OA Week: The Troubling U-turn of Open Access

 

Who Owns Our Knowledge? Troubling trends have emerged.

As academics, media producers, and authors: Who Owns Our Knowledge? I present two troubling scenarios. Each of these have happened in the past few decades and is a heady mix of hypocrisy and gross power imbalance.

Intellectual Property Rights!

2006: RIAA Persecutes people for downloading music.

2013: Aaron Schwartz is persecuted for downloading JSTOR articles, resulting in his suicide.

2025: Technology companies use intellectual property without author permissions to train Large Language Models (LLMs). Everyone celebrates tech company profit margins, and LLMs can drive some people to suicide. 

Which of these things is not like the other? To be fair, the final example (in red text) is at the expense of legacy publishers and intellectual property laws. But that is the point. Intellectual property rights are enforced in ways that totally benefit the largest entity. 

Open Access to the.....logical endpoint?

Once upon a time, people were excited about radical open access. Post a preprint, post-peer review, and eliminate the bias of prestige journals. Now, it is the prestigious journals that enjoy Gold (!!) open access (for an exorbitant fee).

Although there are a number of options outside of this paradigm (e.g. Green Open Access), the goals of the open access reform movement seem to have become obscured. More specifically, the transition from words and slogans to institutional normalization has not been smooth.

So is the highlighted scenario the logical endpoint for open access? Probably not, but more work is needed. Not the easy work, but the harder work of changing systems and institutions.

That is all.

Can these scenarios be stopped? This is up to us.

Orthogonal Lab Annual Report for 2024

Another year of the Orthogonal Research and Education Laboratory (2024). We have had a great year! I posted a summary video on YouTube that covers activities related to Saturday Morning NeuroSim, our Open Science/Open-source interest group, the Computational Developmental Systems interest group, the Representational Brains and Phenotypes interest group, and the Cybernetics interest group. I also discuss our educational initiatives and conference/publication activities.

The seminal activity of the lab is the Saturday Morning NeuroSim meeting, which happens on Saturdays at 10AM ET (North America). This is based on the Saturday Morning Physics educational events, which originated in Germany and are popular in Physics departments and US National Labs. We had 45 meetings in 2024, and covered all manner of intersections between computational, neuroscience, social science, molecular biology, and complexity theory. 

The Computational Developmental Systems interest group can best be described as Neuro-Devo-Psych. This combines our work on Computational Critical Periods and Computational Developmental Biology (DevoWorm-associated). This also intersects with work in the Representational Brains and Phenotypes interest group and the Developmental Neurosimulation approach. 

Our Open Science/Open-source interest group sponsors Google Summer of Code participation in addition to assorted activities in the research practice and open-source project management spheres. The rejuvenation of our Cybernetics interest group features a reading group and other academic activities. 

OAWeek 2024: Intrinsic and Extrinsic Approaches to Open Access

This post is in celebration of Open Access (OA) Week 2024. The theme for this year is "Community over Commercialization". 

How do we incentivize people to adopt Open Access practices? We can take lessons from motivational Psychology to think about routes to better practice. Before doing so, we need to consider the current (and often sorry state) of open access.

It could be argued that in some important ways, Open Access has failed. The system of access to academic goods as currently structured is built on significant benefits to publishers and costs to libraries and authors. This benefit has been accrued by publishers due to reputational benefits: being published in Nature, Science, or Cell is highly prestigious. Yet the benefits of this prestige are necessarily limited to a few groups with lots of resources. And the beneficial attributes of open access have been captured by commercial entities. Similar problems plague the open-source community, a shift to the open ethos is the only way out.  

The different types of open access also play different roles in the marketplace of academic goods. Green open access, or self-archiving artifacts, are community goods. While this can be susceptible to the tragedy of the commons, proper social investment can ameliorate maintenance and growth imperatives. This is often seen as the highest standard for open access but requires community investment. Building a sustainable infrastructure of preprints, open peer review, and overlay journals has been elusive.

