December 25, 2014

Does the Concept of "Paradigm Shift" Need a Rethink?

A faux relationship between the paradigm shift and the theoretical resynthesis. Although in terms of advancing theory, perhaps they indeed do arise from a common ancestor.

As someone who is interested in both evolutionary and "meta-" theory I read a recent comment paper in Nature [1] called "Does Evolutionary Theory Need a Rethink?" with great interest. In fact, I discussed this paper a bit in a Synthetic Daisies post from last month. There are some interesting issues here regarding the role of "extended evolutionary synthesis" ideas in making evolutionary inferences and predictions. However, the real issue here is whether theory best proceeds through soft "paradigm shifts" (in this case, extending the framework) or through "resynthesis" (in this case, relentless synthesis). As an emerging approach to evolutionary theory, the extended evolutionary synthesis includes ideas not typically embraced by the modern evolutionary synthesis [2, 3]. These might include developmental plasticity, evolvabilityepigenetic phenomena, genetic assimilation, and cultural evolution. The primary argument is not just that evolution involves more than just changes in allele frequencies over time, but that such mechanisms should take a more central role in the process of evolutionary change [4].

The landscape of how evolutionary theory might be rethought. WHITE: Darwin's core contributions, LIGHT GRAY: modern evolutionary synthesis, DARK GRAY: extended evolutionary synthesis. Notice that this diagram implicitly favors the addition of rather than a shift towards new topical areas (e.g. resynthesis over paradigm shift). COURTESY: Figure 1.1 in [2].

But why do we need to rethink theories anyway? The classic observation of theoretical change comes from Thomas Kuhn [5], who advocated the dual concepts of "theoretical paradigms" and "paradigm shifts". In the evolution of a given scientific field, many new findings and concepts are introduced over time. Yet there is also an so-called essential tension between traditional and upstart concepts. Only very occasionally, a set of findings or concepts takes root that sweeps away the prevailing worldview. Paradigm shifts are thus low-frequency events that are nonetheless transformative in the way people think about a given scientific field. As events in intellectual history, paradigm shifts can often be a neccessary progression in the history of a scientific field. This is due to both the integrative nature of theory itself and conceptual inertia from the scientific establishment.

Although less appreciated by Kuhn, the integrative nature of theory thus serves to act as a form of conceptual inertia. In terms of theoretical evolution, incremental changes are hard to come by as singular findings and propositions do not often stand on their own. To really understand what is going on, the incremental progress of empirical science must coalesce into an intellectually coherent framework. According to paradigm shifters, prevailing theoretical models tend to be established through what is often called "saltationist" or non-gradualist change. Yet I would argue that whether such advances occur through paradigm shift or through resynthesis requires an underlying set of favorable conditions in the existing literature.

Yet perhaps the predominance of paradigm shifts throughout the history of science is largely based on assumption. Earlier, I mentioned a tension between "soft paradigm shifts" and "resynthesis". It may seem that paradigm shifts are neccessary in order to enable the novel insights in understanding. However, suppose that instead of acting as a neccessity for theoretical change, the paradigm shift served as a bias for those who would build theory itself. This might explain why all too often there is an expectation that new ideas either paradigm shift a field or languish insignificantly.

As an alternative to the paradigm shift, theoretical resynthesis allows for additional information to be incorporated into an existing theoretical framework. While more conservative, it may be no less transformative. In Darwin's original formulation of evolution by natural selection, the concept of heredity was without a formal mechanism [6]. The modern evolutionary synthesis was formulated in part to reconcile the ideas of evolution by natural selection and heredity by independent assortment. While a paradigm shift might give us a sorely needed new perspective, it can also live up to the idiom of throwing out the baby with the bathwater. It is worth noting that while it may be possible to achieve an extended evolutionary synthesis through theoretical resynthesis, the tone of contemporary arguments for an extended synthesis (e.g. the Altenberg 16) tend to be biased towards a soft paradigm shift.

An example of a directed conceptual network, in this case featuring the intellectual evolution (1940s-present) of cybernetics and systems science. As we can see, there are several distinct intellectual traditions that cross-fertilize the field to various degrees and at various points in time. COURTESY: Castellani, Wikimedia Commons.

To answer the question of whether or not evolutionary theory needs a rethink, a literature mining exercise might be helpful [7]. This type of approach would allow us to characterize to what extent extended synthesis concepts are being considered alongside modern evolutionary synthesis concepts and vice versa in the same context. This can be characterized using a conceptual network of empirical studies. In our conceptual network topology, the overall connectivity of (e.g. linkages between) various concepts would represent their relative conceptual integration in empirical studies and literature reviews, which in turn provides a basis for theoretical advances. Think of such pre-existing linkages as the histroical contingencies of theoretical change. This is not typically considered in the paradigm shift model, but has consequences for resynthesis and paradigm shifts alike.

To illustrate how this approach might be useful, I will give two examples from the contemporary biological literature. For example, how often does a published paper consider population genetics alongside evo-devo? Alternatively, how often does cultural evolution get characterized as part of an integrated evolutionary process? In the case of the former, relatively few studies seem to sufficiently bridge population genetics and evo-devo [8]. In the case of the latter, there are only but a few established approach for using the mathematics of population genetics to characterize both genetical and cultural evolution in the same framework [9].

