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* full papers have an 8-page maximum length and should report on new, unpublished work.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. More recently, an article in Nature [2] 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 [2].

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 [3, 4, 5] 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 [6]. 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] Arns, M.   Open accss is tiring out peer reviewers. Nature, 515, 467 (2014).

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

[4] 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).

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

[6] 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).