I'm on the move

Times, they are (and have been) a-changin'.

I've decided to move operations (and sandboxes) to Wordpress. Please visit my new home over here for more musings on science, technology, and everything in between (well, not food. that's staying where it is for now - right, um, here.) I promise to make more of an effort to update, as well. It's on my belated New Year's resolution list (from 2010 ... I'm a little behind).

Head over there (yes, another pointer) for more on where I am now and what I'm focusing on. I hope to see you all over on the other side. Do come join, the weather's just fineeee.

Sayonara, sniffing the beaker. It's been real.

- KT

Hipatia issue on Open Access

I'm currently in San Jose, Costa Rica, for aCCCeso - a seminar on creativity, community and science. The event was held from 11-13 November and largely featured representatives from Latin American countries such as Nicaragua, to Peru, Columbia, Chile, Argentina, etc. My colleague Eric Steuer (Creative Director, Creative Commons) joined me from the States to talk about some of our work at Creative Commons. Stay tuned for more about the event in the coming weeks.

On to Hipatia. Early in 2009 I was asked to contribute to an issue of Hipatia, a resource out of ONG Derechos Digitales in Chile. The issue is dedicated to Open Access and the need for more efficient knowledge sharing. Seeing Claudio (Ruiz) from CC Chile this week reminded me of it, and it looks like it came out in February.

So here it is, better late than never :) Many thanks to those at Derechos Digitales for compiling this very important issue. Outstanding work.

(And slides for this past week's presentation are now posted, as well.)

Data sharing: a look at the issues - Trieste

Here is the second talk of last week, again at "Scientific Information in the Digital Age: Access and Information" at the ICTP, Trieste. The week-long workshop was hosted by the ICTP, eIFL and UNESCO.

The talk below refers to the presentation last Wednesday (14 Oct) on Creative Commons and knowledge sharing, largely highlighting our Open Access policy and how that applies to not only content, but biological materials and data.

The application of FLOSS (Free/Libre/Open) licenses for data can often have the opposite effect over the data, breaking interoperability and making larger barriers to entry for researchers to use and reuse information. The presentation below looks at the legal, technical and semantic issues to keep in mind.

Overall, the audience was made up of representatives from developing countries, chosen by UNESCO. Bandwidth and access are their main concerns, and even moving beyond an idea of access consisting of available online to additional permissions echoed in the BBB definitions of OA is a huge task. The talk below stressed those points, and also the need to keep such issues in mind as steps are made to build systems to accommodate their needs as the digital divide is (hopefully) lessened. Video available here, in the 10-10:59 block after Andres under 16 Oct.

Data sharing: a look at the issues - Trieste

View more documents from Kaitlin Thaney.

Creative Commons: Access and Knowledge Sharing -- Trieste

Today's presentation on access and knowledge sharing, given at "Scientific Information in the Digital Age: Access and Dissemination" at the ICTP, Trieste, Italy.

(More below...)

Creative Commons: Access and Knowledge Sharing

View more documents from Kaitlin Thaney.

A little bit of information about me that you may or may not already know ...

I get the heebie jeebies when my talks are taped and livestreamed.

Let me explain a bit ... I fully support the practice and dissemination, I do. Hands down. It's just the minor hiccups, the technical difficulties or other human errors that often occur during a live presentation, and the thought of having them not only broadcast, but *viewed* by others that makes me the wee bit embarrassed. I know, it's terrible. But, 'tis the truth. It's a personal thing. I'll get over it.

With that said, the video is online from the latest overview of Creative Commons and overview of our OA work. Please be kind. :)

More information on 'Scientific Information in the Digital Age'

Ah, the joy of workshops in computer labs. Here's more information about this week's workshop, the participant breakdown, and up-to-date program.

There's even a free book available on a variety of topics relevant to this audience and access to scientific materials through Open Access. It's available under a Creative Commons license, visible below the all rights reserved, traditional copyright logo. Can't win 'em all. :)

No surprise, there's still quite a bit of confusion in the ever muddy pool of understanding as to what "Open Access" denotes. With any luck, my talk after lunch will help clarify.

Day 1 (for me, Day 3 for the rest) -- Trieste, Italy

Today's my first full day at "Scientific Information in the Digital Age: Access and Dissemination" at the International Centre for Theoretical Physics in Trieste, Italy. I've been invited by Iryna Kuchma of eIFL, to give two long sessions broadly marked as "Open Science and Science Commons Project."

The first will give an introduction to Creative Commons and Science Commons, then segue into our work regarding access and dissemination of content (OA, access to research materials, etc). Data sharing issues will be the focus of Friday's presentation. From what I've been told, the event is in the style of a workshop, with representatives from various developing countries in attendance (less than 50 from the participant list). It's hosted by UNESCO.