In terms of a network topology, each of these examples would represent sparsely connected and a bit more densely connected concepts, respectively. This also illustrates the difference between the need for a paradigm shift and room for accomodation via resynthesis. On the other hand, perhaps the state of the literature serves to predict which outcome is more or less likely. Even in cases like the cultural evolution example, examples of resynthesis might not be representative of the dominant approach.

[1] Laland, K., Uller, T., Feldman, M., Sterelny, K., Muller, G.B., Moczek, A., Jablonka, E., Odling-Smee, J., Wray, G.A., Hoekstra, H.E., Futuyma, D.J., Lenski, R.E., Mackay, T.F.C., Schluter, D., and Strassmann, J.E.   Does evolutionary theory need a rethink? Nature, October 8 (2014).

[2] Pigliucci, M. and Muller, G.B.   Evolution: the extended synthesis. MIT Press, Cambridge, MA (2010).

[3] Muller, G.B.   Evo-devo: extending the evolutionary synthesis. Nature Reviews Genetics, 8(12), 943-949 (2007).

[4] Lamb, M.J. and Jablonka, E.   Evolution in Four Dimensions. MIT Press, Cambridge, MA (2006).

[5] Kuhn, T.S.   The Structure of Scientific Revolutions. University of Chicago Press, Chicago (1962).

[6] For more, please see: Charlesworth, B. and Charlesworth, D.   Darwin and Genetics. Genetics, 183(3), 757-766 (2009) AND West-Eberhard, M.J.   Toward a modern revival of Darwin's theory of evolutionary novelty. Philosophy of Science, 75(5), 899–908 (2008).

[7] I am merely offering the suggestion for a full-scale analysis rather than providing one.

[8] Based on a cursory survey of PubMed entries for the terms "evo-devo" + "population genetics" (21 results). Also:

a) Two reviews that provide a verbal analysis of evo-devo's theoretical underpinnings (circa early 2000's) can be found here: Arthur, W.   The emerging conceptual framework of evolutionary developmental biology. Nature, 415, 757-764 (2002) AND Gilbert, S.F.   The morphogenesis of evolutionary developmental biology. The International Journal of Developmental Biology, 47, 467-477 (2003).

b) There is also a burgeoning but small field called "micro evo-devo". For more, see: Nunes, M.D.S., Arif, S., Schlotterer, C., and McGregor, A.P.   A Perspective on Micro-Evo-Devo: Progress and Potential. Genetics, 195, 625-634 (2013).

[9] The approaches established by Boyd and Richerson (Culture and the Evolutionary Process) and Cavalli-Sforza and Feldman (Cultural Transmission and Evolution: a quantitative approach) are illustrative of such resyntheses. However, other models of culture are less integrative, and one might argue that these examples are not the most complete or parsimonious way to integrate of biology and culture.

December 18, 2014

Piketty Reviews: the year in review

Thomas Piketty's book "Capital in the Twenty-first Century" became quite the phenomenon this year. Originally published in French, it was translated into English in 2014 and has since elicited a large amount of feedback. I have collected a series of book reviews over the course of this year that provide a bit of perspective on the book. This could either prove to be prophetic, or another "End of History and the Last Man". The diversity of responses presented here suggests that the relationship between inequality and economic growth will become a defining social issue in years to come.

Even at 696 pages and a large number of graphs, it is quite a captivating read. Piketty synthesizes data from multiple sources and arrives at a fundamental set of relationships between concentrations of capital (e.g. inherited wealth) and economic growth (e.g. the diffusion of capital into the broader economy). Based on this intellectual synthesis, Piketty's presents two laws of inequality [1, 2]. These laws are drawn from the cross-national and historical data analyses. In particular, the second law serves as shorthand for the book's main thesis. While people might debate how exactly to define "wealth" and "growth" or how well this framework describes the macroeconomic present, Piketty's book gives us the conceptual tools to discuss these issues more clearly.

Piketty's insight is quite simple: there is a proportional and often unbalanced relationship between wealth and growth that transcends both nation and historical era. When the returns on inherited wealth exceeds income growth generated by resource exploitation, entrepreneurship, or innovation, high degrees of social and economic inequality result (W > G -- see Figure 1). This often occurs when growth is slow or nonexistant, and the rate of return on inherited capital exceeds growth by default. In terms of social relations, the W > G scenario allows for inherited wealth to triumph over social mobility and new wealth creation. By limiting social mobility, a host of related factors act to reinforce income inequality [3]. Yet this relationship does not always hold. For example, historical periods during which opportunities for economic expansion and social mobility exceed the power of inherited wealth (such as the latter half of the 20th century) tend to be characterized by high rates of conventional growth (e.g. increases in GDP). While the power of inherited wealth is curbed by growth, it might also be curbed by taxation policy. In any case, the second half of the 20th century scenario can be formulated as G > W, or growth exceeding wealth.

Figure 1. Extreme inequality, shown in both artistic and symbolic logical form.

Piketty arrives at this conclusion by using historical data. These data suggest that the slow growth and high levels of inequality which characteerize the early 21st century will recapitulate a pattern typical of the 19th century or even the European middle ages. The predominance of rentier behavior amongst the 21st century elite is indeed reminiscent of the medivel era, where the primary source of wealth generation came from rents paid to a landed gentry [4]. While the mode of wealth generating is variable from century to century, the basic tension between inherited versus newly-generated wealth is predicted to govern economic dynamics. And in this context, inequality can inflence a host of societal characteristics, from social stratification to technological innovation [5].

