Aaron Swartz Day 2018: The Inside Story – Part 2: Danielle Robinson From the Dat Project and Code for Science & Society

Danielle Robinson will be presenting at the Sixth Annual Aaron Swartz Day & International Hackathon in San Francisco,  on Saturday November 10, 2018) and also that night, during our Saturday Evening Event, where she and Karissa McKelvey will explain why the distributed web is so important.

    Saturday Schedule & Evening Event   Projects To Hack On

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Above: Danielle Robinson from the Dat Project and Code for Science & Society@daniellecrobins

By Lisa Rein

Danielle Robinson is the Co-Executive Director of Code for Science & Society, supporting and advising folks desiring to create open source technologies in the public interest. She received her PhD in Neuroscience from Oregon Health & Science University, while studying the role of phosphoinositide signaling in myelination for her dissertation project.

As a Mozilla Fellow for Science, she ran “Working Open Workshops“, explored decentralized approaches to data sharing and preservation, and advocated for policies that facilitate open access to research.

I originally contacted Danielle strictly on her professional reputation, after I asked Tracey Jaquith at the Internet Archive who would be a good person to explain why the distributed web is so important and in the public’s best interest.

During our email exchange, Danielle shared with me how much she had been influenced by Aaron and his work. It was all quite interesting, so I asked Danielle if she would share her story here.

Lisa Rein: Danielle, thank you so much for talking openly about this. I know these stories can be very personal. You mentioned that Aaron and his work meant a lot to you?

Danielle: Yes, I was a second year PhD student when he died. I was already disillusioned with academia and just beginning to see how I could put that energy to use. Aaron’s work had a big impact on my life and I would not be doing what I do today without his influence.

LR: Really? How did he influence you?

DR: Well, although I did not know Aaron Swartz personally, on a fundamental level, Aaron’s work on open access issues set the stage to grow the movement. I became a part of that movement and it changed my life. Aaron’s work impacted me and many of my colleagues at Dat (https://datproject.org/) the broader Code for Science & Society community, and in the open access movement.

Along with my colleague Joe Hand, I run Code for Science & Society, a nonprofit that supports public interest technology. We work with projects like Dat to build capacity, develop partnerships, and build software centered in the public’s interest.

Note that our next Code for Science & Society Community Call will be on Friday Sept 7 9am PST. Interested folks can join our mailing list or follow @codeforsociety on Twitter for more details about tuning in. These meetings are always super fun and newcomers are welcome to attend.

More on this last “Community Call” (photo below) here in the Recap.

Names top to bottom, L to R Chris Ritzo and Georgia Bullen from Measurement Lab
Hugh Isaacs II, Nokome Bentley from Stencila, Naomi Penfold from eLife, Danielle Robinson,
Yoshua Wuyts, Rik Smith-Una, Mathias Buus Madsen.

DR: Aaron’s story had a huge impact on me on a technical level as well. The Dat Project began as a peer-to-peer (P2P) file sharing tool for moving around large scientific datasets. As the Dat community has developed, use cases have grown to include the Beaker Browser – a P2P browser, ScienceFair – a P2P publication sharing application, and Mapeo – offline friendly mapping software developed to help protect indigenous land rights. There’s even a Dat-based decentralized data sharing pilot project with Internet Archive, California Digital Library, and San Diego Supercomputer Center.

I’m a believer in the potential of P2P technologies and the decentralized web to change the way knowledge is disseminated. I consider open science/scholarship to include equity, justice, and opening the profession of scholarship to historically marginalized communities. Building offline-friendly tools, baking in free access, and creating decentralized communities can help open the profession of research and scholarship. A personal goal is to build systems that provide free access to knowledge.

Working with the open access movement via OpenCon, the Code for Science & Society community, and projects like Dat, ScienceFair, and the decentralized data sharing project – I am privileged to wake up everyday and work towards that goal.

LR: You mentioned that Aaron’s death happened at a time when you were becoming “disillusioned with academia.” Would you mind expanding on what you meant exactly?

DR: I started a PhD program in 2011, after working for about three years as a technician I thought I understood the system and rather naively imagined my PhD as a time of intellectual freedom. I am sure it is for some folks.

