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.
September 29, 2021
OpenWorm Annual Meeting 2021 (DevoWorm update)
October 20, 2020
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.
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.
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!
October 14, 2020
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).
February 16, 2017
A Peripheral Darwin Day post, but Centrality in his Collaboration Graph
Having not decided on what to post for Darwin Day 2017 in advance (and thus being late to the party with my annual post), I will be taking a rather circular approach to this post. I recently read a blog post on a TEDMED talk by Artem Kazneechev [1] on how theorists offer opportunities for collaboration across multiple research domains and existing research communities. The most extreme case is that of Paul Erdos, for whom the term "Erdos number" was coined [2]. The Erdos number defines a degree of association on a collaboration graph between a given author and Erdos as defined through co-authorship [3]. The role of theorists in such collaboration graphs is intriguing, and involves their role as hubs (highly-connected nodes) in a scale-free network topology [4]. In terms of the scientific community, such hubs often serve as connectors between disciplinary groups and sub-communities.
As Kazneechev [1] points out, sometimes one need not be as prolific as Paul Erdos to serve as a connector. Henri Poincare was a bit less prolific, and certainly did not live out of a suitcase, but serves as a scientific connector nonetheless. In fact, all theorists are at an advantage in this regard. This makes me wonder what a collaboration graph centered on Charles Darwin would look like. While I do not have the neccessary data, I would imagine it would quite different from Erdos' graph. This is because Darwin (as far as I know) did not publish collaborative papers. However, a citation network [5] in which documents rather than scientists serve as the nodes might better capture Darwin's role as an influencer, and thus partially recapitulate the topology of an Erdos-based collaboration graph.
Lately, I have been doing some unfocused research on polymathy [6]. One of the things that has fascinated me is the distinction between "domain-specific" knowledge and "general" knowledge, particularly as it relates to specialization. One criticism of modern science is that it suffers from hyper-specialization. The trend towards hyper-specialization has been constant over historical time, and now contrasts sharply with the scientists of the 16th and 17th century. This trend has been countered in a number of ways, particularly through interdisciplinary initiatives. Yet all too often, interdisciplinarity is reduced to groups of specialists gathered in the same room talking past one another.
NOTES:
[1] Kazneechev, A. (2012). Theorists as Connectors: from Poincare to mathematical medicine. Theory, Evolution, and Games Group blog, November 4.
[2] Newman, M.E.J. (2004). Who Is the Best Connected Scientist? A Study of Scientific Coauthorship Networks. Lecture Notes in Physics, 650, 337–370.
[3] Alicea, B. (2011). Academic Connectivity and the Future of Scientific Ideas. Synthetic Daisies blog, September 9.
[4] Newman, M.E.J. (2001). The structure of scientific collaboration networks. PNAS, 98(2), 404-409.
[5] More information about citation networks and their usefulness to the practice of science can be found in: Editorial (2010). On citing well. Nature Chemical Biology, 6, 79.
[6] A few popular readings on polymathy: Arbesman, S. (2013). Let's Bring the Polymath -- and the Dabblers -- Back. Wired, December 13 AND Mazie, S. How to be a Polymath. Big Think blog.
January 18, 2017
More Badges to Earn, Hackathoners!
Check out the Hackathon badges today! For people unaccostomed to earning badges, badges are a quick credential earned by working through the evidence points and submitting an answer in the form of short pieces of computer code, images/graphs, or links acquired through working with a piece of technology. The points of evidence are meant to encourage problem-solving and learning on your own, so there is no time limit on completion. Let me know if working through this badge encourages you to host a Hackathon event of your own.
NOTES:
[1] Badges must be earned in sequence: Hackathon I, Hackathon II, and Hackathon III.
[2] Hackathons can also be used to collaboratively solve interdisciplinary problems in a short period of time. For more information, please see: Marshall, J. (2016). In first 72 Hours of Science, SFI postdocs test the limits of transdisciplinary science. Santa Fe Institute News, April 20.
