April 17, 2017

Breaking Out From the Tyranny of the PPT

Player 1 vs. Powerpoint (with a screenshot of the game Breakout). The image itself was made in PowerPoint, but I promise this post will not be recursive nonsense.


By now, you have probably chosen a side in the PowerPoint debate: namely, does it enhance or hinder scholarly communication? I will present both sides of this argument, but not argue to moderation. Rather, I will show that PowerPoint is good (or good to get rid of) only if you define your own style of presentation. In either case, you will need to "break out" of the box containing typical advice for creating PowerPoint presentations.


A number of people have argued (both rhetorically and in practice) that PowerPoint represents an enforced tyrrany on presented information. It forces big ideas into small compartments, defined by slide optimization and bullet points. What follows are a few examples of PowerPoint tyranny, or cases in which the default style of organization imposes constraints on communication and the exchange of ideas. 


A few years ago, Franck Frommer wrote a book on how PowerPoint makes us stupid [1]. Frommer's definition of stupid refers to impovrishing our ability to communicated logical flow, contextual detail, and the confusion of opinion and fact. Supprting this position is Peter Norvig's Gettysburg Address analysis, which suggests that the cognitive style of PowerPoint and its visual gimmickry often obscure rather than enhance the logical flow of a larger idea.


Example slide from the Gettysburg Address as a PowerPoint presentation.


Education might also benefit from breaking away from PowerPoint tradition. In fact, there is an argument to be made that the use of PowerPoint in education reduces course content to an overly-simplified, pre-packaged learning experience [2]. Dr. Chris Waters at Michigan State University has moved to eliminate PowerPoint lectures altogether in his undergraduate Microbiology course. He is instead adapting the existing presentations into a series of chalk talks which are more conducing to communicating scientific ideas. 


Perhaps the failures of PowerPoint are not about varied styles of communication across different domains of knowledge (scientific, business, legal), but more about the relevance of ideas and their overall structure. Relevance theory (Dan Sperber and Deidre Wilson) suggests that are biased according to what seems relevant [3]. Some of this is mediated by the cognition of attentional resources, but there is also an underappreciated role of cultural preferences and constraints. In the realm of science communication, the narrowly-defined relevance of typical PowerPoint design practice might encourage some aspects of scientific practice (science as memorization of facts, still images, simple graphs) at the expense of others (experimentation, data exploration, theory-building). 


The tyrrany of representational orthodoxy, PowerPoint style. On the other hand, this is actually pretty good in terms of available clip art. While perfectly suitable for business-oriented communication (e.g. team-building, simple storytelling), this may or may not be suitable for other domains of knowledge.


So how does one break out from the restrictions of PowerPoint? One way forward is shown by the artistic community's use of PowerPoint as an expressive medium. Like the latter-day explosion of animated .gif art on Tumblr [4], artists have been using PowerPoint to create animations and short videos. Interestingly, the limitations of PowerPoint for representing alternate forms of argumentation does not seem to limit artistic innovation [5]. Perhaps this has to do with the use of symbols rather than the ambiguity of linguistic syntax. 

A more argumentative-based way to approach PowerPoint is to adopt the Lessig Method of presentation [6], which presents ideas in only a few words in a large font. One example of this is Larry Lessig's "Free Culture" lecture, which connects a sequence of court cases and landmark ideas in sparse blocks of text. Whether this solves the ambiguity issue is not clear to me, but does provide a way to simplify without losing information.


The last several talks I have given include a final "Thanks for your Attention" Acknowledgements slide which features a graphic that has something to do with attention (visual illusion and/or obscure reference). This is one such example featuring Marshall McLuhan (e.g. breaking the message out of the medium).

UPDATED (4/23): Here is a presentation to the Association of Computational Heresy by Tom Wildenhain on how to construct a Turing Machine with PowerPoint. While it is a lot of fun, it does bring to mind some more creative uses of PowerPoint.


NOTES:
[1] Frommer, F. (2012). How PowerPoint Makes You Stupid: The Faulty Causality, Sloppy Logic, Decontextualized Data, and Seductive Showmanship That Have Taken Over Our Thinking. New Press, New York.

[2] Ralph, P. (2015). Why universities should get rid of PowerPoint and why they won’t. The Conversation, June 23.