Perhaps these consequences of inequality are simply a consequence of an over-domineering financial industry, which provides massive returns to investment income relative to labor productivity. In this sense, history is more contextual than cyclical. But history can also parallel broadly-stated theoretical predictions. This state of affairs can be compared with the prediction made by Karl Marx with respect to the end of capitalism itself [6]. As capitalism matures (so-called "late stage" capitalism), we can expect most forms of labor to become devalued. While this is not something that Piketty predicts for the future, this devaluation is due to both various resource consolidations promulgated by the owners of capital and a by-product of technological innnovation (particularly automation -- see [7]). Piketty's solution to countering this type of structural inequality is wealth redistribution, which is something America pioneered [8], but is needed on a global scale to avoid the predicted negative consequences of economic growth stagnation [9].

Here is my collection of Piketty reviews

Introducing Piketty:
Galbraith, J.K.   Kapital for the Twenty-first Century? Institute for New Economic Thinking blog, March 31 (2014).

Frankel, J.   Piketty's Fence. Jeffrey Frankel's blog, September 22 (2014).

Yglesias, M.   The Short Guide to Capital in the 21rst Century. Vox blog, April 8 (2014).

Dorman, P.   Piketty for Dummies. EconoSpeak blog, April 26 (2014).

Wolf, M.   "Capital in the Twenty-first Century", by Thomas Piketty., April 15 (2014).

R.A.   Thomas Piketty's "Capital", summarized in four paragraphs. Economist, May 4 (2014).

Cowen, T. and de Rugy, V.   Why Piketty's Book Is a Bigger Deal in America Than in France. NYTimes The Upshot, April 29 (2014).

Eakin, E.   Capital Man. Chronicle of Higher Education, April 17 (2014).

Broader Economic Implications:
An Interview with Adair Turner: "Which Capitalism for the 21rst Century?". Institute for New Economic Thinking blog, November 12 (2013).

Hutton, W.   Capitalism simply isn't working and here are the reason why. The Guardian, April 12 (2014).

Boucoyannis, D.   Adam Smith is not the antidote to Thomas Piketty. WaPo Monkey Cage blog, April 22 (2014).

Cassidy, J.   Forces of Divergence: is surging inequality endemic to capitalism? The New Yorker, March 31 (2014).

Krugman, P.   Why we're in a New Gilded Age. New York Review of Books, April 10 (2014).

Shenk, T.   Thomas Piketty and Millenial Marxists on the Scourge of Inequality. The Nation, April 14 (2014).

Faux, J.   Thomas Piketty Undermines the Hallowed Tenets of the Capitalist Catechism. The Nation, April 18 (2014).

Rosenberg, P.   Thomas Piketty terrifies Paul Ryan: Behind the right’s desperate, laughable need to destroy an economist. Salon, April 30 (2014).

Ritholtz, B.   Piketty vs John Stuart Mill’s Marketplace of Ideas. The Big Picture blog, May 1 (2014).

Kaminska, I.   Inequality and Hyperinflation. Dizzynomics blog, April 25 (2014).

Criticisms: In May, there was a post on the Financial Times' Money Supply blog that claimed to find flaws in Piketty's data analyses and basic aproach to studying inequality. The following articles are a rebuttal to these claims.

Piketty, T.   Appendix to Chapter 10. Inequality of capital ownership. Addendum: response to FT. May 28 (2014).

Buchanan, M.   Economists, Show your Assumptions. Bloomberg View, May 6 (2014).

Irwin, N.   Everything You Need to Know About Thomas Piketty vs. The Financial Times. NY Times The Upshot, May 30 (2014).

Winship, S.   Financial Times vs. Piketty on US. Smoke, No Fire. Forbes, June 2 (2014).

Return to an Ancien Regime?
So is growth truly over? Or are we transitioning to a new mode of production? Perhaps it is not the nature of growth that guides thinking about this but the existential need for a powerful ruling class. Such a desire for oligarchy mirrors many popular interpretations of Piketty's main thesis, but in a more fatalistic manner. This hidden cultural theme might explain the recent (and disturbing) trend towards neo-reactionary thought amongst certain segments of Western society [10, 11]. So-called neo-reactionary thinking involves a combination of radical libertarianism with dictatorship. In and of itself, this would be a fairly predictable reaction to a period of great social and economic change. Yet this movement even has legions in the technology industry, a social milieu that a) represents the "new" economy and a prime source of future economic growth, and b) represents an industry that could help us overcome the limitations of traditional growth. This might reflect an inability to think innovatively about social and cultural change, or perhaps it shows how inerred we truly are to old ideas.

[1] Galbraith, J.K.   Unpacking the First Fundamental Law. Economist's View blog, May 25 (2014). AND Krussell, P. and Smith, T.   Is Piketty's "Second Law of Capitalism" Fundamental? Vox blog, June 1 (2014).

[2] von Schaik, T.   Piketty's laws with investment replacement and depreciation. Vox blog, July 6 (2014).

[3] Krugman, P.   Piketty Day Notes. Conscience of a Liberal blog, April 16 (2014).

[4] Kaminska, I.   The Tyrrany of Land. Dizzynomics blog, February 5 (2014).

[5] Hanlon, M.   Why has human progress ground to a halt? Aeon Magazine, December 3 (2014).

[6] Jeffries, S.   Karl Marx's guide to the end of capitalism: a primer. The Guardian, October 20 (2008).