But the reality of my PhD was quite different, I was working on the grants of my advisor and didn’t have a lot of freedom. Rather than being empowered to pursue knowledge and share information, there was a competitive and secretive culture which extended from lab meetings (opportunities for intellectual take-downs) to keeping our work under wraps for fear of getting scooped.

On top of this, everyone in my research group felt tremendous pressure to publish in Cell, Nature, Science (CNS) journals. The students and postdocs worked all hours (quite unsustainably) to try to get projects done and papers out. There was lots of talk along the lines of “this is not ideal, but it’s the way things are and you can change it when you’re in charge.”

At the time, I had never heard of the open access movement, but the secrecy and focus on CNS papers still seemed antithetical to the spirit of science. In short, I was disappointed and disillusioned. I wound up changing labs to complete my PhD but this experience informed my perspective on academia. I saw the pressure on early career researchers as coming directly from a system that positioned itself as a meritocracy (to incentivize folks at the bottom to work harder) but was in fact something closer to a pyramid scheme heavily influenced by money and market forces. Over the years, I’ve heard similar stories form others. I now see this a systemic problem with the academic system. I should add here that I love science and because I love it I have focused my work on the larger structural issues that influence how science and research gets done.

LR: And how did Aaron’s story have “a big impact” on your life?

DR: I first heard about Aaron’s work in the early days of my PhD during his prosecution for downloading academic papers from JSTOR via MIT. I’d been insulated from most of the activism around science and research before this. I worked in a lab and saw how publishing and other academic incentives played out in the academy, but I didn’t know that that an entire community of people was working to change things and fighting for access to knowledge as a human right.

Like many people, I felt Aaron’s actions were justified and in line with the spirit of science and research. While the actions of MIT, JSTOR, and the federal government appeared to be motivated by a desire to restrict access to academic work for the protection of moneyed interests. This was the first time I’d heard about the open access movement and first exposure of activism around academic issues. I saw that the problematic incentive structure I experienced in my lab were part of a much larger issue that impacted global access to knowledge. Aaron’s writing on open access inspired me, in part because he focused on what a person could do today.

As a graduate student at a US institution, I was in a relatively privileged position to impact the system. I was inspired to find the community of scholars and activists working on open access issues around the world. I found my local open access community though Robin Champieux at my home institution’s library, got involved in the OpenCon and Mozilla Science communities, and found the way to put my disillusionment to work.

Danielle with her comrades from “Mini-Working Open Workshops with Mozilla” Top row: Ryer Banta, Teon Brooks, Javier Jonas Mendoza, Daniela Saderi, Tavita Garrett, Antoinette Foster, Allison Schaser, Itallia Pacentine, Khadidiatou (Khady) Sall, Asia Mitchell. Bottom row: Ted Laderas, Robin Champieux, Samantha Hindle, Danielle Robinson, Jess Schamek, Luci Moore.

Here’s the website for this workshop (Mozilla Science Lab MiniWow PDX).

Mozilla WOW Montreal

LR: You mentioned that the circumstances of Aaron’s death also struck you personally in many ways?

DR: Yes. It’s hard for me to consider his work without thinking about his death. Although there is nothing I can say about his death that is new or insightful. Any suicide leaves pain, sadness, and questions unanswered. It’s a reminder that life is messy, and messed up, and often too short. I’ve also struggled with depression. Who hasn’t? I got treatment at a critical point after the birth of my son. Depression isn’t rational. It’s deeply irrational. My personal goal is to be honest about my own experiences and try to support my colleagues and friends (and myself) to do work that (hopefully) matters in a world that doesn’t make sense.

LR: Your 2016 dissertation is not available for download until Tuesday, March 4 of the year 2020. What’s going on there?

DR: Yes. Sadly my PhD advisor is not an open access believer, so until my paper is out of review my dissertation is under embargo, which drives me nuts.

To give you more context regarding my dissertation being embargoed: I understand the incentives that lead my PhD advisor to prefer to keep unpublished work, such as what’s contained in a dissertation, under wraps. I get it. But I think it’s the wrong path for science, in the big picture. It’s also personally frustrating to me, as I know how long it took to get some of those protocols working and I’d prefer preprints or the dissertation to be freely available. I want to save some other researcher that time.