The Economic Benefits and Costs of Different Colored Access

Black open access using tools such as Sci-Hub is considered piracy (hence the "black" label). From an economic perspective, piracy is symptomatic of a dysfunctional market. Indeed, part of open access' failure is due to the dominant position of publishers and their own economic imperatives. In fact, black open access can be considered a rational response to closing access to article in a research culture of sharing and finding alternate routes to success [1-3]. 

To focus more on the publisher's advantage, and the failure point of open access more generally, is the current state of Gold, Diamond, and Platinum open access. Gold open access involves payment of an APC (Article Processing Charges) fee to the publisher. This often reduces the burdens on libraries, as they previously paid excessive subscription fees. This is because APCs actually increase the burden on individual authors, with disappointing results on the prestige economy. Without market power for the authors (or home institutions), there is no incentive to build Diamond and Platinum access systems. In such systems, no APC fee is paid, and we get the prestige that people seek. One barrier to this is shifting the burden back to publishers, but with proper management of community resources it is the least bad option.

Up to this point, I have been speaking in economically coded language. Without thinking about various motivations, however, we cannot fully understand ways to move forward. Let's think about various intrinsic/extrinsic motivations of authors and their institutions to reclaim open access. Intrinsic motivations are properties of individual cognition, while extrinsic motivations are things that motivate individual behaviors from the outside world.

Intrinsic motivations

There are many intrinsic motivations that drive acceptance and adoption of open access. But there are many that do not, and these motivations often come into tension. Positive drivers include striving for a better community, an imperative for sharing results with the community, the ability to provide different platforms for scientific communication (datasets, hypotheses, theory, out-of-scope studies), and recognition for unsung components of the scientific process (such as technical reports or negative results). Negative drivers include a need to satiate cultural traditions, an inability to convey prestige through open means, a conflation of open access with fraud and low-quality work, and an inability to meet the quality needed to do open access successfully.  

Extrinsic motivations

The multitude extrinsic motivations include institutional support, the need for career promotion, community rewards and prestige, the pressure for cost savings, and technological ease of adoption. These can be a mix of positive and negative drivers that make adoption of open access hard to justify. Interactions with open-source software can also drive open access adoption, as the commitment needed to develop shared data and code can be easily extended to other academic artifacts.

What is the path forward? 

Sometimes considering motivations are not enough, and the community is much pettier and more irrational than we like to admit. It is worth thinking about eLife's model in open peer review, which in part lead to a backlash against the editorial staff [4, 5] by less sympathetic members of the scientific community (and barely-disguised corporate interests). Part of this is a disagreement about open strategies, but this is also about the gatekeeping nature the scientific community itself. The eLife model allows for papers to be preprinted, and then peer reviewed. The paper remains live on eLife's website even if the reviews recommend rejection (although the rejection is noted) [6, 7]. This is not novel amongst open peer review platforms but has rankled the more hierarchically oriented members of the scientific community. Perhaps we need to also consider "irrational management strategies", or what intrinsic motivations drive decisions that favor obsolete conventions.

References:

[1] Melvin et.al (2020). Communicating and disseminating research findings to study participants: Formative assessment of participant and researcher expectations and preferences. Journal of Clinical and Translational Science, 4(3), 233–242.

[2] Casci and Adams (2020). Research Culture: Setting the right tone. eLife, 9, e55543.

[3] Nosek et.al (2015). Promoting an open research culture. Science, 348(6242), 1422-1425.

[4] eLife latest in string of major journals put on hold from Web of Science. RetractionWatch. https://retractionwatch.com/2024/10/24/elife-latest-in-string-of-major-journals-put-on-hold-from-web-of-science/

[5] Abbot (2023). Strife at eLife: inside a journal’s quest to upend science publishing. Nature News, March 17. https://www.nature.com/articles/d41586-023-00831-6

[6] F1000 Staff (2022). Open peer review: establishing quality. March 7.  https://www.f1000.com/blog/peer-review-establishing-quality

[7] McCallum et.al (2021). OpenReview NeurIPS 2021 Summary Report. https://docs.openreview.net/reports/conferences/openreview-neurips-2021-summary-report

OAWeek 2022: Managing Virtual and Hybrid Meetings

Welcome to International Open Access Week, 2022 edition! Last year, we discussed the vision of a distributed research organization. This year, we will explore this theme a bit further. One aspect of distributed organizations is the need to work both synchronously and asynchronously. This brings the real-world experience closer to the collaborator without the travel, carbon emissions, or expense of being at a centralized institute. As our collaborators live in many time zones and have different lifestyles, it is important to capture their full attention in different ways. 