[7] Gordon, R.J.   Is U.S. Economic Growth Over? Faltering Innovation Confronts the Six Headwinds. NBER Working Paper No. 18315 (2012).

[8] Geier, K.   Taking Aim at Inequality. Blog of the Century, March 12 (2014) AND Yglesias, M.   If growth is dead, we need radical redistribution. Moneybox blog, October 7 (2013).

[9] Cowen, T.   "Unified Growth Theory" by Oded Galor. Marginal Revolution blog, June 9 (2011) AND Kuznets Curve. Wikipedia. December 30 (2013).

[10] Pein, C.   Mouthbreathing Machiavellians Dream of a Silicon Reich. The Baffler, May 19 (2014).

[11] Brin, D.   "Neo-Reactionaries" drop all pretense: End democracy and bring back lords! Contrary Brin blog, November 26 (2013).

December 11, 2014

May You (and your Lineage) Have a Long (Artificial) Life!

The nested pun is my way of announcing the arrival of ECAL 2015Since I will be on the program committee for ECAL (European Conference for Artificial Life) 2015, I have been asked to publicize the call for papers, abstracts, and workshops. Here it is below — if interested, please consider submitting and attending.


“Embodiment, Interaction, Conservation”

The 13th European Conference on Artificial Life (ECAL 2015) will be held in York, United Kingdom, 20-24 July 2015, hosted by the York Centre for Complex Systems Analysis at the The University of York.

ECAL 2015 will showcase a wide range of topics in Artificial Life, bringing together world-leading researchers to discuss the latest advances in Artificial Life.  Artificial Life is an interdisciplinary field, and as such welcomes submissions from across the spectrum of scientific and humanities disciplines, that consider the main conference themes of “Embodiment, Interaction, Conservation”. 

THE ECAL programme committee invite you to submit full papers (8 pages) or abstracts (1 page) in the area of Artificial Life.  All submissions will undergo a detailed peer review process.  Full papers will be reviewed for relevance, scientific and/or engineering quality, sound methodology and use of appropriate analysis techniques. Abstracts will be reviewed for relevance and quality.

I M P O R T A N T   D A T E S   A N D   I N F O R M A T I O N

Submission papers:    Monday 2nd March, 2015
Notification of Acceptance: Friday 17th April, 2015
Paper CRC required:    Monday 18th May, 2015
Main Conference convenes: 20-24 July, 2015

Contact email for queries: ecal2015

S U B M I S S I O N   F O R M A T

There are two options for submission: either full paper or abstract. Note that the format is exactly the same for both options. The only difference resides in the number of pages and type of contents:

* full papers have an 8-page maximum length and should report on new, unpublished work.

* abstracts are limited to a 1-page length and can report on previously published work, but offer a new perspective on that work. We encourage the use of LaTeX for the production of papers. 

Submission will be via the Easy Chair system.

Papers and abstracts will be selected for oral or poster presentation, with no distinction being made between full papers and abstracts.


General Chair: Prof. Susan Stepney
Technical Chair: Prof. Jon Timmis
Workshop Chair: Dr. Simon Hickinbotham
Special Sessions Chair: Dr. Leo Caves
Tutorial Chair: Dr. Fiona Polack
Local Chair: Dr. Paul Andrews
ISAL Summer School: Dr. Rene Doursat

December 8, 2014

What Kind of Jurassic World Do We Live In?

Free-association and creative license at geologic timescales......

In a world where Gondwana has not yet fully drifted apart.....

COURTESY: Australian Museum.

And features a long-suffering movie idea that will probably end up being mediocre.....

Here is the "Jurassic World" trailer. COURTESY: Universal Pictures.

Satire still exists! Sort of.

A cynical take on the whole Jurassic World enterprise. COURTESY: xkcd.

December 4, 2014

Tales of an Academic Start-Up (Orthogonal Research)

This content is cross-posted to my personal website reboot. Previous updates and allusions to Orthogonal Research can be found (in chronological order) here, here, here, here, and here.

Myself, Represented Orthogonally
From January 2014 to November 2014, my primary affiliation was as Primary Investigator at Orthogonal Research [1]. Upon running out of funding at my previous position (Cellular Reprogramming Lab at Michigan State University), I decided to formally found an academic start-up. The idea was to have an affiliation and continue doing research while looking for a more formal position. However, with an open mind, an interest in research innovation, and some background in research commercialization, I decided to turn this into a more formal opportunity. I managed to turn out several papers, become a formal grant-making institute, and begin a long-term, large-scale distributed collaboration (DevoWorm). In fact, this collaboration led to my current position at UIUC.

While I now have a formal position, I am retaining the organizational identity as a secondary affiliation (much as some academics are "Chief Science Officers" at a start-up). I generated a number of reports to document the activities of an "academic start-up". This was stylized in the form of Quarterly Reports, which were based on three month intervals of the calendar year and summarized my academic activities during the period in question. These reports can be downloaded here: Q1, Q2, Q3, Q4 (coming soon).

Why call it a "Start-up"?
Why do I call it an academic start-up? Three things distinguish this from a more traditional start-up: fundraising, non-tangible vs. tangible outcomes, and business plan. While regular start-ups have multiple rounds of fundraising, the academic start-up is a bit more flexible. We can use cross-subsidization, grant money, and crowdsourcing [2] as a starting point. It is harder to fundraise when you have many non-tangible outcomes. The quarterly reports stress the tangible outcomes (papers, presentations, peer reviewing). However, academic work (particularly of the scientific variety) involves significant learning, internalization, experimentation, and reflection. 