Here's the program:

Scientific Information in the Digital Age: Access and Dissemination

ICTP – Trieste, Italy from 12 to 16 October 2009

PROGRAM Workshop

Mon 12 Oct 2009
-———————————————————————————————-

* 08:30 – 11:15 Registration and Administrative Matters
* 11:15 – 11:30 Opening Address – SDU Team (ICTP)
* 11:30 – 12:30 Introduction to Open Access – Iryna Kuchma (eIFL.net)
* Lunch
* 14:00 – 15:00 Open Repositories – Iryna Kuchma (eIFL.net)
* 15:00 – 16:00 PLOS, Semantic Enrichment Tools, Database and Literature Integration – Philip Bourne (UC San Diego, USA)
* 16:00 – 16:15 ICTP Computer Facilities – Johannes Grassberger (ICTP)
* Coffee Break
* 16:45 – 17:45 How the Internet Works – Les Cottrell (SLAC, USA)

Tue 13 Oct 2009
-———————————————————————————————-

* 09:00 – 10:00 How the Internet is Performing – Les Cottrell (SLAC, USA)
* Coffee Break
* 10:30 – 11:30 Network Measurements – Les Cottrell (SLAC, USA)
* 11:30 – 12:30 Setting up the repositories, Policies and Legal Issues, Expanding Content and Increasing Usage – Iryna Kuchma (eIFL.net)
* Lunch
* 14:00 – 15:00 Content Management in a Web 2.0 Environment – Philip Bourne (UC San Diego, USA)
* 15:00 – 16:00 DSpace software I – Iryna Kuchma (eIFL.net)
* Coffee Break
* 16:30 – 17:30 DSpace software II – Iryna Kuchma (eIFL.net)

Wed 14 Oct 2009
-———————————————————————————————-

* 09:00 – 10:00 Case Studies/Presentations by Participants I
* Coffee Break
* 10:30 – 12:30 Case Studies/Presentations by Participants II
* Lunch
* 14:00 – 15:00 Open Science and Science Commons Projects I – Kaitlin Thaney (Science Commons, USA)
* 15:00 – 16:00 Open Source Journal Management and Publishing Systems I: PKP Software – James MacGregor (SFU, Canada)
* Coffee Break
* 16:30 – 17:30 Open Source Journal Management and Publishing Systems II: Open Journal Systems – James MacGregor (SFU, Canada)
* 19:00 Get Together Reception

Thu 15 Oct 2009
-———————————————————————————————-

* 09:00 – 10:00 Quantifying the Digital Divide as seen Through the Internet – Les Cottrell (SLAC, USA)
* Coffee Break and Group Photo
* 10:30 – 11:30 e-Math and e-Physics for Africa I – Anders Wandahl (physics.golonka.se)
* 11:30 – 12:30 scivee.tv: Science Community Site – Philip Bourne (UC San Diego, USA)
* Lunch
* 13:30 – 14:00 YOUnipr: A Video Server 2.0 – Sara Valla (Servizio Supporti Informatici per la Didattica e E-Learning, Univ. Parma, Italy)
* 14:00 – 15:00 ePrints Software I – William Nixon (Univ. Glasgow, UK)
* 15:00 – 16:00 ePrints Software II – William Nixon (Univ. Glasgow, UK)
* Coffee Break
* 16:30 – 17:30 Automated Open Webcasting with Linux I – Livio Tenze (Univ. Trieste)
* 17:30 – 18:30 e-Learning and Science – Donald Clark (UK)

Fri 16 Oct 2009
-———————————————————————————————-

* 09:00 – 10:00 e-Math and e-Physics for Africa II – Anders Wandahl (physics.golonka.se)
* 10:00 – 11:00 _Automated Open Webcasting with Linux II _ – Livio Tenze (Univ. Trieste)
* Coffee Break
* 11:30 – 12:30 Open Science and Science Commons Projects II – Kaitlin Thaney (Science Commons, USA)
* Lunch
* 14:00 – 15:00 e-Learning and Generation Y – Donald Clark (UK)
* 15:00 – 16:00 ICTP Diploma Course On-line – Carlo Fonda (ICTP-SDU)
* 16:00 Final Discussion and Certificates to Participants

----

Only a few hiccups so far, with a significant amount of participants traveling here (myself included) luggage-less thanks to Alitalia. Other than that, there's a remarkable view of the Adriatic about 30 steps out of the Guesthouse, which puts you right on the water. Here's hoping the logistical aspect works itself out. Stay tuned.

