Friday, February 09, 2007

Essays: Connections : Web focus : Nature

Web page with free access to previous two posts

Essays: Connections : Web focus : Nature:

"Essays: Connections

From cell biologists to quantum physicists, researchers are struggling to work out how systems involving large numbers of interacting entities work as a whole. In this collection of Essays, scientists explain how a systems approach, in parallel with the reductionism that dominated twentieth-century science, promises to yield fresh insight, and in some cases, to challenge the most widely held concepts of their field."

A twenty-first century science : Article : Nature

Essay

Nature 445, 489 (1 February 2007) | doi:10.1038/445489a; Published online 31 January 2007
ConnectionsA twenty-first century science

Duncan J. Watts

1. Duncan J. Watts is at the Department of Sociology and the Institute for Social and Economic Research and Policy, Columbia University 420 W. 118th Street, 8th Floor, New York, NY 10027, USA.

If handled appropriately, data about Internet-based communication and interactivity could revolutionize our understanding of collective human behaviour.

Few would deny that many of the major problems currently facing humanity are social and economic in nature. From the apparent wave of religious fundamentalism sweeping the Islamic world (and parts of the Western world), to collective economic security, global warming and the great epidemics of our times, powerful yet mysterious social forces come into play.

But few readers of Nature would consider social science to be the science of the twenty-first century. Although economics, sociology, political science and anthropology have produced a plethora of findings regarding human social behaviour, they have been much less successful than the physical and life sciences in producing a coherent theoretical framework that can account for their discoveries. This is not because social scientists are less clever than their peers in other fields, but because social phenomena are among the hardest scientific problems to solve.

Social phenomena involve the interactions of large (but still finite) numbers of heterogeneous entities, the behaviours of which unfold over time and manifest themselves on multiple scales. It is hard to understand, for example, why even a single organization behaves the way it does without considering (a) the individuals who work in it; (b) the other organizations with which it competes, cooperates and compares itself to; (c) the institutional and regulatory structure within which it operates; and (d) the interactions between all these components. To draw an analogy with physics, one must solve the equivalent of quantum mechanics, general relativity and the multi-body problem at the same time — even string theorists don't have it that bad! Fortunately, recent developments in network science auger some hope for the future.

For the past 50 years or so, sociologists have thought deeply about the importance of interactions between people, institutions and markets in determining collective social behaviour. They have even built a language — network analysis — to describe these interactions in quantitative terms. But the objects of analysis, such as friendship ties, are hard to observe, especially for large numbers of people over extended periods of time. As a result, network data have historically comprised one-time snapshots, often for quite small groups. And most studies have relied on self-reports from participants, which suffer from cognitive biases, errors of perception and framing ambiguities.

The striking proliferation over the past decade of Internet-based communication and interactivity, however, is beginning to lift these constraints. For the first time, we can begin to observe the real-time interactions of millions of people at a resolution that is sensitive to effects at the level of the individual. Meanwhile, ever-faster computers permit us to simulate large networks of social interactions. The result has been tremendous interest in social networks: thousands of papers and a growing number of books have been published in less than a decade, leading some to herald the arrival of a 'science of networks'.
A twenty-first century science

J. KAPUSTA/IMAGES.COM

This label, unsurprisingly, has attracted its share of critics, and with some justification. Some of the ideas are not as new as sometimes advertised; many of the popular models are too simplistic to stand up to scrutiny; and even the more sober-looking empirical studies tend to use data that happen to be available, rather than obtained with a specific research question in mind. As a result, despite the avalanche of publications and breathless headlines, it is probably true that little has been learned about real social processes.

Nevertheless, the near future looks promising, especially if a few fundamental features of social networks can be emphasized. First, social networks are not static structures, but evolve in time as a consequence of the social and organizational environments in which they are embedded. Second, they are not unitary, but multiplex, meaning that people maintain a portfolio of types of ties — formal, informal, strong, weak, sexual, business and friendship — each of which serves different functions. And finally, network structure must be understood within the larger framework of collective social dynamics. People do not just interact: their interactions have consequences for the choices they, and others, make.