[3] Sperber, D. and Wilson, D. (1995). Relevance: Communication and Cognition. Blackwell Publishers, Oxford, UK.

[4] Alicea, B. (2012). Moving the Still, courtesy of the .gifted. Synthetic Daisies blog, October 19.

[5] Greenberg, A. (2010). The Underground Art of PowerPoint. Forbes, May 11. Some examples of PowerPoint art (converted to YouTube videos) include:

a) "Infiltration" by Jeremiah Lee.

b) "Joiners" by blastoons.


[6] Reynolds, G. (2005). The "Lessig Method of Presentation". Presentation Zen blog, October 7.

April 4, 2017

100 years of Growth and Form!


This year marks the 100th anniversary of "On Growth and Form" [1] by the biologist/ mathematician D'arcy Thompson. "On Growth and Form" has always been an intriguing book from both a historical and technical perspective [2]. This includes the integration of fields such as physics, developmental biology, and geometry. There is an entire website dedicated to the centennial, which demonstrates that his ideas are still useful today [3].

Four bony fish phenotypes related through evolution and transformed through phenotypic deformation. 

D'arcy Thompson provided an account of what we now call evo-devo [4] as a series of mathematical transformations. On the one hand, this provides a mathematical model for the static geometry of the developmental phenotype across species. On the other hand, Thompson provided few if any evolutionary, nor any genetic mechanisms, even in a time when both were becoming ascendant [5]. His physical approach to biological form and morphogenesis has not only been useful in biology, but also as inspiration for computational modeling approaches [6].


NOTES:
[1] Thompson, D.W. (1917). On Growth and Form. Cambridge University Press, Cambridge UK.

[2] Alicea, B. (2011). The Growth and Form of Pasta. Synthetic Daisies blog, October 11.

[3] Much of the contemporary innovation in this area is in the field of architecture. In modern evo-devo, it has taken a back seat to genetic manipulation. Given what we now know about evolution and genetics, there are some potentially interesting biological simulation to be done at the interface of regulatory mechanisms in development and phenotypic fitness based on biomechanical parameters.

[4] Arthur, W. (2006). D'Arcy Thompson and the theory of transformations. Nature Reviews Genetics, 7, 401-406.

[5] Deichmann, U. (2011). Early 20th-century research at the interfaces of genetics, development, and evolution: reflections on progress and dead ends. Developmental Biology, 357(1), 3-12.

[6] Kumar, S. and Bentley, P.J. (2003). On Growth, Form, and Computers. Elsevier, Amsterdam.

March 18, 2017

Almost time for GSoC Applications!

Your chance to join the DevoWorm group is almost upon us. If you are a student, the Google Summer of Code (GSoC) is a good opportunity to gain programming experience. Applications are being accepted from March 20 to April 3. If selected, you will join the DevoWorm group, and also have the chance to network with people from the OpenWorm Foundation and the INCF.

The best approach to a successful application is to discuss your skills, provide an outline of what you plan to do (which should resemble the project description), and then discuss your approach to solving the problems at hand. We are particularly interested in a demonstration of your problem-solving abilities, since many people will apply with a similar level of skill. You can find an application template in outline form here.


You can apply to work on one of two DevoWorm projects: "Physics-based Modeling of the Mosaic Embryo in CompuCell3D" or "Image processing with ImageJ (segmentation of high-resolution images)". If you have any questions, comment in the discussions or contact me directly.

March 15, 2017

A Tree of Deeper Experiences -- the Authorship Tree

One of the most difficult aspects of academic publishing with multiple authors is in determining the order of authorship. In many fields, authorship order is the key to job promotion. Unfortunately, these conventions vary field, while the criteria for authorship slots often varies by research group. Since a responsible accounting of contributions are key to determining authorship and authorship order [1], it is worth considering multiple possibilities for conveying this information.

Example of an Authorship list (with affiliations)

A mathematics or computer science researcher might also see the problem as one of choosing the proper representational data structure. The authorship order, no matter how determined, is a 1-dimensional queue (ordered list). Even though some publishers (such as PLoS) allow for footnotes (an inventory of author contributions), there is still little room for nuance.