One way this is done is through the live attendance and replay of group meetings. The Orthogonal Research and Education Lab (OREL) offers a number of regular topical meetings, in addition to a general meeting on Saturdays, that engages collaborators from all over the world using a number of different pedagogical and technological techniques. 

An example of a virtual distributed meeting with collaborators dropping in from different parts of the globe.

An open meeting has a number of moving parts that need to be thoughtfully considered to ensure success. The first of these is choosing a meeting platform. OREL has found success with Jitsi, as it is lightweight and free to use (open source). While Jitsi can be used as a service, installing it on your own server opens up its many customizable features. Jitsi even works with Virtual Reality, with interactions between the 2-D meeting world and immersive 3-D being available in the Wolvic browser and Meta Quest casting option.

Sample scenes from screensharing within Meta Quest and the casting option.

Secondly, programming the meeting is a non-trivial detail that can make the most of your time. For our Saturday Morning NeuroSim meetings, we have settled on the following format: updates, light features, discussion, open collaboration, and finally, papers of the week. Agenda-setting should be flexible with respect to your attendee's availability. Not everyone can make an entire meeting, so allowing them to "drop into" participation is encouraged. 

Notetaking and live feeds are also good for augmenting our meetings. The OREL Lab Manager (Jesse Parent) We use notetaking tools such as Obsidian and Notion with allied feeds (Slack and Discord) for coordinating the various fragments of ideas and themes that emerge during meeting time. Feed technology is also good for sharing papers, and the vision of a stream feed is key to realizing the multimedia aspect of real-time meeting immersion, even when attendees are asynchronous.     

Different types of notetaking and stream feeding within a meeting (from the Cognition Futures Reading Group).

As a tool for participatory engagement, this can be done in a number of different ways. Lead by Daniel Ari Friedman and Bleu Knight, the Active Inference Institute has taken the route of invited livestreams and summary podcasts. These materials introduce collaborators to difficult academic concepts while making them more accessible. While YouTube has options for live streaming, it is not always the best option. I use OBS Studio (free and open source) to compose a desktop recording and edit before making it public. 

Recorded meetings are also good for coding demos, particularly when they do not go as planned. One can either prepare a recording in advance to include in the meeting recording or strip the demo down to a minimal approach using a CoLab notebook. This reduces the friction of failed screenshares and execution errors, while also easing the burden of performing in front of a group.

Coding demos from a recent Saturday Morning NeuroSim meeting.

But completely virtual experiences are not the only option for bringing people together from around the world. OREL has been experimenting with hybrid meetings. This type of meeting brings the ethos of virtual meetings to more traditional in-person meetings. This enables more inclusive participation from distant geographical points. Last Spring, we experimented with our own virtual meeting experience at the New York Celebration of Women in Computing (NYCWiC), hosted live at Fort William Henry, NY. The hybrid session "Frontiers in Data Privacy and Tech Ethics" featured a buffet of topics on AI and technology ethics. Soem of the participants were live, while others were virtual (recorded or located in different parts of the globe). For this type of meeting, experimenting with ways to optimize live/virtual synchronization and media capture quality are essential. We plan to experiment with this more in the near future. 

Virtual (top) and in-person (bottom) components of the session.

OpenWorm Annual Meeting 2021 (DevoWorm update)

This week we had our OpenWorm Annual Meeting for 2021, which featured administrative business as well as updates from our research groups and educational initiatives. Much activity going on inside of the OpenWorm Foundation -- join the OpenWorm Slack or follow OpenWorm on Twitter for more information. Below are the slides I presented on progress and the latest activities in the DevoWorm group. If anything looks interesting to you, and you would like to contribute, please let me know. Click on any slide to enlarge.