July 24, 2016
Catching up on Free Alife
Here are the Proceedings from the previous Alife conference (XIV), held in NYC during the Summer of 2014.
June 17, 2015
Breaking the Threshold of 150,000 Reads
When I started Synthetic Daisies, it was loosely modeled on a style typical of the science blogosphere in 2008 (with a bit more casual approach). I was also (and have been since the late-90s) inspired by what Wired's approach to web content. This landscape has changed quite a bit, and so has Synthetic Daisies. Having my own blog has allowed me to address my own set of interests in my own style. I've also been presented with unique opportunities for scholarship which are not typically "blog-like", but interesting nonetheless.
Post Name
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Type
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Reads
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Blogroll
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9677
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Blogroll
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5426
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Essay
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2168
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Feature/Cartoon
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1696
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Blogroll
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1460
|
|
Theoretical
Essay
|
975
|
|
Feature/Cartoon
|
820
|
|
Essay
|
788
|
|
Theoretical
Essay
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689
|
November 16, 2014
Thought (Memetic) Soup: November edition
The modern notion of disruptive innovation does not make the distinction between the effects of innovation in different industries, nor are all so-called "disruptions" equally as valuable. Schumpeter's model of disruptive innovation resembles a power law, while the modern conception of disruptive innovation argues that transformative changes are ubiquitous. Here are some readings on the myth and controversies surrounding the concept:
Lepore, J. The Disruption Machine. New Yorker, June 23 (2014).
* a critique of the "disruption" industry.
Bennett, D. The Innovator's New Clothes: Is Disruption a Failed Model? Bloomberg Businessweek, June 18 (2014).
* perhaps Lepore is right -- disruption for disruption's sake is not a viable model of economic change.
Bennett, D. Clayton Christensen Responds to New Yorker Takedown of 'Disruptive Innovation'. Bloomberg Businessweek, June 20 (2014).
* a rebuttal to the Lepore article from the modern "disruption" guru.
[1] Pliny the In-Between Theistic evolution. Evolving Perspectives blog, July (2014).
[2] Why There are Still Monkey (fake book in the Dummies series). Timothy McVeins Twitter post, June 20 (2014).
October 20, 2014
October, 21, 2015 is roughly 365 days away!
Screenshot courtesy of Back to the Future Countdown and Hero Complex. Are we approaching yet another "temporal paradox"? Or is it just a multiverse? Ah, I see. Someone must have gone back and changed something....
May 1, 2012
Carnival of Evolution #47 is live
Next Month's CoE (#48) will be hosted by PZ Myers at Pharyngula (no Gorillas, but probably LOTS of squid and octopii). And you are interested in hosting your very own Carnival of Evolution (I believe there is an open spot for July), contact Bjorn Ostman at the Carnival of Evolution head office.
March 30, 2012
A graphical, parallel biological world.....
This is a different approach to using CUDA architectures, which for most scientists is all about solving their mathematically-intensive problems faster. My interest is a bit more philosophical. I wish to understand the connections between parallelism and high-powered graphics processing (e.g. image rendering) in the service of designing novel data structures for analyzing scientific data. In this case, I am interested in what we can learn from a host of biological systems (ranging from population biology to cell biology).
Perhaps this approach can be leveraged to better understand the self-organization and underlying context that characterizes many biological systems. This talk represents a first step in this synthesis, but should be interesting in any case.
February 3, 2012
Hard-to-define Events (HTDE) Workshop
It should be a good session, but I need to procure a lineup of participants. I am currently recruiting people to present their work in the context of hard-to-define events: the plan is to think about how one's research might involve hard-to-define events, and then consider how we might design analytical tools and/or measurement techniques to discover them.

November 3, 2011
Carl Sagan Day
It seems there is a "cult of Sagan" brewing. I'm looking forward to the upcoming remake of "Cosmos" involving Seth MacFarlane and Neil DeGrasse Tyson (supposedly arriving on our planet in 2013). Next up, Richard Feynman day (May 11).
Below are several printable poster (.pdf format) announcing the event: