Showing posts with label general-events. Show all posts
Showing posts with label general-events. Show all posts

September 29, 2021

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!

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.


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!

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 AbtahaJainal09RaviKarriRudRajit1729Joel-Hansonshreyraj2002Malvi-Mkrishnakatyal, 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

Happy Darwin Day-ish! COURTESY: Kapil Bhagat

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.

Darwin at the center (a hub with a high degree of centrality) of a hypothetical collaboration graph. Image is actually of an evolutionary amplifier, a computational structure from Evolutionary Graph Theory. Image of Darwin is from Dinochick's blog.

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.

A "T" shape skillset in terms of employment skills and educating talent. COURTESY: T-Summit 2014.

I am interested in taking a landscape model approach to modeling polymathy as a function of expertise and semantic specialization. In getting there, we have to understand the relationships (various dimensions) of specialization and generalized knowledge. According to the education and tech literature, the traditional polymath can be modeled as a "T". In fact, the T-shaped skillset is back in vogue in some fields (e.g. design, project management). It is somewhat difficult to make the leap from abstract skills to specific facts and other knowledge that facilitates (or constrains) scientific collaboration. 


Components of the "I" shape in terms of academic influence and expertise. More information on this work to come.

To help this along, I have worked out an ontological and semantic model of scientific expertise. In the figure above, I show the bivariate model as a shape representing the relative "depth and "breadth" of a particular style of scientific practice. While there are "Is" (specialists) and "Ts" (generalists with a single specialty), there are also "combs" (generalists with multiple specialties) and "dashes" (pure generalists). "Combs" are most analogous to the traditional polymath, but it is interesting to ask where Charles Darwin (and other theorists) would fit into this type of scheme. 


While Darwin has shaped the thinking of many scholars in multiple fields (both traditional and upstart) over the past 150 years, he was also influenced by a variety of thinkers. Even more than a scientific specialist, the essence of theorists can be captured by multiple-input, multiple-output (MIMO) graphs of major ideas. This can extend even beyond the lifetime of the scientist. The following graphical example of influencers and the influenced (inputs and outputs) is from Semantic Scholar, and shows Charles Darwin's position in a semi-directed citation network within the Computer Science community.

Charles Darwin's academic influence as MIMO graph. See profile for details on how graph is computed.


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!

Several months ago, I posted on the beginnings of the OpenWorm Foundation's badge system. Contributions have been made by several senior contributors, including myself (see the Literature Mining series). Another of my contributions is a series of three badges focused on planning and executing a successful Hackathon [1]. Hackathons are get-togethers of expertise for the purpose of facilitating social coding and solving big, multistep problems. These types of events can be held live or via Skype, and even involve non-coding problem domains [2].

An active in-person Hackathon. 

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 three Alife-related resources to catch up on, some new and some not yet posted to this blog:


Alife XV just concluded, and was hosted in Cancun by Carlos Gershenson and the Self-organizing Systems Lab at UNAM. The proceedings are available here.


Here are the Proceedings from the previous Alife conference (XIV), held in NYC during the Summer of 2014.


And here is the Spring 2016 issue of Artificial Life journal, which features selected papers from the Alife XIV conference (held in NYC in 2014). Be sure to check out the paper "An Informational Study of the Evolution of Codes and of Emerging Concepts in Populations of Agents", which I reviewed.

June 17, 2015

Breaking the Threshold of 150,000 Reads

Great news! According to Blogger analytics, Synthetic Daisies blog has just surpassed 150,000 reads! This calls for a milestone post -- as a cake with candles would be logistically and conceptually difficult. In addition, Synthetic Daisies now has 300+ posts in the archives.

Most recent logo design, trite subtitle.

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.

Allowing myself to be myself since December 2008.

