May 18, 2017

Innovation, Peer Review, and Bees

This post was inspired by a couple of Twitter conversations by people I follow, as well as my own experience with peer-review and innovation. The first is from Hiroki Sayama, who is contemplating a range of peer review opinions on a submitted proposal.


I like the using the notion of entropy to describe a wide range of peer-review opinions based on the same piece of work. This reminds me of the "bifurcating opinion" phenomenon I sketched out a few years ago [1]. In that case, I conceptually demonstrated how a divergence of opinion can prevent consensus decision-making and lead to editorial deliberation. Whether this leads to subjective intervention by the editor is unclear and could be addressed with data.

Hiroki points out that "high-entropy" reviews (wider range of opinions) represent a high degree of innovation. This is an interesting interpretation, one which leads to another Twitter conversation-turned complementary blog posts from Michael Neilsen [2] and Julia Galef [3] on the relationship between creativity and innovation.


In my interpretation of the conversation, Michael point out that there is a tension between creativity and rational thinking. On one side (creativity) we have seemingly crazy and irrational ideas, while on the other side we have optimal ideas given the current body of knowledge. In particular, Michael argues that the practice of "fooling oneself" (or being overly confident of the novel interpretation) is critical for nurturing innovative ideas. An overconfidence in conventional knowledge and typical approaches both work to stifle innovation, even in cases where the innovation is clearly superior.

Feynman though that "fooling oneself" was generally to be avoided, but also serves as a hallmark of scientific rationality. However, the very act of thinking (cognitive processes such as focusing attention) might be based on fooling ourselves [4], and thus might define any well-argued position. 

Julia disagrees with this premise, and thinks there is no tension between rationality and innovative ideas. Rather, there is a difference between confidence that an idea can be turned into an artifact and confidence that it will be practical. Innovation is stifled by a combination of overconfidence in practical failure combined with a lack of thinking in terms of expected value. I take this to be similar to normative risk-aversion by the wider community. If individual innovators are confident in their own ideas, despite the sanctions imposed by negative social feedback, they are more likely to pursue them.

Nikola Tesla's approach was "irrational", it was also a sign of his purposeful self-delusion and perhaps even his social isolation from the scientific community [5]. Remember, in the context of this blogpost, these are all good things.

Putting this in the context of peer review, it could be said that confidence or overconfidence is related to the existence and temporary suspension of sociocultural mores in a given intellectual community. A standard definition of social mores are customs and practices enforced through social pressure. In the example given by Michael Neilsen, fooling oneself in order to advance a controversial position requires an individual to temporarily suspend social mores held by members of a specific intellectual community. In this case, mores are defined as commonly-held knowledge and expected outcomes, but can also include idiosyncratic practices and intuitions [6]. From a cognitive standpoint, this may be similar to the requisite temporary suspension of disbelief during enjoyable experiences.

While this suspension allows for innovation, violations of social mores can also lead to a generally negative response, including moral panics and the occasional face full of bees [7]. Therefore, I would amend Hiroki's observation by saying that innovation is marked not only by a wide range of peer-review opinion, but also by universal rejection. Separating the wheat from the chaff amongst the universally rejected works is work for another time.

The price of innovation equals a swarm of angry bees!

NOTES:
[1] Alicea, B. (2013). Fireside Science: The Consensus-Novelty Dampening. Synthetic Daisies blog, October 22.

[2] Nielsen, M. (2017). Is there is tension between creativity and accuracy? April 8.

[3] Galef, J. (2017). Does irrationality fuel innovation? Julia Galef blog, April 7.

[4] Scientific American (2010). How We Fool Ourselves Over and Over. 60-second Mind podcast, June 19.

[5] Bradnam, K. (2014). The Tesla index: a measure of social isolation for scientists. ACGT blog, July 31.

[6] Lucey, B. (2015). A dozen ways to get your academic paper rejected. Brian M. Lucey blog, September 9.

[7] "Face full of bees" is a term I just coined to describe the universal rejection of a particularly innovative piece of work. "Many bees on face" = "Stinging rebuke".

May 10, 2017

Embryology Special Issue

Me and my colleagues are pleased to announce an upcoming special issue of the journal Biology (Basel). The topic is "Computational, Theoretical, and Experimental Approaches to Embryogenesis" (see announcement). Our view of what constitutes embryogenesis research is rather broad, spanning experimental studies, cellular reprogramming, bioinformatics, and artficial life. Therefore, we seek submissions from a wide variety of researchers and article types.


As the lead editor, I will take any questions you might have about interesting ideas, types of articles, or if you are interested in peer-review. As noted on the poster, the deadline for submissions is August 31, 2017. Looking forward to an excellent issue.

UPDATED (5/17):
With the initial dealine fast approaching, we have decided to extend the submission deadline to December 31. 

May 4, 2017

Announcing our Google Summer of Code 2017 Students


As mentioned in a previous post, the OpenWorm Foundation (and DevoWorm group) has been receiving application for this year's Google Summer of Code. We have now selected our student applicants and projects to be awarded the internship. We had a very good group of applicants this year, so congratulations go out to everyone who applied!


Shubham Singh will be working on the model completion dashboard project, which is a general tool for the OpenWorm community. Siddharth Yadav will be working with me and the rest of the DevoWorm group to quantify and analyze secondary microscopy data that capture the process of embryogenesis for C. elegans and other organisms [1]. Good luck!

Thanks to the INCF for coordinating the selection process!


NOTES: 
[1] For more reading on the promise of this approach, please see: Chi, K.R. (2017). Picking out Patterns. The Scientist, May 1 AND Rizvi, A.H., Camara, P.G., Kandror, E.K., Roberts, T.J., Schieren, I., Maniatis, T., and Rabadan, R. (2017). Single-cell topological rNA-seq analysis reveals insights into cellular differentiation and development. Nature Biotechnology, doi:10.1038/nbt.3854.

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.

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