Because of this flexibility and departure from conventional business thinking, the academic start-up does not operate by means of a formal business plan. In the case of Orthogonal, a path forward was made through exploration, tying up the loose ends of previous research, and working with collaborators to generate new productivity. In a sense, an academic start-up is a lot like a creative web endeavor such as programming a YouTube channel or administering blog content (which is part of the Orthogonal Research portfolio).

The workflow and productivity of an academic start-up, enabled by information technology.

Things I learned from this experience
1. There are significant economic "barriers to entry" in the field of research. As I was aware when starting Orthogonal, the University provides much of this infrastructure at significantly reduced cost. A University affiliation is to benefit from numbers (of fellow researchers) and (institutional) prestige. Orthogonal Research occupies a space in which the barriers to entry have fallen enough to do research at a very low cost (e.g. secondary analyses, modeling and simulation, collaborations, theory-building).

2. There is a need to combine academic start-ups with alternative funding methods [3], particularly for researchers who and projects that do not fit in well at more traditional academic institutions. Alternately, an academic start-up can be used as an auxiliary affiliation, to conduct work and collaborations outside the scope of one's Uni affiliation. In any case, this might serve the research workforce and local Universities well, much as research parks can have a synergistic effect with the University. While not everyone will agree that such partnerships are a good development, the small-scale nature of my initiative provides an avenue for high-risk or hybrid projects. Particularly when cross-subsidized, academic start-up might actually catalyze research innovation by not forcing research to conform to any single model.

3. What happens when a large number of independent researchers all have their own organizations, whether or not it is registered as a LLC? They can do things such as share equipment and resources, broker agreements with the local Uni, and provide collaborative support to each other. Here are two examples of how this has become more common:

a. one of my long-term collaborators (Dr. Steven Suhr) is in the process of starting up a biotech/ gene construct business called Biomilab LLC. Part of the purpose for this is to match an impressive skill set with resources that are outside the scope of traditional Uni research opportunities and funding regimes. While he is independent, he also collaborates with with University-affiliated people.

b. in the DevoWorm project, none of the collaborators (excluding myself) have a formal academic affiliation beyond graduate student. One is affiliated with a start-up called MetaCell, LLC, another is the proprietor of New Light Industries, Ltd., and a third is retired from academia but affiliated with Gulf Specimen Marine Lab (non-profit educational institute) in Florida.

[1] "Orthogonal" means "at right angles", "perpendicular", or alternately, "statistical independence". I chose this name to reflect the diverse research I have been fortunate enough to engage in over the years (a fair amount of it in the areas of mathematical and computational modeling). While my research work typically represents an interdisciplinary synthesis, there is always the feeling that the different components are "perpendicular" or "statistically independent" to one another. There is also referential meaning in the oddly- defined relationship between "Independent" and "Affiliated" research.

[2] My feelings about crowdsourcing are mixed. On the one hand, it is a good way to raise money quickly, and it is catching on amongst researchers. On the other hand, there is a tangibility (or hipster) bias, and (at least to me) resembles an inbred capital market (see below).

Diagram of an inbred capital market, or, “why do seemingly ridiculous Kickstarter projects raise large sums of money". Distinct from the phenomena of large corporate entities using the idle time of social groups for fun and profit.

[3] My forays into alternative funding methods have been largely theoretical. However, check out my stock presentation on the topic (from January 2013, so it might be time for a revision). It is called "A New Route to Science Innovation", and lays out the visionary case for the why and how with respect to the alternative funding of science research.

November 29, 2014

Neo-proprietarians + Conceptual Obfuscation = To What End?

It's been an interesting/bizarre month with respect to the open source/open access ethos [see disclaimer in 1]. The first part of the month saw two events. One was the posthumous birthday of Aaron Schwartz, and the other was a social media kerfuffle that represents part of a more general conservative backlash to net neutrality [2]. More recently, an article in Nature [3] argued that increases in the number of published papers in recent years (partially enabled by open-access publishers), has diluted the quality-control process enforced through peer-review.

What do these three events have in common? They all involve brushes with neo-proprietarianism, or the advocacy of intellectual property (IP) rights through a simple assumption: private ownership/management of IP is always somehow morally superior to open access. This might range from overzealous prosecutors and politicians to earnest, well-meaning scientists. The result is oddly-placed criticism of ideas that are potentially more beneficial to society than to private owners or firms. At times, people with no direct stake in the IP rights defend the claims of rights holders, which seems odd except in the light of neo-propietarianism (or defending the mere idea of ownership rather than its drawbacks and consequences).

In the case of both Aaron Schwartz and the aforementioned Nature article, the issue at hand is open access to scientific articles. The Nature article is well-meaning and raises some good points about how scientists might be compensated for work such as peer review. However, the tone and overall argument is reminiscent of another critique of open access publishing published last year in Science. Furthermore, there are some issues with making a link between publication quantity and the overall quality of the scientific literature. This is particularly true when the argument is made in a Nature article, lest it be interpreted as a conflict of interest [3].

Whether this is simply the act of conflating "the best of the best" with a restrictive paid-access model of publishing or an implicit argument for the infallibility of peer-review elitism is unclear. However, blog posts and data analyses by two biologists (one being Michael Eisen) and a bioinformatician [4, 5, 6] provide a very different (and more nuanced) view of the open-access journal phenomenon. This includes a rebuttal of the argument that the explosion of open-access journals is bad for the quality of the scientific literature and a burden on peer reviewers.