Finally, aside from the ten pages hosted here, the nine most read posts (circa June 2015, courtesy Blogger Analytics) are as follows:
Post Name

Type
Reads

Blogroll
9677

Blogroll
5426

Essay
2168

Feature/Cartoon
1696

Blogroll
1460

Theoretical Essay
975

Feature/Cartoon
820

Essay
788

Theoretical Essay
689



November 16, 2014

Thought (Memetic) Soup: November edition

This content is cross-posted to Tumbld Thoughts. Here are a few short observations on the state of the world and data, circa Summer 2014. Haven't gotten around to cross-posting these yet. The meta-theme is social disruption, evolutionary change, and economic dynamics, in spite of ideonational bias. These include Disruption du jour (I), Satire Makes it Doubly Skewed (II), and Ideonational Skew - Satire = Epistemic Closure? (III).


I. Disruption du jour


Is the idea of disruptive innovation a useful concept, or is it largely a misapplied buzzword. In the original definition of "creative destruction", Joseph Schumpeter described a process of innovation that resembled an avalanche or an earthquake. For example, most innovations do not reshape their respective industries, but a few key innovations (born out of creative ferment) do.



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.


II. Satire Makes it Doubly Skewed

Two (intentionally) skewed views on Evolution [1, 2]: God does not do art, and monkeys still exist. Or something like that. Anyways, here is a sampling of creationism satire from Summer 2014.

[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).



III. Ideonational Skew - Satire = Epistemic Closure?


Statistical conspiracy theory? Here is a link to John Williams' Shadowstats site and (appropriately) three readings [1-3] that critique the overall approach. For example, in one reading, it is suggested that the "shadow" in the Shadowstats name consists of an inappropriate modeling methodology.



[1] Aziz   The Trouble with Shadowstats. Azizonomics, June 1 (2013).

[2] Krugman, P.   Always Inflation Somewhere. Conscience of a Liberal blog, July 19 (2014).

[3] Hiltzik, M.   A new right-wing claim: Obama must be lying about inflation. The Economy Hub, Los Angeles Times, July 23 (2014).

October 20, 2014

October, 21, 2015 is roughly 365 days away!

Or 365.37708 days away, to be a bit more precise.


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

I've officially passed on the baton. The new Carnival of Evolution, #47 (All the News that's Fit to Blog) went live today on the "Evolving Thoughts" blog. It is organized around a "newsmedia" theme. As you will see upon visiting, I have two posts from this month prominently featured there.


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 Wednesday (April 4) at 2pm Pacific time, I will be presenting a lecture entitled "Scenes from a grahical, parallel biological world" to the Embryo Physics groups in Second Life. The lecture (see slides here) will be an excursion into the world of GPU (graphical processing unit) computing. I have been interested in GPU computing for a few years now, and interested in computer graphics for significantly longer.

 Scene from the Embryo Physics course (between classes).


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.

UPDATE (4/4): A blogscript of the talk is available on this page.

February 3, 2012

Hard-to-define Events (HTDE) Workshop

I just found out that the workshop I am trying to organize for Artificial Life XIII on hard-to-define phenomena was accepted by the program committee. Hard-to-define events are events in a complex system that set up major transitions or obvious features. Signatures of hard-to-define events are related to natural fluctuations, embedded patterns, and rare events of large magnitude. Unlike the underlying patterns and information revealed by machine learning techniques, hard-to-define techniques require alternative approaches not yet formalized.

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.

I am interested in having people participate from any number of fields. Of particular interest is how this idea might apply to the biological, cognitive, and social sciences. I have launched a webpage devoted to the latest news on the session. Please check it out, and if you are interested in participating contact me for more information. If you are in the Midwest on the weekend of July 19-22, you should try to attend (see previous blog post for more information).

November 3, 2011

Carl Sagan Day

November 7th is Carl Sagan Day (on what would have been his 77th birthday). Fun fact: our birthdays are three days apart. This tradition (or rather periodicity) was started by the Fort Lauderdale branch of the CFI (Center for Inquiry) several years ago. It has since become a nationwide event sponsored by the CFI. As Carl Sagan might say, be there or be superstitious.

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:

Printfriendly