June 18, 2017

Loose Ends Tied, Interdisciplinarity, and Consilience

LEFT: A network of scientific disciplines and concepts built from clickstream data. RIGHT: Science mapping based on relationships among a large database of publications. COURTESY: Figure 5 in [1] (left) and SciTech Strategies (right).

Having a diverse background in a number of fields, I have been quite interested in how people from different disciplines converge (or do not converge) upon similar findings. Given that disciplines are often methodologically distinct communities [2], it is encouraging when multiple disciplines can exhibit consilience [3] in attacking the same problem. For me, it is encouraging because it supports the notion that the phenomena we study are derived from deep principles consistent with a grand theorizing [4]. And we can see this is areas of inquiry such as learning and memory, with potential relevance to a wide variety of disciplines (e.g. cognitive psychology, history, cell biology) and the emergence of common themes according to various definitions of the phenomenon.

Maximum spanning tree of disciplinary interactions based on the Physics and Astronomy Classification Scheme (PACS). COURTESY: Figure 5 in [5].

The ability to converge upon a common set of findings may be an important part of establishing and maintaining coherent multidisciplinary communities. Porter and Rafols [6] have examined the growth of interdisciplinary citations as a proxy for increasing interdisciplinarity. Interdisciplinary citations tend to be less common than within-discipline citations, while also favoring linkages between closely-aligned topical fields. Perhaps consilience also relies upon the completeness of literature inclusion for people from different disciplines in an interdisciplinary context. Another recent paper [7] suggests that more complete literature citation might lead to better interdisciplinary science and perhaps ultimately consilience. This of course depends on whether the set of evidence itself is actually convergent or divergent, and what it means for concepts to be coherent. In the interest of not getting any more abstract and esoteric, I will leave the notion of coherence for another post.


NOTES:
[1] Bollen, J., Van de Sompel, H., Hagberg, A., Bettencourt, L., Chute, R., Rodriguez, M.A., and Balakireva, L. (2009). Clickstream Data Yields High-Resolution Maps of Science. PLoS One, 4(3), e4803. doi:10.1371/journal.pone.0004803.

[2] Osborne, P.  (2015). Problematizing Disciplinarity, Transdisciplinary Problematics. Theory, Culture, and Society, 32(5-6), 3–35.

[3] Wilson, E.O. (1998). Consilience: the unity of knowledge. Random House, New York.

[4] Weinberg, S. (1993). Dreams of a Final Theory: the scientist's search for the ultimate laws of nature. Vintage Books, New York.

[5] Pan, R.J., Sinha, S., Kaski, K., and Saramaki, J. (2012). The evolution of interdisciplinarity in physics research. Scientific Reports, 2, 551. doi:10.1038/srep00551.

[6] Porter, A.L. and Rafols, I. (2009). Is science becoming more interdisciplinary? Measuring and mapping six research fields over time. Scientometrics, 81, 719.

[7] Estrada, E. (2017). The other fields also exist. Journal of Complex Networks, 5(3), 335-336.

June 5, 2017

"Hello World", project version

The DevoWorm group has two new students that will be working over this summer on topics in computational embryogenesis. To begin their projects, I have asked each student to prepare a short presentation based on their original proposal, which serves as a variant of the traditional "Hello World" program. We will then compare this talk with one they will give at the end of the summer to evaluate their learning and accomplishment trajectory.

One student (Siddharth Yadav, who is a current Google Summer of Code student) is interested in pursuing work in computer vision, machine learning, and data science, while the other (Josh Desmond, a Google Summer of Code applicant) is interested in pursuing work in computational biology and modeling/simulation. You may view their presentations (about 20 minutes each) below, and follow along with their progress at the DevoWorm Github repository [1].

Siddharth Yadav's project talk  YouTube

Josh Desmond's project talk  YouTube

NOTES:
[1] Siddharth's project repo (GSoC 2017) and Josh's project repo (CC3D-local).

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.

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