Short Threads of Reading Queue

Here are some academic papers, articles, and blog posts I have put into my reading queue over the past few weeks that I have found interesting and/or comment-worthy. I have organized them into threads (e.g. streams of consciousness) here:

Short thread on cell biology and genomics:

[1] Xie, J. et.al   Autocrine signaling based selection of combinatorial antibodies that transdifferentiate human stem cells. PNAS, doi:10.1073/pnas.1306263110 (2013).

[2] Williams, R.B.H. et.al   The influence of genetic variation on gene expression. Genome Research, 17, 1707-1716 (2007).

In [1], the researchers use a combination of receptor antibodies to reprogram a cell's fate. Yet more evidence that cellular reprogramming is not only possible, but involves more than just a few transcription factors or a spontaneous transformation. The science in [2] is a pre-RNA-seq study on the effects of standing genome variation on steady-state gene expression. A good early review, although there is now more current/specific work available.

Short thread on economics, markets, and technology:

[1] Yglesias, M.   Who gets rich when robots take our jobs. Moneybox blog, May 13 (2013).

Mr. Spacely from "The Jetsons". He's rich and George Jetson is not.

[2] Falk, A. and Szech, N.   Morals and Markets. Science, 707, 340 (2013).

After reading [1], I come away with the impression that the only thing that can be economically gained from automation is a bolstering of the arbitrary claim (e.g. Russian roulette) to genius (e.g. even patent trolling qualifies). Apparently, it is more relevant (and fleeting) than ever. This is part of a trend that has lead to productivity gains of the last 40 years becoming locked up in corporations and/or an executive elite. Again, automation has helped this trend along, although automation does not always result in this outcome.

In [2], a curious finding is reported. If you are part of a market, you are more likely to let a mouse die for a lower amount of money. A novel addition to the experimental moral philosophy field. Not quite sure if this is an exercise in mutually-assured moral behavior (e.g. bystander effect), or a call to make judgments about economic value in isolation. Is there more than meets the eye to this simple set of experiments? As an aside, how does this relate to the psychology of auctions?

Short thread on subjectivity in the brain:

[1] Wittmann, M. et.al   The neural substrates of subjective time dilation. Frontiers in Human Neuroscience, doi:10.3389/neuro.09.002.2010 (2010).

[2] Schurger, A. et.al   Reproducibility distinguishes conscious from nonconscious neural representations. Science, 327, 97 (2010).

Apparently, 2010 was a good year for investigating subjectivity in the brain. How do we measure engagement with a piece of art or the practice of culture? In [1], changes in activity patterns among the "cognitive control" and "default activity" brain networks mediate subjective responses to visual motion. In [2], neural activity related to conscious, neural correlates of subjectivity must be both of a certain duration and intensity as well as being reproducible. While subjective experiences can be transient and unique, their neural correlates are not.

Happy 50th birthday, Chaos theory!

[1] Arbesman, S.   The Fiftieth Anniversary of Chaos. Social Dimension blog, May 17 (2013).

[2] Lorenz, E.N.   Deterministic Nonperiodic Flow. Journal of Atmospheric Science, 20, 130-141 (1963).

[3] Motter, A.E. and Campbell, D.K.   Chaos at Fifty. Physics Today, May, 27 (2013).

This feature got a pretty decent response on my micro-blog, Tumbld Thoughts: happy 50th birthday to the study of chaos [1]. A worldview first proposed (in formal fashion) by Edward Lorenz in a landmark paper on weather prediction called “Deterministic Nonperiodic Flow” [2]. Later, the field would grow to encompass analytical strategies such as nonperiodic attractors, bifurcation maps, and fractals.

As a new way to describe physical phenomena and complex systems with a high degree of nonlinearity and subtle unpredictabilities (e.g. the butterfly effect), chaos shattered the notion of a clockwork universe [3]. As a paradigm shifting concept, chaos theory has the potential to enrich all areas of science [4].

Image on left is from [1], and image at the right is from [3]. For the latest work in the field, check out the journal “Chaos: an interdisciplinary journal of nonlinear science”.

For examples from brain science, see the following two articles and book:

* Robson, D.   Disorderly genius: How chaos drives the brain. New Scientist, June 29 (2009). YouTube video.

* Kitzbichler, M.G., Smith, M.L., Christensen, S.R., Bullmore, E.   Broadband Criticality of Human Brain Network Synchronization. PLoS Computational Biology, 5(3), e1000314 (2009).

* Freeman, W.J.   Neurodynamics: an exploration in mesoscopic brain dynamics. Springer, Berlin (2006).

Intriguing evolution stuff:

Zimmer, C.   Enlisting a virtual pack, to study canine minds. New York Times, April 22 (2013).

The Dognition website.

This is a story about Dr. Hare, the Anthropologist (the study of humans) interested in canine cognition. Can we throw any more species in there? Oh yes -- apparently dogs are more intelligent than their wolf wild-type cousins (determined by something called the "pointing test"). So to make this assessment more scientific, Dr. Hare came up with a test for dog intelligence. He also founded a company called Dognition, which is collecting data from dogs worldwide. But there's no such thing as a Dog IQ just yet. It will be interesting to see how intelligence corresponds with breed and degree of artificial selection for specific traits.

Evolutionary "gut check":

Burger, O. et.al   Human mortality improvement in evolutionary context. PNAS, doi:10.1073/ pnas.1215627109 (2013).

This is a paper that I could not quite figure out. My gut says that something is not quite right/being accounted for here. Are they using ethnographically-observed hunter gatherer populations to derive an evolutionary baseline? If so, can they truly demonstrate that these populations actually represent such a baseline? Also, it seems to me that increases in life expectancy may involve the elimination of early mortality (due to warfare, violence, and disease) rather than a biological or cultural adaptation (particularly one on the order of those that distinguish between sister taxa, as the one that distinguishes human hunter-gatherers and chimps).

...and, finally, actual robots!

ICRA 2013 Conference website. Held in Karlsruhe, Germany, and sponsored by IEEE.

Erico Guizzo reports for IEEE Spectrum from ICRA (Robotics Conference), and brings us (among many other interesting things) a feature on Entropica:

LEFT: Screenshots of Entropica configurations (social network interactions and a pole balancing task). RIGHT: real-world (e.g. Primate) behaviors (termite dipping/tool use and stock market trading).

Wissner-Gross, A.D. and Freer, C.E.   Causal Entropic Forces. Physical Review Letters, 110, 168702 (2013).

Hewitt, J.   The emergence of complex behaviors through causal entropic forces. Phys.org, April 22 (2013).

Using a robotic model, it can be demonstrated that general intelligence (in the form of causal generalization) may be amplified or otherwise result from entropy maximization. This is related to work done on ant trails, showing that they conform to Fermat's principle of least time.