Sometimes quality control is a good thing. This paper was accepted by a so-called "predatory publisher" (maybe you stop bugging me for solicitations to your journal, maybe I won't embarrass you) . In discussions that revolve around publishing "quality" and "prestige", it is common to lump predatory publishers in with all other open-access publishers. Do you need an elite publishing model to prevent things like this from happening? (Answer: a rhetorical "no"). COURTESY: David Mazieres, Eddie Kohler, and Peter Vamplew.

For more reflection on the life of Aaron Schwartz, see this event hosted by the Electronic Freedom Foundation (EFF) called "Hacking for a Better World". And for some less ideonational views on net neutrality, see the two readings on the subject in [7]. Should November be known henceforth as "Open Information Month". In light of this year's events, perhaps.

[1] For purposes of this post, no finer distinctions will be made between true (e.g. the technical definition of) "open access" and Net Neutrality. Particularly as defined by the current debate, Net Neutrality is not equivalent to "open access".

However, for some recent thinking in this area, please see: Godwin, M.   How Wikipedia Zero will serve and promote network neutrality. Mike Godwin's LinkedIn blog, December 1 (2014).

[2] Pendleton, A. and Lannon, B.   One group dominates the second round of net neutrality comments. Sunlight Foundation, December 16 (2014).

[3] Arns, M.   Open accss is tiring out peer reviewers. Nature, 515, 467 (2014).

[4] Taylor, M.   Open-access megajournals reduce the peer-review burden. Sauropod Vertebra Picture of the Week blog, November 27 (2014).

[5] Eisen, M.   Contrary to what you read in Nature, Open Access has not caused the growth in science publishing. It is NOT Junk blog, November 27 (2014).

[6] Saunders, N.   Growth in free and closed scientific publications 2000-2013. Neil Saunders' Rstudio Notebook, November 28 (2014).

[7] Madrigal, A.C. and LaFrance, A.   Net Neutrality: A Guide to (and History of) a Contested Idea. The Atlantic, April 25 (2014) AND Bergstein, B.   Q&A: Lawrence Lessig. MIT Technology Review, October 27 (2014).

November 23, 2014

Ratchets, Constructions, Games, and Borg in the Reading Queue

Here are a few new (or new to me) papers that are evolution-related from my reading queue. There is a loose theme to these papers (indicated in the title of this post). I will give you my impressions and insights as the post proceeds.

Varieties of uni- and multicellular relationships amongst different species of green algae. COURTESY: Figure 1 in [1].

1. Libby, E. and Ratcliff, W.C.   Ratcheting the Evolution of Multicellularity. Science, 346, 426-427 (2014).

This short paper in a recent issue of Science deals with the transition to multicellularity and associated "ratcheting" mechanisms in what is a complexity theory take on evolutionary transitions and ratchets. According to Libby and Ratcliff's model, the transition to multicellularity involved a transfer of fitness costs from individual cells to groups of cells. This could also be seen as an overall change in the level of selection from individual cells to cell populations [2]. In this case, a so-called ratcheting mechanism is also proposed that provide a mechanism for how such transitions occur. Group living allows for certain group traits to emerge and limits reversion to the single-celled state, a so-called "de-Darwinization" of individual-level cell behaviors [3].

While individual cells transition from being autonomous to being mutually reliant, this occurs only in the context of its fitness effects. For the complexity ratchet to work, there must be opposite effects on fitness. Group living in the form of a colony formation provides a fitness benefit that is not at all present with individualistic cells. Social arrangements such as division of labor can encourage these fitness effects. The authors point to apoptosis as a trait which, while having a high fitness cost to the individual, can be beneficial to the group. Namely, relaxed group selection on apoptosis allows for the growth and nutrient constrains of a population to be circumvented. There are other traits for which individual and group selection differ -- changes in these selective pressures (much like what one would see in a shift to a new environmental niche) are what drive the evolutionary transition.

Do cultural practices (such as dietary innovations) have an influence on human evolution? COURTESY: Frank Stockton, Smithsonian Mag.

2. Laland, K.N., Odling-Smee, J., and Myles, S.   How culture shaped the human genome: bringing genetics and the human sciences together. Nature Review Genetics, 11, 137-148 (2010).

Transitions to group living also involve new sources of fitness costs, distinct from those that exist at the individual level. In this lengthy review article (from 2010), Laland, Odling-Smee, and Myles argue that culture can modify fitness costs for a given trait. The article authors are also advocates of niche construction theory and a post-synthesis evolutionary theory [4], which is clearly seen in their treatment of how culture interfaces with evolution. The mediating effects of culture on population genomics and evolutionary dynamics can be seen in gene-culture coevolution, but also suggests that there is another dimension to group selection in animal species that possess culture. These authors might also argue that cultural selection pressure is a key factor in human uniqueness, something we will come back to in the next section.

While the examples given in the article are muddied with more standard environmental selection pressures, the argument for cultural selection is that some environmental pressures are specifically related to cultural construction [5]. For example, natural selection due to dietary practices are reinforced by human modification of the environment (e.g. harvesting animal milk for general consumption). While genes and culture are viewed as interacting forms of inheritance, it is not so clear as to how they can be disentangled. In cases where cultural boundaries shape population genetics, the answer is relatively easy. However, in cases where cultural dynamics influence the frequency of host-pathogen interactions or heat shock genes, removing the signal from the noise is less clear.

