), where the cost of buying science kits and instruments can be an obstacle to amateur science, I keep thinking back to how science was done many years ago. What were the tools used? What were the different reagents of the day? How can this lost knowledge be applied today to circumvent barriers to modern reagent and instrument access?

I remember when I was a tech at MIT, back in the late 80s. There was an old Worthington molecular biology catalog with reagents and enzymes. For restriction enzymes, there were two: EcoRI and BamHI. Talking around the lab, our PI told me how "in the day" everyone had to purify their own restriction enzymes. 

To me, that was fascinating. By the late 80s, the New England Biolabs catalog was already full of a ton of enzymes and kits. And, huh, it was so easy to sequence DNA by doing nested deletions of M13 vectors and using the kit's primers. And then you could purify plasmids with CsCl gradients and gobs of Ethidium Bromide in milligram balanced tubes and a wicked cool ultra-centrifuge. 

State of the art, man!

As the junior tech in that lab at MIT, I was also responsible for keeping the fly stocks alive, transferring them on a regular basis from old bottles to new bottles. As per fruit fly science convention of the time, the flies were kept in small glass milk bottles, with cardboard plugs. I wonder how old our bottles were, but I was told that it was getting harder to find the bottles or even the cardboard plugs.

When I went over to the Whitehead to do some experiments, I saw that they all had plastic containers - in the shape of a milk bottle. It was the future, but in the image of the past. I wonder if folks today know why they still use such oddly shaped bottles to store flies in.

Straddling the past and future, that lab was a treasure trove of old stuff. I once opened a drawer at the lab and found a ton of capillary tubes with different color markings and sizes. These were actually glass micro-pipettes, calibrated and used with a mouth adapter (oh, my!), and eventually replaced by Gilsons with disposable plastic tips.

In summary, there are a ton of techniques and tools that have been knocked aside by kits and newer instruments, mostly for convenience (because I am a science history enthusiast, I have a ton of these stories). For those enterprising neo-natural philosophers, if you long for some kit or instrument, imagine back to the day when you got your hands dirty and didn't just buy your reagents. You might find some ideas how to create your own reagents and tools.

Image of pigments from hyperscholar, to remind you that "in the day" artists ground and mixed their own pigments to make paint. No kit for them!

Don't guess the future of the social Web, read it right here.

Chris Messina and Jyri Engeström wrote a brilliant article on the Arctic Startup site (hey, Ville and Antti, nice catch!). Both of them have been actively pushing forward the concept, philosophy, and hard-core standards for a more person-centric Web.

Link: The Web At A New Crossroads
It’s 2009, going on 2010. For the past three years, the web has been morphing into a real-time and people-centric place. We’ve seen this trend among individual users — through their actions and demands for better social experiences — but also increasingly among companies and developers. We want a web that’s more “like us” than the old model was. We want a web where people are as important to the architecture of the system as documents.

They chart out the history of the Web and point to where it must go.

There have been some recent indicators, for example, an excellent article from Marshall Fitzpatrick (who is also brilliant and a watcher in this space), Opera's Unite, the anger at Facebook's purchase of Friendfeed, the rise of the Cloud, and the social meltdown the day Facebook and Twitter were down from DoS attacks (and some indicative comments of data ownership, and network ownership in some of my posts on Nokia Conversations). We seem to be passing a conceptual hurdle and behind-the-scenes coding (gosh, I had wished for DiSo back in 2008!) and finally seeing some real motion towards a more peer-to-peer style of social networking.

I was explaining to my son that in the old days, computing was done on main frames via terminals, much like social networking today is done from a dumb browser with servers in the Cloud. What Chris and Jyri are driving is just as liberating as PCs were to folks tied to mainframes - bringing power, choice, control, and the like back to the user, unmediated by proprietary services.

This isn't geeky dreaming. Chris, who had created Flock, which in some ways reflected a person-centric form of browsing, has been able to pull together Facebook, Myspace, Six Apart, and Google to back him up. And Jyri and Brad (who helped with the article) are key players in this and both work for Google (last I checked).

I admit I have not been following this as much as I used to. Other than the occasional article from Marshal that I pick up, in the past year or so, the most I have discussed this was at a lunch at Web 2.0 (where indeed, Chris, Jyri, and David Recordon, among others, were there going over all this stuff). So I am not sure what other articles these two have written.

In any case this article they have written will be part of the People-centric Real-time Web manifesto.

Will you be a part of it?

Original image here.

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.