Looking at the field today, open access, preprints, and other approaches to make research freely available are becoming the norm in neuroscience research. It’s a huge change from when I started my degree in 2011. The work isn’t done, and the embargoed dissertation illustrates that for me (on a very personal level).

These cultured cells have been stained to show the myelin (red) and the cell nuclei (blue). The green is a virally induced expression of green fluorescent protein.

LR: Now tell me what’s going on in these images. (1) Above and (2) Below.

DR: These images show cultured neurons and Schwann cells. The Schwann cells make insulation for a neuron’s axon. In the body, this helps electrical signals travel fast along long axons – to send information out to the periphery or in to the central nervous system.

These cultured cells in the image above have been stained to show the myelin (red) and the cell nuclei (blue). The green is a virally induced expression of green fluorescent protein.

LR: I’m including some quick links so folks can read a few sentences on each of them and better understand what you are explaining. I know I understood much better, after I did so.

DR: Ok thanks. Just to finish up: This specific research project attempted to understand the root causes of abnormal myelination in one type of “Charcot Marie Tooth peripheral neuropathy,” an inherited condition that involves abnormal Schwann cell myelination, demyelination of axons, and loss of peripheral nerve function.

This myelin photograph has been stained red so it can be assessed for its morphology.

LR: One of your bios says that you collect terabytes of microscopy data and love fancy microscopes – what’s the story there?

DR: During my time at the bench (slang for science that’s done in a lab, as opposed to field work or computational work) I got to work with a lot of really cool microscopes and imaging methods, including two photon and spinning disc microscopy, transmission and scanning electron microscopy, and photo activated localization microscopy (PALM). Microscopes were a part of my job and it was always fun to learn about the hardware, physics, and computational processing that made each approach unique. But what I really enjoyed was developing sampling and analysis methods to try to answer questions quantitatively. This usually requires a lot of samples and a lot of images, hence the terabytes of data!

I do really love fancy microscopes. It’s always fun to look at samples, even on the most low tech ‘scope. I have the most affection for a 1993 Phillips CM10 transmission electron microscope that I worked with from 2009-2011. I learned how to do all the routine maintenance on that ‘scope and believed it took better images than the newer machines. It was the first microscope that I knew how to fix, and could often fix it when others got stuck with it. The PALM ‘scope probably taught me the most, as I had to learn MatLab to work with it – my first experience with code!

LR: You mentioned to me that “It’s important to note that legal action similar that taken against Aaron Swartz still happens.” –> which case were you referring to?

DR: In 2017, after three years of fighting in Columbian and US courts, Diego Gomez was cleared of charges related to sharing a paper online.

LR: Glad he is okay. Thanks Danielle!

 

References:

1. The Dat Project: https://datproject.org/

2. Beaker Browser https://beakerbrowser.com

3. Code for Science & Society https://codeforscience.org/

4. Code for Science & Society Mailing list: http://eepurl.com/dj7pnj

5. Recap of June 11, 2018 Community Call:

https://blog.datproject.org/2018/06/11/may-community-call-recap/

6. Mozilla Science Fellowship Website:

https://science.mozilla.org/programs/fellowships/fellows

7. Mozilla Science Lab MiniWow PDX:

https://daniellecrobinson.github.io/mini-wow-pdx/

8. Working Open Workshops 2017 (Mozilla Science Lab):

https://mozillascience.github.io/WOW-2017/

9. Working Open Workshops Git Hub repository:

https://github.com/mozillascience/working-open-workshop

10. A Dat-based decentralized data sharing pilot project with Internet Archive, California Digital Library, and San Diego Supercomputer Center https://blog.archive.org/2018/06/05/internet-archive-code-for-science-and-society-and-california-digital-library-to-partner-on-a-data-sharing-and-preservation-pilot-project/

11. Danielle’s Dissertation (Abstract – Available for Download March 2020) The Role of the Myotubularin Pseudophosphatase MTMR13 in Myelination and Disease: https://digitalcommons.ohsu.edu/etd/3885/

12. ScienceFair – sciencefair-app.com – a P2P publication sharing application

13. Mapeo – https://www.digital-democracy.org/mapeo/– offline friendly mapping software developed to help protect indigenous land rights

14. Setting the Record Straight – Aaron Swartz Day.org – (Facts about the case.) https://www.aaronswartzday.org/aaronswartzfacts/

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