Episode 256: Thomas Karagianes & Jonathan Romano on crowd-sourcing RNA research with Eterna

Guest Thomas Karagianes | Jonathan Romano Panelist Richard Littauer
Show Notes In this episode, host Richard Littauer discusses the
journey and impact of Eterna with developers Jonathan Romano and
Thomas Karagianes. The conversation revolves around Eterna's role
in RNA research through user-contributed puzzle solutions,
emphasizing community engagement and educational outreach. Topics
include the integration of hybrid intelligence, where human
intuition complements AI in scientific discovery, and the
significance of explainable AI in motivating player participation.
The episode also touches on the ethical considerations in
collaborating with for-profit entities, the development of
accessible COVID vaccines, and low-cost tuberculosis diagnostics.
Hit download now to hear more! [00:01:24] Jonathan describes
Eterna, a platform where players solve puzzles to contribute to RNA
research. [00:02:12] Thomas explains that Eterna focuses on RNA
complexity and its importance in modern science, like mRNA vaccines
and how Eterna engages players in folding RNA sequences and testing
them in labs. [00:04:36] Richard asks if the project is open source
and Jonathan says its partially open source and explains the
technical limitations that prevent full openness. [00:05:26] We
learn about Eterna’s community with around 100,000 total players,
and a core group of about 30-40 who regularly engage in scientific
challenges. [00:07:31] Thomas discusses ongoing efforts to make the
game more accessible and increase community engagement through
educational outreach and simplifying the tutorial system, and
Eterna is used in classrooms as a teaching tool. [00:09:47]
Jonathan explains how some Eterna players become code contributors,
staff members, and even lead authors on academic papers. [00:13:32]
We hear about the funding of the community. [00:15:56] Thomas
discusses how Eterna integrates AI to assist players but stresses
the importance of human intuition in tackling unique challenges and
Jonathan explains how Eterna uses hybrid intelligence, combining AI
and human input for better research outcomes. He highlights how
Eterna’s community has contributed to important research, including
COVID-19 vaccine development and tuberculosis diagnostics.
[00:22:29] Thomas shares that Eterna attracts players who enjoy
breaking the model or exploring boundaries, making the game
engaging and motivating for them. [00:27:48] Jonathan and Thomas
discuss the ethical considerations of partnerships, especially with
for-profit companies, and the need to engage the community in
decision-making processes. [00:31:41] Jonathan shares how you can
contribute to Eterna and how to join the developer community on
GitHub. Quotes [00:10:10] “Minimally, whenever there is a
scientific publication that comes out of Eterna from players
contributions, there is a consortium author on the paper. That will
include everyone who has submitted a solution.” [00:14:21] “There’s
definitely this pattern - and you can even see it in the code-
where open source code passes from grad student to grad student.”
[00:19:14] “Hybrid intelligence is an underused buzzword.”
Spotlight [00:33:16] Richard’s spotlight is The Internet Archive.
[00:34:23] Jonathan’s spotlight is txircd, a modular IRC daemon
written in Python. [00:35:32] Thomas’s spotlight is Bioconda. Links
SustainOSS (https://sustainoss.org/) podcast@sustainoss.org
(mailto:podcast@sustainoss.org) richard@sustainoss.org
(mailto:richard@sustainoss.org) SustainOSS Discourse
(https://discourse.sustainoss.org/) SustainOSS Mastodon
(https://mastodon.social/tags/sustainoss) SustainOSS LinkedIn
(https://www.linkedin.com/company/sustainoss/?trk=public_profile_volunteering-position_profile-section-card_full-click&originalSubdomain=in)
Open Collective-SustainOSS (Contribute)
(https://opencollective.com/sustainoss) Richard Littauer Socials
(https://www.burntfen.com/2023-05-30/socials) Thomas Karagianes
LinkedIn (https://www.linkedin.com/in/thomaskaragianes/) Jonathan
Romano Website (https://luxaritas.com/) Jonathan Romano LinkedIn
(https://www.linkedin.com/in/luxaritas/) Eterna
(https://eternagame.org/) Eterna Project Information
(https://eternagame.org/about) Eterna OpenVaccine
(https://eternagame.org/challenges/10845741) Eterna OpenTB
(https://eternagame.org/challenges/10845742) Eterna OpenKnot
(https://eternagame.org/challenges/11843006) Eternagame-GitHub
(https://github.com/eternagame) Foldit (https://fold.it/) RNA
(https://en.wikipedia.org/wiki/RNA) Hybrid Intelligence (Springer
Link article)
(https://link.springer.com/article/10.1007/s12599-019-00595-2)
Mapping Citizen Science through the Lens of Human-Centered AI
(Human Computation article)
(https://hcjournal.org/index.php/jhc/article/view/133) Practical
recommendations from a multi-perspective needs and challenges
assessment of citizen science games (PLOS ONE article)
(https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0285367)
Mountains Beyond Mountains by Tracy Kidder
(https://en.wikipedia.org/wiki/Mountains_Beyond_Mountains) Internet
Archive (https://archive.org/) txircd
(https://github.com/elementalalchemist/txircd) Bioconda
(https://bioconda.github.io/) Reamde by Neal Stephenson
(https://en.wikipedia.org/wiki/Reamde) Credits Produced by Richard
Littauer (https://www.burntfen.com/) Edited by Paul M. Bahr at
Peachtree Sound (https://www.peachtreesound.com/) Show notes by
DeAnn Bahr Peachtree Sound (https://www.peachtreesound.com/)
Special Guests: Jonathan Romano and Thomas Karagianes.