Chimps playing the Prisoner's Dilemma. COURTESY: Science Magazine.

3. Martin, C.F., Bhui, R., Bossaerts, P., Matsuzawa, T., and Camerer, C.   Chimpanzee choice rates in competitive games match equilibrium game theory predictions. Scientific Reports, 4, 5182 doi:10.1038/srep05182 (2014).

3a. Lopata, J.   How Star Trek may show the emergence of human consciousness., November 18 (2014).

3b. Helbing, D., Yu, W., Opp, K-D., and Rauhut, H.   Conditions for the Emergence of Shared Norms in Populations with Incompatible Preferences. PLoS One, 9(8), e104207 doi:10.1371/ journal.pone. 0104207 (2014).

Here is an interesting collection of readings, which make sense in the context of the Martin paper. In Martin, the authors compare equilibrium expectations for Prisoner's Dilemma (PD) game [6] play with actual outcomes for both humans and chimps. It was found that when chimps play the game, the result is closer to the theoretical expectation than when humans play the game. This suggests that chimpanzee decision-making is more homogeneous than human decision-making, at least in the context of interactions that involve theory of mind. While the result is curious, there are two more recent items that might provide useful speculation about these outcomes.

In a recent article published in (3a), it is postulated that early human cognition (and perhaps cognition in the human-chimp common ancestor) resembled that of the Borg from Star Trek. It is argued that our ancestors were Borg-like in their ability exhibit little individuality across populations. In terms of the PD game, the theoretical equilibria often results from a convergence upon pure strategies. This may not so much a improvement upon an individual's ability to predict what their opponent will do next as the lack of heterogeneity in behavior over time. Thus, a species that exhibits much heterogeneity with respect to behavioral innovation (e.g. humans) would deviate from the theoretical expectation [7].

But does that mean the PD model is not really valuable in modeling human behavior? After all, the original formulation was modeled on human behavior. In addition, the model implicitly relies upon behavioral traits possibly unique to human cognition (such as theory of mind). In 3b, we can see that even though humans have a great diversity of preferences, sets of shared norms may emerge that serve to unify the behavioral outcomes of a population [8]. Despite our great individuality, some aspects of human culture can serve to reduce human heterogeneity.

We were a bit like the Borg (sans hive mind-style collective consciousness), once... COURTESY: Star Trek Online Pictures.

[1] Michod, R.E.   Evolution of individuality during the transition from unicellular to multicellular life. PNAS, 104(S1), 8613-8618 (2007).

[2] Of course, there is plenty of debate regarding the role of group and multilevel selection in the evolutionary process. For more on the virtues of these types of selection, please see: Traulsen, A. and Nowak, M.A.   Evolution of cooperation by multilevel selection. PNAS, 103(29), 10952–10955 (2006) AND Goodnight, C.J.   Multilevel selection: the evolution of cooperation in non-kin groups. Population Ecology, 47, 3-12 (2005).

[3] The term "de-Darwinization" refers to the relaxation of selection for a given trait or level of selection. Please see: Godfrey-Smith, P.   Darwinian Populations and Natural Selection. Oxford University Press, New York (2009).

[4] Laland, K., Uller, T., Feldman, M., Sterelny, K., Muller, G.B., Moczek, A., Jablonka, E., Odling-Smee, J., Wray, G.A., Hoekstra, H.E., Futuyma, D.J., Lenski, R.E., Mackay, T.F.C., Schluter, D., and Strassmann, J.E.   Does evolutionary theory need a rethink? Nature, October 8 (2014).

[5] Richerson, P.J. and Boyd, R.   Natural Selection and Culture. BioScience, 34(7), 430-434 (1984) AND Bell, A.V.   Why cultural and genetic group selection are unequal partners in the evolution of human behavior. Communicative and Integrative Biology, 3(2), 159–161 (2010).

[6] Johnson, D.D.P., Stopka, P., and Bell, J.   Individual variation evades the Prisoner's Dilemma. BMC Evolutionary Biology, 2, 15 (2002).

[7] Herbert-Read, J.E., Krause, S., Morrell, L.J., Schaerf, T.M., Krause, J., and Ward, A.J.W.   The role of individuality in collective group movement. Proceedings of the Royal Society B, 280(1752), 1-8 (2013).

[8] Such norms, such as sharing, exhibit species differences in children. For an example, please see: Hamann, K., Warneken, F., Greenberg, J.R., and Tomasello, M.   Collaboration encourages equal sharing in children but not in chimpanzees. Nature 476, 328–331 (2011).

November 16, 2014

Thought (Memetic) Soup: November edition

This content is cross-posted to Tumbld Thoughts. Here are a few short observations on the state of the world and data, circa Summer 2014. Haven't gotten around to cross-posting these yet. The meta-theme is social disruption, evolutionary change, and economic dynamics, in spite of ideonational bias. These include Disruption du jour (I), Satire Makes it Doubly Skewed (II), and Ideonational Skew - Satire = Epistemic Closure? (III).

I. Disruption du jour

Is the idea of disruptive innovation a useful concept, or is it largely a misapplied buzzword. In the original definition of "creative destruction", Joseph Schumpeter described a process of innovation that resembled an avalanche or an earthquake. For example, most innovations do not reshape their respective industries, but a few key innovations (born out of creative ferment) do.

