The conditions of a mass biotech DIY movement

The idea of doing biological experiments with current biotechnological methods and conducting research projects at home is quite new. There are already many names in use referring to the same concept: bioDIY, home biology, biotech DIY, garage biology.

We have a detailed case example which can be considered as the first registered, high profile biotech DIY activity starting the era of useful garage biology: Recently Hugh Rienhoff amplified his daughter’s DNA at home to help doctors figure out her genetic disorder. From the Nature cover article:

“So he bought a used PCR machine, a microcentrifuge, some small-volume pipettes and a brand new gel box. All told, the equipment cost him about $2,000. With these simple tools and some sequence-specific DNA primers of his own design, he could pick the relevant genes out of his daughter’s genome and amplify them enough for sequencing. Freezing the samples and packing the tiny tubes on ice, Rienhoff sent them off for sequencing at about $3.50 a pop. He prepared upwards of 200.”

Another suggested project was the How to isolate amniotic stem cells from the placenta, at home! but so far I haven’t heard of anybody who really did that at home and I only isolated the cells at the lab.

In my coming series I’d like to examine the following conditions of a mass biotech DIY movement: acquiring skills, affordable kits, tools, hardware, motivations, business opportunities and impact.

acquiring the how to skills:

- good education tools, protocols, videos, howto-s on the web

- short intensive academic or industrial lab courses available for every citizen

- self-education in community: forming Homebrew Biotech Clubs

available, affordable tools, hardware:

- cheap kits: based on the Rienhoff example, a very basic home lab can be set up out of 2-3000 dollars, which is the price of a good laptop.

says Mr. Rienhoff in an email: I bought all the equipment used from a local vendor who buys equipment at auction and from universities. All the gear is at least ten years old so it was very used and low throughput. But given that my project was incredibly focused I did not need the more sophisticated equipment.

- used equipment network:

Biotechies at O’Reilly ETech, March 3 - 6, San Diego

The O’Reilly Emerging Technology Conference (ETech) is on and this year they had a growing number of biotech related sessions. Fellow SciFoo Campers like Hugh Rienhoff and Timo Hannay, Makers like Phil Torrone and Limor Fried, Brain Hackers like Ed Boyden are visiting and many more.

Will JoVE’s new science blog service reinvent the genre?

The pioneer biological video publishing site JoVE (covered here many times) will soon launch a blogging platform and a community site. Nikita Bernstein, the main nerd behind JoVE is building the code and the platform - as Anne Kushnir informed me - should hopefully go live in the next couple of weeks. At least that is what can be known publicly.
The expectations are high and the JoVE guys (co-founders Moshe Pritsker and Nikita) themselves raised the bar with the quality and concept of video-protocols. As JoVE is a startup, not an established company with big inertia, they could be experimental but within the limits of their investors’ patience and money.

The real question for me whether JoVE’s blogging service can renew the genre of science blogging or at least bring a previously non-existing color into it? Points:

- Who will become JoVE’s first generation bloggers? Fresh blood? If yes what will be the source? Senior scientists, high school students, postdocs in the U.S.A., discovering the web?

- Existing bloggers who’d like to syndicate their content? Bloggers from Scienceblogs, Nature Network or from the DNA Network? Independent bloggers from outside theses established circles? Journalists? What will be the bait? For existing bloggers, who are tempted to commercialize their activity somehow the crucial question is whether they can generate any revenue out of this new platform? Will they be paid by traffic, and if yes how competitive are the tariffs? Is it possible to install paid ads, banners on the blogs and the bloggers could be paid based on pay per click methods just like Google AdSense?

- What about content rights? Exclusive, non-exclusive, et cetera? Would there be any topic restrictions? How can quality science blogging and credit is maintained in the long term?

Tim O’ Reilly at Nature: science meets bored tech-savvyness to find new things

As a biotech geek blogger and occasionally Make contributor, who stands at the intersection of science and technology with a (life) science bias, it is more and more exciting to see how the attractive brands of the 2 sides are building the bridge and creating a shared channel. So far, the biggest manifestation of this shared channel was the SciFoo Camp, organized by Nature and O’Reilly, hosted by Google. Now Tim O’Reilly, a native of Cork, Ireland turned Californian tech publisher visited the Nature Headquarters and talked about his angle on the web and tech publishing (giving me an incentive to finish the story of my earlier visit at Nature at September). You can read the informal account of Timo Hannay on the meeting at Nascent (picture: my shot on Tim and Timo summarizing the SciFoo experience at the Googleplex).