Soliciting help in doing some research

As many of you know, there are a plethora of reasons why I came to work at Science Commons years ago (3 years this August, so says my paycheck).

Part came from my background in another form of "open information" - from my time at Reporter's Committee working on Freedom of Information issues, covering First Amendment cases, Katrina aftermath, and Open Government.

Part was curiosity, having not trained as a scientist, but being very interested in the cross-section of scientific research and knowledge sharing, about the philosophy behind, the history and of course - the actual research. My work with Hal Abelson back when I was (gasp) still finishing up college gave me a bird's eye view into this world, starting with applications of education technology that crossed all disciplines, from the social sciences, to the hard sciences and back.

And part was personal. Very personal. From the early days at Science Commons, we've worked very closely with the neurodegenerative disease community and on a broader scale, the rare and neglected disease network. Two people very close to me have been / are afflicted with degenerative muscle and/or genetic diseases - one my grandfather who passed away when I was in elementary school, and the other one of my very dear friends Jameson - whose doctors stumbled upon his Marfan Syndrome diagnosis when he was 18 and at Berklee.

Jameson let me in during some of the most difficult times following the diagnosis, leading me to throw myself into researching as much as I could about the disease to better understand. Marfan Syndrome is a genetic disorder of the connective tissue, that leads to the break down of this tissue affecting in some cases just a few areas of the body but in more severe cases is extremely debilitating. It's painful to watch from the sidelines, but also compelling. Jameson has been managing this disease ever since, still doing what he loves down in Florida - playing music and living his life.

To this day, I'm still not entirely sure what my grandfather had, despite asking my mother about it. This is where I need your help, because I want to understand. And with the resources available now, I want to read more, since his affliction is still a mystery to me. Let's see if pharming this out to the web and you all can help me figure this out, some 20 odd years later.

Here's what I know / remember:

- From what I recall (remember, I was young), my grandfather was a healthy man, with no prior history of illness, genetic disorder, etc. Granted, technology wasn't what it is today back then.
- He was an avid carpenter / woodscrafter, and worked at Kodak for his career.
- His symptoms only appeared following an accident where he fell out of a tree while doing some regular yardwork in the backyard, breaking both wrists. This is where I remember it all going downhill.
- Relatively rapidly from there, he went from being my healthy, loving grandfather, to losing muscle function (or so it was explained to me) bit by bit, until he was bedridden, without the ability to speak, and only able to blink his eyes. It reminds me now of something similar to ALS, but then again I can't be sure.
- My mother said, over the phone, that it was "super neuromuscular palsy" but I'm not sure if I got that down right, or if that was the formal name for it.

Any insight into this would be greatly appreciated. As many family members, friends, or patients of those with such diseases - I just want to understand. Can you help?

** Update: Thanks to my older cousin Rob, now know the correct name of the disease - Progressive supranuclear palsy.

Sciencecommons.org in top 20 list of sites scientists should know

Sciencecommons.org has been listed as one of the Top 20 Web sites every scientist or engineer should know by Baltimore Examiner. It's an informal list, including resources to find papers (ahem, sadly not OA), sort through the acronym soup so many of us find ourselves in daily, and Grants.gov (everyone needs moo-lah).

Nevertheless, we're happy to be cited, and I encourage you all to check out our site. Over the next few months we will be working to make the site more accessible and useful, and will be asking for feedback on what exactly you, our users, need. Keep an eye out for more on that this summer.

$120m - will it help, and a look at the greater issues

The last few months have consisted of a blur of meetings, round table discussions, presentations, and impromptu conversations on the train and at universities - all largely revolving around a few key topics. There's been the open science and knowledge sharing in the sciences dialogue, data policy and drafting codes of conduct, and innovation and access models for rare and neglected disease research.

The last of those topics surfaced this week, after catching an item on Scientific American's 60-Second Science Blog. The post deals with drug development and NIH's recent commitment of $120 million over five years for drugs and therapies for rare and neglected diseases. Woo hoo. I support that. But the real question, surfaced in this post as well - will that make a difference?

One of these meetings I attended over the last 3+ months of travel was a recent summit on innovation and access by the National Organization of Rare Diseases (apparently "neglected" is implied? :) ) The crowd - independent disease foundations that were members of NORD, FDA representatives, folks from the Office of Orphan Products, biopharma, and other medical professionals, among others. It was their annual meeting, and as somewhat expected, included an initial 1.5 hour "congratulations" and offering of thanks to one another for their "contributions to rare disease research" as a kickoff to the meeting.