The modern notion of disruptive innovation does not make the distinction between the effects of innovation in different industries, nor are all so-called "disruptions" equally as valuable. Schumpeter's model of disruptive innovation resembles a power law, while the modern conception of disruptive innovation argues that transformative changes are ubiquitous. Here are some readings on the myth and controversies surrounding the concept:

Lepore, J.   The Disruption Machine. New Yorker, June 23 (2014).

* a critique of the "disruption" industry.

Bennett, D.   The Innovator's New Clothes: Is Disruption a Failed Model? Bloomberg Businessweek, June 18 (2014).

* perhaps Lepore is right -- disruption for disruption's sake is not a viable model of economic change.

Bennett, D.   Clayton Christensen Responds to New Yorker Takedown of 'Disruptive Innovation'. Bloomberg Businessweek, June 20 (2014).

* a rebuttal to the Lepore article from the modern "disruption" guru.

II. Satire Makes it Doubly Skewed

Two (intentionally) skewed views on Evolution [1, 2]: God does not do art, and monkeys still exist. Or something like that. Anyways, here is a sampling of creationism satire from Summer 2014.

[1] Pliny the In-Between   Theistic evolution. Evolving Perspectives blog, July (2014).

[2] Why There are Still Monkey (fake book in the Dummies series). Timothy McVeins Twitter post, June 20 (2014).

III. Ideonational Skew - Satire = Epistemic Closure?

Statistical conspiracy theory? Here is a link to John Williams' Shadowstats site and (appropriately) three readings [1-3] that critique the overall approach. For example, in one reading, it is suggested that the "shadow" in the Shadowstats name consists of an inappropriate modeling methodology.

[1] Aziz   The Trouble with Shadowstats. Azizonomics, June 1 (2013).

[2] Krugman, P.   Always Inflation Somewhere. Conscience of a Liberal blog, July 19 (2014).

[3] Hiltzik, M.   A new right-wing claim: Obama must be lying about inflation. The Economy Hub, Los Angeles Times, July 23 (2014).

November 6, 2014

The Top 100 Needles in a Haystack

A week or so ago, Nature News published a feature on the Top 100 (e.g. most-cited) articles of all time [1]. Interesting read, even if you don't agree with their methods or conclusions. Briefly, a Science Citation Index (SCI) was used to generate a list, the top 100 articles of which were considered the most highly-cited papers. Another more inclusive list was generated for comparison using Google Scholar. The outcomes were then evaluated.

The top papers-as-mountain peak analogy. COURTESY: Nature Publishing.

So which type of papers dominated the top of the list? As you might have guessed, papers that describe the details of a now-ubiquitous method dominate the top 100. Articles on methods such as single-step RNA isolation (#5) or density-functional thermochemistry (#8) have been cited in the neighborhood of 50-60,000 times because they provide a simple description of a method that has now become widespread. As it is considered good form to cite the source article for a given method, these are the top articles in this index. It may seem a bit disingenuous to count these articles as the most influential in science. For example, the Watson and Crick paper [3] describing the structure of DNA does not make the top 100. But, this methodology allows us to see the relative diffusion of such methods in the literature. Normalizing the number of citations by their respective age gives us a citation rate, which in turn allows us to estimate the velocity [4] of a given method through the scientific community.

Number 12 on the list is the paper that introduced the BLAST genome alignment method [2]. COURTESY: Nature Publishing.

For comparative purposes, the Nature News article also provides an alternate index, one compiled by Google Scholar. This index not only includes books, but deals with citations that are more conceptual in nature. For example, the top 100 citations of all time includes: Thomas Kuhn's "Structure of Scientific Revolutions" (#7), Claude Shannon's "Mathematical Theory of Communication" (#9), Rogers' "Diffusion of Innovations" (#17), "The Rat Brain in Stereotaxic Coordinates" (#23), and Zadeh's "Fuzzy Sets" (#29). Much like the SCI method, the Google Scholar method results in a long-tailed distribution, with a few papers far exceeding the rest of the literature in terms of citations. While it is less dominated by methods papers (and books), most of the top references on the list have nevertheless had a major influence on a number of fields. 

But what does all this mean for your recent publication? Will your recent paper on the mathematical structure of inter-neuronal conversion be worthy of one of these top spots at some point in the future? One interesting exercise might be to predict the future citation rates and diffusion velocities for recent papers and books (published within the last 10 years). While not at the very top of the list, these papers would demonstrate how the middle of the distribution lives. And for all of those papers with only a few citations even after years of being published, don't despair. It could be that your paper does not fit the criterion of a "top" paper (e.g. covers a series of clever but non-landmark studies), and so has not gained a high profile. Citation patterns are a curious thing.

[1] The relevant databases have limited this to the 20th and 21st centuries. Article citation: Van Noorden, R., Maher, B., Nuzzo, R.   The Top 100 Papers. Nature News, October 29 (2014).

[2] Full citation: Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J.   Basic local search alignment tool. Journal of Molecular Biology, 215, 403-410 (1990).

[3] Watson, J.D. and Crick, F.H.C.   A Structure for Deoxyribose Nucleic Acid. Nature, 171, 737-738 (1953).

[4] Calculating method or publication "velocity" involves mapping the citation rate (per unit time) to a metric space or graph the represent the "shape" of the scientific community (disciplines, interest areas, etc). This is intentionally vague, as various community shapes are contingent on many factors.