Example from "The Academic Family Tree"

But is there a better way? Academic genealogies provide one potential answer. A typical genealogy can be thought of as a 1-dimensional order, from mentor to student. In reality, however, an academic have multiple mentors, influenced by a number of predecessors. The construction of academic family trees [2] is one step in this direction, turning the 1-dimensional graph into a 2-dimensional one.


Picture of the Authorship tree cover. COURTESY: "The Giving Tree" by Shel Silverstein

This is why Orthogonal Lab has just published a hybrid infographic/paper called the The Authorship Tree [3]. This is a working document, so suggestions are welcome. The idea is to not only determine the relative scope of each contribution, but also to graphically represent the interrelationships between authors, ideas, and scope of the contributions.

As we can see from the example below, this includes not only our authors, but also people from the acknowledgements, funders, reviewers, authors of important papers/methods, and funders. While the ordering of branches along the stem suggests an authorship order, they are actually ranked according to their degree of contribution [4]. To this end, there can be equivalent amounts of contribution, as well as inclusion of minor contributors not normally included in an authorship list.

Example of an authorship tree (derived from original 1-D author list).

NOTES:
[1] Cozzarelli, N.R. (2004). Responsible authorship of papers in PNAS. PNAS, 101(29), 10495.

[2] David, S.V. and Hayden, B.Y. (2012). Neurotree: A Collaborative, Graphical Database of the Academic Genealogy of Neuroscience. PLoS One, 7(10), e46608. doi:10.1371/journal.pone.0046608.

[3] Orthogonal Lab (2017). The Authorship Tree. Figshare, doi:10.6084/m9.figshare.4731913.

[4] For more on the point system convention, please see: Venkatraman, V. (2010). Conventions of Scientific Authorship. Science Issues and Perspectives, doi:10.1126/science.caredit.a1000039.

March 4, 2017

Open Data Day Activities

Today is International Open Data Day, which was first proposed in 2010. To do my part, we will discuss a few open data-related items. Namely, what can you do to make this day a success?

Logo of the Open Knowledge Foundation (based in London), who offer a host of Open Data Day acitivities.

1) You can host some of your unpublished data (whether they are linked to publications or not) at an open data repository. You can do this through a general repository such as Dryad or Figshare, or a specialized repository such as Open fMRI [1].

* another part of publishing data is the need for annotation and other metadata. This is a barrier to opening up datasets, but the benefits of doing so may outweigh the initial investments [2].
2) You can join a open access communities such as data.world, a new social media network that allows people to share datasets of all types and sizes.

3) You can commit to creating more systematic descriptions of your research methods (e.g. the things you do to create data). This can be done by creating a set of digital notes or protocol descriptions [3], and making them open through Jupyterhub and protocols.io [4], respectively.

4) You can host your own virtual Hackathon. Unsure as to how you might do this? Then you can earn any (or all) in a series of three badges (Hackathon I, Hackathon II, Hackathon III) created in conjunction with the Open Worm Foundation.

5) You can petition or get involved with municipal and state/provincial governments to ensure their committment to open public data.

Of course, there are other things you can do, and more innovation is needed in this area. Have some ideas or planning an event of your own. Let me know, and I will invite you to the Orthogonal Lab's new Slack channel on Open Science.


NOTES:
[1] This choice, of course, depends on the field in which you are working. I used this example because fMRI data seems to have good community support for data sharing. Consult the Open Access Directory to learn more about the specifics for various disciplines.

For more information about data sharing in the field of neuroimaging, please see: Iyengar, S. (2016). Case for fMRI Data Repositories. PNAS, 113(28), 7699-7700.

[2] Based on a paper recently posted to the bioRxiv, and based on some material from a recent talk. For more information, please see: Alicea, B. (2016). Data Reuse as a Prisoner's Dilemma: the social capital of open science. bioRxiv, doi:10.1101/093518.

[3] Olson, R. (2012). A short demo on how to use IPython Notebook as a research notebook. Randal S. Olson blog, May 12.

[4] In terms of witing better and more accessible protocols, please see the following examples:

Protocols.io (2017). How to make your protocol more reproducible, discoverable, and user-friendly.
February 25. dx.doi.org/10.17504/protocols.io.g7vbzn6

Daudi, A. How to Write an Easily Reproducible Protocol. American Journal Experts, http://www.aje.
com/en/arc/how-to-write-an-easily-reproducible-protocol/, Accessed February 27, 2017.


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