One thing seems more visible to me: Tim is bored about his original business and industry and is looking for some new which he seems to find in…. science (see Craig Venter and Tim O’Reilly chat: when 2 worlds meet).

The computer industry was a very exciting place, and then it became boring, because it became consolidated. ..There is going to be a lot of consolidation, the man will take over (he might be idealistic like google), it is going to get a lot more boring. The interesting question is what will happen when google’s growth slows down?
But you have to have a belief in people’s ability to find new things. There are going to be a lot new areas coming out of science, one thing we can do is to help to birth the future.

or: What happens when folks from synthetic biology meet hedge fund hackers meet roboticists and makers?

Tim’s boreness is really good (not the burned out part) for scientists like me. For instance, one of my ideas (an idea briefly communicated to Phil Torrone at the Austin Maker Faire) is to collect enough bioDIY projects like the “Make stem cells from the placenta at home” together, that is enough to set up an exclusive “sciencey” BioMaker Faire.

Let’s build Stem Cell Labs on the Globe with Google My Maps!

Stem Cell Labs on the Globe is a would-be map of important, worldwide stem cell locations made by Google My Maps. Let us help to build it further in order to easily find all the interesting academic stem cell places that you need to know.

With Google My Maps you can create personalized, annotated, customized maps using the well-known Google Maps. Ever since Google My Maps has launched in April, 2007 I committed myself to the idea of building a comprehensive stem cell labs map with it, share it in order to fill the map with useful information for stem cell scientists… uploaded by stem cell scientists themselves. Finally I allocated one hour to set up the initial map with 5 placemarks: Center for Gene Therapy (Prockop lab), Bernstein Laboratory at UCSF, Scadden lab at Mass. General Hospital, Wake Forest Institute for Regenerative Medicine, California Institute of Regenerative Medicine. These placemarks are good hints on what would be desirable to be included on the Stem Cell Labs on the Globe map: stem cell labs, the basic, functional units of stem cell science, academic institutes, departments with the information that is needed to put them not just on the real geographical map, but on your mental map too. All you need to start with is a little trial and error and the use of the Google My Maps User Guide, I swear that it is a no-brainer even for non-geek types. If you would like to participate in this project and instantly upload good stem cell related locations with some important data (exact address, name of the PI and lab website) email me at stemcelllabsmap@gmail.com, which is the account of Stem Cell Labs on the Globe, and I send you back the password and you can start to upload your favourite lab…..

You can open the map in Google Earth on the desktop too.

Forget about submitting your scientific papers written in Word 2007

Wow, I feel fresh air, although I am not sure whether the following news is a beginning of any deeper changes or not: From Science Authors Guideline: “Because of changes Microsoft has made in its recent Word release that are incompatible with our internal workflow, which was built around previous versions of the software, Science cannot at present accept any files in the new .docx format produced through Microsoft Word 2007, either for initial submission or for revision. Users of this release of Word should convert these files to a format compatible with Word 2003 or Word for Macintosh 2004 (or, for initial submission, to a PDF file) before submitting to Science.”

Tips: Undernews: SCIENCE PUBS REJECT ARTICLES WRITTEN IN WORD 2007
O’Reilly Radar: Science and Nature rejecting Word 2007 Manuscripts

One commenter in Undernews said: “This isn’t just Science and Nature. All Wiley journals now include the instructions: “[Journal] does not accept Microsoft Word 2007 documents at this time. Please use Word’s “Save As” option to save your document as an older (.doc) file type.” So don’t think it’s a singular problem — I’m sure if you visited all the science journal publications, you’d find similar instructions as well.”

What can I say: Prepare for the age of Google Office manuscripts and figures! All you need is a gmail account.

P.S. I made an attempt to coedit my ongoing first author article (desperately waiting for submission) by publishing the draft on Google Docs and adding the coauthors as collaborators, but only one coauthor (a med student) was kind enough to make one little correction this way. The rest is….well the majority of science people are living within the narrow world of Microsoft Office.

Second Annual Maker Faire this weekend and expecting the First BioMaker Faire…

Builders, Hackers, Do-It-Yourselfers are gathering around this weekend at the most visible embodiment of the Maker spirit, the Maker Faire 2007 at San Mateo Fairgrounds, California. I remember the inquisitive and incredulous eyes of the traditional tech makers, coders, engineers while presenting my placental stem cell project at Euro Maker Faire last year. Now imagine a similar Faire for Biotech DIYers with open lab spaces… If you can imagine it, you can make it! Links: Make Blog, Phillip Torrone’s Flickr Stream, Maker Social Network, Wired.