The last slide is in recognition of OpenWorm's 10th anniversary, or at least the first release of  OpenWorm 10 years ago this month. Looking forward to what the next 10 years will bring! 

But in terms of what the next month will bring (for DevoWorm), we are hosting our second annual Hacktoberfest! Check out README files in our pinned repositories on DevoLearn and devoworm/digital-bacillaria to get started!

ASAPBio Session on the "Past, Present, and Future of Preprints"

For Open Access Week 2020, Synthetic Daisies will feature an exciting panel discussion on preprints. On Monday (19th), I was part of a panel called "Past, Present, and Future of Preprints", hosted by ASAPBio. I live tweeted the event from the Orthogonal Research and Education Lab Twitter account. If you were not able to attend in person, the recording is on YouTube! The session started with a short introduction from each of our participants: Antonis Rokas, Soumya Swaminathan, Richard Sever, Ross Mounce, and Anjana Badrinarayan.

Yamini Ravichandran and Marco Fumasoni started us off with a short introductory presentation, followed by an introduction by each of our panelists. This part of the session culminated with Marco posing an initial question to the panel.

It turns out that there are many contributing factors to preprint adoption. Some of them involve legacy patterns from manuscript submissions and publications. But preprints also democratizes access to both the production and consumption of scientific literature. It turns out that cultural traditions (within fields and countries), researcher agency, and community incentives are also quite important.

The theme of research culture came up time and time again. But research culture is not only a motivating factor; pro-preprint behaviors can lead to other virtuous practices. For example, Ross Mounce suggests that preprints can encourage a culture of versioning, where different versions of a paper are viewed as important steps in the research process rather than simply being erratum.

There was also a discussion of the role traditional journals play in the research dissemination process. One future direction of preprint culture is to decouple papers from journals. Towards the end of our session, we heard a choice quote from Antonis Rokas and the Rokas Lab.

This combines nicely with observations earlier in the session regarding citation metrics: with the movement towards iteratively-developed preprints with multiple supporting components (open data sets, supplemental figures and notes), there will be a need to distinguish article quality from journal quality. Altmetrics are one path forward, but a more robust system is needed. 

Thanks to everyone for participating! Thanks also go to Sarah Stryeck, Jessica Polka, and of course Iratxe Puebla for being a great community manager! Happy Open Access Week! 

UPDATE (11/3): A recording of the session is now on YouTube!

Hacktoberfest now live!

Welcome to Hacktoberfest! Check out our DevoLearn repositories and our DevoLearn AI resources. Contribute from now until the end of October. Make five commits during the course of October, and Github [1] has something for you!

Want to participate in Hacktoberfest @ DevoWorm? Look at our issue board for Group Meetings, or look at the contribution guidelines for DevoLearn and contribute a Data Science demo. 

Select issues on the Group Meetings issue board (DevoWorm) and the Community Board for DevoLearn are also marked with the "Hacktoberfest" label. Once you decide where to contribute, issue a pull request or communicate your interest as a comment in the issue you want to address!

Thanks to Mauyukh Deb and Ujjwal Singh for their administration efforts, and Github users Abtaha, Jainal09, RaviKarri, RudRajit1729, Joel-Hanson, shreyraj2002, Malvi-M, krishnakatyal, and jesparent for their commits so far!

[1] Github offers a T-shirt as incentive for contributing. Offer only applies to labeled repositories (most of the DevoLearn repositories are eligible).

OpenWorm Annual Meeting -- DevoWorm Slides

Today we held the OpenWorm Annual Meeting, which is a time for the Board of Directors and Senior Contributors to meet and discuss the latest developments within the foundation (in this case, activities over the past 1.5 years). Overall, a very inspiring meeting! Here are the slides I presented on progress and the latest activities in the DevoWorm group. If anything looks interesting to you, and you would like to contribute, please let me know.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.

Click to enlarge.