Studies that combine all these features are currently beyond the state of the art, but two of my group's recent projects indicate tentative progress. The first used the anonymized e-mail logs of a university community of around 40,000 people to track daily network evolution over a year as a function of existing network structure, shared activities (such as classes) and individual attributes. Dynamic data of this type may shed light on the relative roles of structural constraints and individual preferences in determining, for example, observed homogeneity of friendship circles.

The second was a Web-based experiment in which 14,000 participants were asked to listen to, rate and download songs by unknown bands. Some participants made their decisions independently, and others could see how many times the songs had been downloaded previously. Experiments of this kind measure not only the influence that individuals have over each others' decisions, but also the consequences of these individual-level effects on macro properties, such as the predictability of 'hit' products.

Clearly, the leap from these still simplistic studies to the 'big questions' of social science remains formidable. In this regard, cooperation between academic researchers and the large Internet companies who currently dominate data collection may be extremely productive. Although such collaborations will encounter challenges, including privacy and intellectual-property issues, the questions are too difficult to be left to intuition, or even experience, alone. We must start asking how the technological revolution of the Internet can lead to a revolution in social science as well.

FURTHER READING

Heyman, K. Science 313, 604–606 (2006).

Duke, C. B. Network Science (The National Academies Press, 2006).

Kossinets, G. & Watts, D. J. Science 311, 88–90 (2006).

Salganik, M. J., Dodds, P. S. & Watts, D. J. Science 311, 854–856 (2006).

Biology's next revolution : Article : Nature

An essay that challenges perceptions of evolution as vertical descent, and biological terms such as organism and species.

Nature 445, 369 (25 January 2007) | doi:10.1038/445369a; Published online 24 January 2007
Connections: Biology's next revolution

Nigel Goldenfeld 1 and Carl Woese 2

1. Nigel Goldenfeld is in the Department of Physics and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, USA.
2. Carl Woese is in the Department of Microbiology and Institute for Genomic Biology, 601 South Goodwin Avenue, Urbana, Illinois 61801, USA.

snippets:

The emerging picture of microbes as gene-swapping collectives demands a revision of such concepts as organism, species and evolution itself.

Recent work suggests that viruses are an important repository and memory of a community's genetic information, contributing to the system's evolutionary dynamics and stability.

A computer scientist might term the cell's translational apparatus (used to convert genetic information to proteins) an 'operating system', by which all innovation is communicated and realized. The fundamental role of translation, represented in particular by the genetic code, is shown by the clearly documented optimization of the code.

Refinement through the horizontal sharing of genetic innovations would have triggered an explosion of genetic novelty, until the level of complexity required a transition to the current era of vertical evolution.

Saturday, January 13, 2007

Human Computation

Human Computation - Google Tech Talk

Luis von Ahn - the creator of captcha (www.captcha.net) talks about using humans to solve problems that are hard for computers, by playing games. Small actions by individual players that are correct/valid because of the game structure add up to a huge well-annotated set.

www.espgame.org
www.peekaboom.org

Saturday, October 28, 2006

Emergence: The Connected Lives of Ants, Brains, Cities, and Software

Emergence: The Connected Lives of Ants, Brains, Cities, and Software, by Steven Johnson, started off a bit too glibly. His messianic enthusiasm for the results in the field felt a bit strange after the tempered practicality of real complex systems researchers such as Barabasi, Duncan Watts, and Kauffman. This might have been an entertaining first book to read about complex self organizing systems. The core ideas were not new to me (how pheromones work) but his descriptions of how the web is NOT showing emergence just go to show how quickly the internet has changed. He was betting his money on feedback systems like Alexa, even Alexa required users to buy into ONE invasive tool (for tracking browsing). Blogs and pingbacks are the new pheromones on the web and were completely unanticipated - which just goes to show how it is VERY difficult to predict anything. The principle that feedback is essential for a complex system still holds though.