Excuse me here for being cynical and a bit brash, but were they congratulating one another for a drug pipeline that a) is insanely costly, b) takes approx. 17 years to get a drug to market IF it succeeds, c) doesn't work in favor of the community they're serving? The fact that a significant portion of patients afflicted with the 6,800 + diseases characterized as "rare" and/or "neglected" use off-label drugs or find other ways to circumnavigate not only the prices of these therapeutics but also the FDA and approval process doesn't seem like a win. Good for finding a way to alleviate symptoms, helping people potentially live longer, but not a win for bringing the price of these treatments down and getting them into the hands of those that desperately need them.

Trust me, even as I sat there in the audience, I was able to find out about a FDA approved hypertension drug that has shown positive results in Marfans patients (which a dear friend of mine has) to maintain muscle growth and lower / maintain TGF-β signaling levels. Some are getting this through basic hypertension diagnoses and prescriptions, whether they have it or not. Talk about working around red tape.

Now, I fully realize that drug companies need to make money, and that a portion of that comes from selling drugs for diseases that affect a large subset of people. The money and logic just isn't there, strictly thinking of $$$, for those diseases that instead of affecting 500,000 a year may only affect 100. I get that. Clinical trials are difficult to conduct with a small sample size. It's difficult, with how expensive it is to bring a drug to market (approx $1 billion), to get any of that cost back. But not admitting that there's a problem with the pipeline? Really?

After the first set of speakers and a keynote by Gov. Tommy Thompson (WI), the moderator opened the floor to a few comments from the audience, giving us each a few minutes to make remarks on the day. At this point, it was two hours into the event ... without mention of "innovation" or "access" outside of "access to $200,000 therapeutics".

For those familiar with our work at Science Commons (and the above opinions are certainly influenced by that work, but are still my own), you know that the concepts of "innovation" and "access" are integral parts of our mantra, our raison d'être, our everyday work. But it seemed like somehow, in the midst of all of the congratulating for thousands of people in their "network" not having any sort of drug or treatment, these two words - the themes of the event - went unmentioned.

I raised my hand to have a turn, puzzled by all of this and made a comment, which was later backed and echoed by Janet Woodcock of the FDA and Francis Collins, the famous geneticist (thanks to both). I talked about the reasons we were all there - to talk about "innovation" and "access" in terms of access to research, accelerating scientific discovery, new "innovative" models to help fix this broken pipeline we all were dancing around, and get therapeutics and results to patients faster, cheaper and more successfully. It was astonishing a) how many people were nodding and smiling when I brought this to the forum and b) the fact that if not said, it may have gone unmentioned for the rest of the meeting. All of a sudden, the tone changed - with Francis Collins emphasizing the importance of Open Access and Janet Woodcock even saying "Put information into the public domain".

Small wins in an area that still needs a bit of coaching (like others, certainly) on making better use of a poorly funded wing of disease research.

Will $120 million over 5 years make a difference? Certainly, in some respect. How large of a difference depends on what model is constructed to hopefully better share the scientific knowledge we're pumping tens of hundreds of thousands of dollars into, the funding model, etc. Perpetuating the "walled garden" approach does not "fix" the system. Offering therapeutics that patients cannot afford does not solve the problem. And 17 years (at a minimum) and $1 billion per drug is just not acceptable. All need to be further addressed, because at the end of the day, in terms of drug development, $120 million is barely a blip on the radar screen.

ROFLDNA up for sale, proceeds to the commons

Prepare yourself for a heavy dose of awesome. In perhaps the most clever Science Commons fundraiser launched by a third party, the folks over at breadpig and DNA11 have brought us ROFLDNA - a set of leading Internet personalities' DNA and autographs, all being auctioned on eBay. And the best part, all proceeds will go to Science Commons.

Among some of the famous Internet superstars out there (is that the correct way to describe? help me characterize) we have Jay "TRON Guy" Maynard, MC Frontalot and the man behind Chuck Norris Facts - Ian Spector, among others. They've all lent their DNA to the cause - to help make scientific research more efficient through our work here at Science Commons.

And I do have to say, I have to agree with the tagline for the site ... this is some deoxyriboneucleic awesome.

What's even more incredible about this is that is shows how far modern technology and collaboration have gone to drastically lower the costs and barriers to DNA synthesis and synthetic biology. The iGEM competition is a leading example I've pointed to in the past, showing the potential out there for the remix culture in the sciences. Hell, we even own a DNA Explorer Kit (his name's "Dean Nay" ... say it fast, see if you get the nerd humor) that we proudly display in the office. Times they are a changing and the potential for explosions of innovation isn't coming. It's here. Many thanks to the people behind this for yet another incredible example of this, and here's hoping we get some bids. ;)