Stem Cell Lab Monitor: post series on excellent stem cell labs

Research in life sciences is more a team effort than ever. If you take a look on an average peer review article, in most cases there are as many as 6 authors and usually from more than 1 lab. But the basic unit and currency of any valuable research contribution is a LAB. Not the principal investigator (although the PI is the most representative voice of a lab) in itself, not a lonely grad or postgrad student, or an assistant, but a working functional and whole LAB, which can consist of 3 people or 10 or 25 people. The same arithmetics applies to the equipment: what makes a lab is not one particular tool (an incredible confocal, a smart PCR machine, a cool laser MicroDissector) but the whole set of the lab tools (picture: my Macbook shot on the Cambridge lab I worked last year).

So here I am happy to inform you on my coming blog post series (column), called Stem Cell Lab Monitor which will introduce the outstanding stem cell labs all over the world through their homepages, projects, interests, members etc., and through interviews (forgot almost: blogterviews) with the PIs and other lab members if possible. I hope you can get a picture on the lab cultures this way. If the focus is not on a definite stem cell lab, rather on a tissue engineering or a mitochondria or any life sciences lab, it’ll be a Tissue Engineering or Mitochondria Lab Monitor, respectively.

These will be my short questions to the PIs in the first round, and they can be modified and specified depending on the lab under investigation.

1. What is your scientific background and how did you get immersed into stem cell research? What was the motivation behind that?

Nature Network Global Beta and social networking 2.0 for scientists

If you are busy building a professional career and want things to get done, it’s time to forget MySpace, Facebook or any other social networking 1.0 sites, that are focusing on friendship, love, spam whatever with a general membership. What you need is social networking 2.0, which is based on the special profession you’re in, or is centered around a special topic. Ning, for instance, is a tool for creating your own social network for anything specifiable.

For the business and technology (mostly IT) sector LinkedIn is a more and more frequent destination. And, at last, there is a social networking starting point for every English-speaking (natural) scientist called the Nature Network (NN), which went global in February, after 7 testing months in the local hub Boston. It is still in Beta, just like all good “web 2.0 and more” apps.

First, I was informed about the plan of Nature Network Global from a comment of Corie Lok, main editor on NN, in the comment section of a Nature Blog in January. Corie was kind enough to share with me some recent initial stats on NN: We have more than 1800 registered users. When we relaunched in mid-February, we had 400. We’ve been growing steadily since February by about 100 to 150 new users registering every week. We’re now at about 100,000 total page views across the whole website. We had about 20,000 in February.

According to the numbers, Nature Network is currently a very small but organically growing strong online community. This is exactly the most exciting period in the life cycle of every forming network, so it is a guaranteed experience and challenge to join and participate - now at least - for people like me, who are eager to test and modulate every flexible beta product.

To get the key parameters and shed light on the prospects standing before NN, I’ve made the following table, which is a comparison of NN with relative and rival professional networking site LinkedIn:

As Gavin Bell neatly summarized the core architecture and aims of NN while writing on Nature Network Boston launches: “Some of the key features of the site are the groups, which allow individual communities to have their own spaces within NNB.

Nature Publishing Editor on the idea of a public scientific multimedia site

Maxine Clarke, Publishing Executive Editor of Nature and blogger of Peer-to-Peer got interested in the problem of “supporting information” and in the idea of an open access, peer-review supporting information aggregator website. She shared with me her valuable thoughts and informations by mail, from which I now publish parts with the permission of Maxine Clarke (emphasis by me).

On the possibility of a community-approved public multimedia site (videos, audios, pictures) with open access supporting information from peer-review journals.

It would indeed be nice for authors and readers to have such a facility. If there were to be a multimedia database, accepted by the community, we’d be happy to consider making deposition mandatory. Our principle is that data described in our papers are freely available, so if there were a community-approved public multimedia site, which included annotatation and curation, we’d be happy to consider making it a condition of publication for movies etc to be deposited in it. It would need to be publisher-independent to work, so that authors could upload multimedia data wherever they’d published their paper.

The main point for us at Nature is that as a publisher we have to be confident that material published off our website is properly curated, archived and preserved. For example, when we introduced the microarray deposition policy we ensured that there was full community support for the two databases (in one of which, authors’ choice, we require deposition) before implementing the policy. So for this video idea to work, the “database” concerned would need to be publicly accessible (not commercial), curated, annotated etc.

On the status of online supporting information at Nature:

Supplementary Information on the Nature website is free, though you have to register. (Confirmed, see screenshot of a 3D supplementary animation showing that the gut-associated lymphoid tissue comprised of different subsets of haematopoietic cells, Veiga-Fernandes et al.)

On the problem and handling of online supporting information: