Lecture to BEACON Center, Michigan State

On May 17th (Friday) at 3:30pm (EST), I will be giving a lecture entitled "Adventures in Quasi-Evolution" [1] to the BEACON Center [2]. The audience is Thrust Group 1 (Genomes, Networks, and Evolvability).

The first half of my talk will be on computational models of cellular reprogramming (e.g. evolutionary modulus, or the engineering on the remnants of evolutionary and developmental variation). The second half is some emerging work I am doing on the cultural evolution of economic value (e.g. evolutionary through the looking glass, or how evolutionary models [3] may explain current economic puzzles).

NOTES:

[1] "Adventures in Quasi-Evolution". Figshare, doi:10.6084/m9.figshare.701463 (2013). I define quasi-evolution as "changes over time not due to reproductive fitness or generational inheritance".

[2] For those who are unfamiliar, the BEACON Center (an NSF-funded center) is a multi-disciplinary, multi-University group interested in the intersection of biology and engineering with relevance to evolution. Catch the lecture at one of these locations:

Michigan State University: Biomedical and Physical Sciences Building, Room 1441 (BEACON seminar room), 3:30pm.

North Carolina A and T University: McNair Hall, Lecture Room 4, 3:30pm.

University of Idaho: Life Sciences South (LSS), Room 144, 12:30pm

University of Texas, Austin: Service Building (SER), Room 321H, 2:30pm.

University of Washington: UW Hutchinson Cancer Center, Building PAA Room 023D, 12:30pm

[3] The cultural evolutionary models used in my research are called Contextual Geometric Structures (CGSs). Contextual Geometric Structures (CGS) will never play chess well, or perhaps at all. They will never beat Ken Jennings on Jeopardy. That's not the point. They exist as soft or fuzzy (e.g. possibilistic, non-transitive) classifiers that capture (or at least reproduce) the structural features of cultural behavior. This is quite different from the dual inheritance models that are common in studies that focus on the geneaology of traits.

The "structure" of culture has been observed and pondered by many cultural anthropologists, from Claude Levi-Strauss to Pierre Bourdieu. Bourdieu used a construct called the "habitus" to characterize the relationship between individuals in a single generation and cultural structures that exist across multiple generations. CGSs provide a measure of computational precision (e.g. a kernel function)  to this and other conceptions of "cultural logic".

As a quasi-evolutionary phenomenon, CGSs are designed to capture neither the dual inheritance of genes and culture nor the connectionism of a traditional cognitive model. The outcomes of CGS agents are not geared towards optimal decision-making. Rather, they classify natural phenomena according to a set of discrete oppositions (or categories).

Some of these are based on premises (e.g. historically-determined preferences), while others are based on biological features of the organism. The CGS agents then use the classificatory state of other agents as a cue to either follow (conform) or disperse (dissent). What results is a form of social learning that can be used to update (or obliterate) the space between the lower-level categories.

CGS simulations can be run either in an liquid-like simulation, or independently. In the original conception, which maps CGSs to geographic and other spatial phenomena, a hybrid model was proposed. In experiments geared towards understanding the social construction of economic value, populations of CGS kernels and their agents are static with respect to spatial position. However, they exchange items and attach value to those items based on repeated interaction.

For more information, please see:
Alicea, B.  Contextual Geometric Structures: modeling the fundamental components of cultural behavior. Proceedings of Artificial Life, 13, 147-154 (2012).

Celebrity Recurrence, Professional Graphs, and Nano-Self-Expression

This has been cross-posted to my micro-blog, Tumbld Thoughts:

First up, it’s time for internet memes to meet mathematical concepts. On the left is a conceptual piece I am calling “The Cage Recurrence”. This is based on the Nick Cage vampire urban legend [1]. The transformations in the image are based on the Poincare recurrence (inset A), originally developed by Henri Poincare [2].

A Poincare recurrence occurs when the state of a volume-preserving flow map (e.g. 2-D image) returns to a close approximation of the initial condition after a period of time (usually very long). Theoretically, this is related to ergodic theory and the evolution of Hamiltonian systems [3]. As such, the dynamics of a Poincare recurrence can also be illustrated as a chaotic Poincare map (inset B, left) or a deterministic Baker’s map (inset B, right).

Next up, LinkedIn has a new feature that allows you to visualize your professional social network. It plots all of your first-order connections on the basis of shared connections and other attributes.

The network tends to cluster by workplace/community, but my network includes a lot of people that do not fall into any one category (as do most, I would imagine). InMaps uses programming tools such as Hadoop for handling large datasets and Processing for visualization. Fun!

Finally, here is a feature on nanoscale movies. In 1990, Don Eigler and other researchers at IBM [4] were able to assemble the letters “I-B-M” out of Xenon atoms using scanning tunneling microscopy (STM) [5].

Now, similar techniques have been used to make the world’s first atomic-scale animated short film “A Boy and His Atom” [6]. A “Star Trek” logo is also possible [7]. 

NOTES:

[1] Google “Nick Cage vampire” for more information.

[2] Image/illustration is courtesy of the Max Planck institute for Complex Systems and Crutchfield, J. et.al   Chaos. Scientific American, December (1986).

[3] it may also be the mechanism behind deja vu in “The Matrix” trilogy.


[4] Eigler, D.M. and Schweizer, E.K.   Positioning single atoms with a scanning tunnelling microscope. Nature, 344, 524-526 (1990).

[5] Johnson, D.   IBM Makes Smallest Movie Ever. IEEE Nanoclast Blog, May 1 (2013).

[6] Pachal, P.   IBM Manipulates Atoms to Create the World’s Smallest Movie. Mashable, May 1 (2013).

IBM Research, “A Boy and His Atom”. YouTube, April 30 (2013).

[7] Kramer, M.  IBM Warps Atoms into Crazy “Star Trek” Art. Space.com, May 3 (2013).

The significance of influence metrics: some fun with Klout and Google Scholar

 

Here is the main Klout interface with my personal Klout score and its trend over time. Klout is (please pick the one that is most applicable):

a) a popularity time-series, like brain electrical activity or stock market performance, and is probably (in an indirect fashion) related to each [1].

b) based on what exactly? I know, this puzzled me initially as well. Find out more here.

c) an excellent way to parlay your Facebook playtime into professorial tenure [2]. Not really. But it would not be at all surprising to me, given the almost-reflexive reverence paid to social media by business and journalistic culture.

d) a way to determine you personal worth, if your life is all about social media. And, really, what person’s life isn’t these days. It’s the new religion. Praise Zuckerberg [3]!

e) all of the above. Hope this raises my Klout score!

UPDATE: Since cross-posting this to Tumbld Thoughts, my Klout score has indeed increased by 8 (it is 40 as of May 5th). Looks like it is due to an increase in Facebook activity (or perhaps more targeted Facebook activity -- suggesting that the Klout score could be incredibly easy to manipulate). World domination, here I come!

Of course, this says nothing about my "official" academic research footprint. Or does it? Perhaps we can learn more about these types of metrics by looking at Google Scholar. Holly Dunsworth at the blog Mermaid's Tale has looked at what exactly constitutes her h-index measurement. In short, just because papers are cited does not mean that they are cited for the same reasons, and thus do not have a uniform degree of influence across citations [4].

My h-index [5] is 1 (across 27 papers -- some being Figshare documents), and is highly asymmetrical. A single Nature Reviews Neuroscience paper accounts for most of the citations taken into account. I'm actually not sure what database they are using to calculate citations (and thus influence), since it is not taking into account a number of peer-reviewed conference papers and book chapters (and blog posts, for that matter - [6]).

Does this dude abide? Apparently, I've only been influencing people in a significant manner since 2011. However, the analytics engine at Academia.edu does things a bit differently. Does this capture additional (and useful) information?

Okay, I have not reached a definitive opinion about this as of yet. It's just food for thought, so please discuss.

NOTES:

[1] Here is a fun paper (for theoretical physicists, at least) on this topic from Marcus Raichle's group: He, B.J., Zempel, J.M., Snyder, A.Z., Marcus E. Raichle, M.E.   The temporal structures and functional significance of scale-free brain activity. Neuron, 66(3), 353-369 (2011).

[2] a very apt April Fools' joke deftly executed by C. Titus Brown on his blog Living in an Ivory Basement.

[3] the classic "Microsoft buys the Catholic Church" internet meme is probably appropriate here.

[4] Here is another critical assessment of citation statistics: Adler, R., Ewing, J., and Taylor, P.   Citation Statistics. arXiv:0910.3529 (2010).

In addition, Audrey Watters at Hack (Higher) Education blog (hosted by Inside Higher Ed) has a post on the problems she's experienced with Google Scholar.

[5] Of course, the h-index is just one possible way to measure research output. But caveats of the h-index and then some apply to all alternative methods.

[6] This was a problem for Jonathan Eisen (Tree of Life blog) as well. At least Google tries to be accomodating in these cases.......

In general, "The Secret History of Rock" by Roni Sarig might enlighen this discussion a bit. In many cases, relatively (or in some cases absolutely) obscure bands such as the Dead Kennedys have served to influence much more popular (but perhaps less influential) musicians and bands. Influence networks serve as the mechanism for absolute vs. relative influence. While the h-index does not capture this phenomenon well, the Klout socre might be better at uncovering this.

Evolving the Tardis: Carnival of Evolution #59

This has been cross-posted to my micro-blog, Tumbld Thoughts:

I've passed the CoE torch yet again. Dirk Steinke from the University of Guelph and blog DNA Barcoding brings us this month’s “Carnival of Evolution” (#59). Continuing with the futuristic/fantasy theme of last month’s carnival, the theme this month is: Dr. Who, evolutionary biologist. Who knows, perhaps he can make sense of Dalek diversity. This edition features the recent Synthetic Daisies post "Replication, Model Organisms, and Evolutionary Signatures".

An analytics update to Carnival of Evolution #58: As of May 3 (since April 1), this version has received 630 hits. Not bad for an academically-oriented blog carnival. Enjoy this month's installment (it should get a fair number of hits as well), and if you wish to host a future edition, please contact Bjorn Ostman.

Freely-associated Earth Day and Outdoor Adventure-related Content

This is being cross-posted to my micro-blog, Tumbld Thoughts.

Here is a recent story on how 70,000 ladybugs have been released in the Mall of America to combat aphid infestations of the interior foliage. At 4.2 million square feet, the Mall of America has developed an incipient ecosystem [1]. The dynamics of this ecosystem will interesting to observe, particularly in light of the work that has been done in the field of biospherics (e.g. Biosphere 2, which is sponsored by the University of Arizona) [2]. Speaking of self-sustaining ecosystems.......

Nice ecosystem animation for Earth Day, courtesy of Google Doodle. Surf the web to find the true meaning of Earth Day, I guess. Speaking of surfing.....

Why it pays to Surf Michigan. No, really! There is a thriving (albeit obscure) surf culture in the US state of Michigan [3]. Lake Michigan surfing (inset on the left, picture from the St. Joseph Pier on Lake Michigan) has been going on for years, usually in the Fall and Spring when gales present waves large enough for surfing on.

When there is significant rainfall (such as during the past few weeks) or Spring snowmelt, the inland rivers (inset on the right, picture from the Red Cedar River in front of the Administration Building at Michigan State University) allow for interesting surf conditions.

Rincon Beach Park, Santa Barbara County, CA. There is also beachfront right across the street from the UCSB campus.

Surfing at Michigan State is a bit like a cold UC Santa Barbara with ducks on a river (odd mental image, I'm sure). Speaking of academically-oriented surfing [4], here is a profile on the "Physics of Surfing" class offered at UC San Diego [5]. Happy outdoor adventuring!

Scenes from the "Physics of Surfing" class, which combines lessons in instrumentation, oceanography, and of course surfing.

NOTES:

[1] this has parallels to ecosystems that emerge due to climatic changes such as the retreat of glaciers.

[2] Allen, J.   People Challenges in Biospheric Systems for Long-Term Habitation in Remote Areas, Space Stations, Moon, and Mars Expeditions. Life Support and Biosphere Science, 8, 67-70 (2002).

[3] Pictures of wetsuit adventurers in interesting conditions courtesy of Matuli Surf Company (Matulis brothers, Midland, MI).

[4] Here is a list of the top 10 surf colleges from Surfer magazine. Michigan State (nor any other Michigan University) is on it. The only odd duck here is NYU, which offers you the opportunity to surf Long Island (and perhaps the sewers). I might add Florida Atlantic University (FAU) to the list, at least during hurricane season.

[5] A few more links about those skeptical of the academic value of studying surfing: 1) a video on the physics of surfing by Kevin Stahl and friends, 2) a white paper called "The Physics of Ocean Waves" by Michael Twardos (courtesy of Snake Gabrielson's Surflibrary.org), 3) a story by John Jeka at the University of Maryland in the "Neuromorphic Engineer" called "Light touch-contact: not just for surfers". The article profiles the role of touch (e.g. somatosensory information) in helping people and other animals keep their balance when moving across a surface.