Four essential features according to Johnson:
Neighbor interaction
Pattern recognition
Feedback
Indirect control

Other authors to follow up based on this book - historical complexity/cybernetics readings - Turing (morphogenesis), Shannon, Weiner, Selfridge, Weaver, Jacobs, Holland, Prigogine.

Friday, September 29, 2006

An Introduction to Genetic Algorithms - The MIT Press

An Introduction to Genetic Algorithms - The MIT Press is an oldie, but goodie. The official text for the University of Edinburgh Informatics course on Genetic Algorithms and Genetic Programming (being taught by Gillian Hayes in Autumn, 2006), it's already got me thinking about how the pairing of candidate chromosomes for the next generation might be achieved as it is in biological systems - i.e. not randomly, but on the basis of some gross characteristics.

Update (2006-10-17): Chapter 4 discusses what problems GAs are good at (and how they find the solution space, using the building blocks hypothesis). This got me thinking of whether Evolution is a good GA problem to solve or not. It might be at a later stage, when the fitness landscape is smooth and crossovers between two good solutions are likely to lead to a better solution. But early on in the evolutionary landscape, it is possible that GAs were NOT the best way of finding a solution (given that there was less complexity/organization in the organisms, hence crossover solutions were less likely to make sense).

Friday, September 22, 2006

Living online: I'll have to ask my friends - opinion - 20 September 2006 - New Scientist Tech

Living online: I'll have to ask my friends - opinion - 20 September 2006 - New Scientist Tech

Given how much Sherry Turkle knows about technology mediated communication, I don't think this is the standard rant of someone who is over 25.

Living online: I'll have to ask my friends

* 20 September 2006
* Exclusive from New Scientist Print Edition.

Is social networking changing the way people relate to each other?

For some people, things move from "I have a feeling, I want to call a friend" to "I want to feel something, I need to make a call". In either case, what is not being cultivated is the ability to be alone and to manage and contain one's emotions. When technology brings us to the point where we're used to sharing our thoughts and feelings instantaneously, it can lead to a new dependence, sometimes to the extent that we need others in order to feel our feelings in the first place.

Our new intimacies with our machines create a world where it makes sense to speak of a new state of the self. When someone says "I am on my cell", "online", "on instant messaging" or "on the web", these phrases suggest a new placement of the subject, a subject wired into social existence through technology, a tethered self. I think of tethering as the way we connect to always-on communication devices and to the people and things we reach through them.

How is it affecting families?

Let me take a simple example. Tethered adolescents are given a cellphone by their parents. In return, they are expected to answer their parents' calls. On the one hand, this arrangement gives the adolescent new freedoms. On the other, the adolescent does not have the experience of being alone, of having only him or herself to count on: there is always a parent on speed dial. This provides comfort in a dangerous world, yet there is a price to pay in the development of autonomy. There used to be a moment in the life of an urban child, usually between the ages of 12 and 14, when there was a first time to navigate the city alone. It was a rite of passage that communicated, "You are on your own and responsible." Tethering via a cellphone buffers this moment; tethered children think differently about themselves. They are not quite alone.
Does it worry you?

Our society tends toward a breathless techno-enthusiasm: "We are more connected; we are global; we are more informed." But just as not all information put on the web is true, not all aspects of the new sociality should be celebrated. We communicate with quick instant messages, "check-in" cell calls and emoticon graphics. All of these are meant to quickly communicate a state. They are not meant to open a dialogue about complexity of feeling. Although the culture that grows up around the cellphone is a "talk culture", it is not necessarily a culture that contributes to self-reflection. Self-reflection depends on having an emotion, experiencing it, taking one's time to think it through and understand it, but only sometimes electing to share it.
Is this a bad thing?

The self that grows up with multitasking and rapid response measures success by calls made, emails answered, messages responded to. In this buzz of activity, there may be losses that we are not ready to sustain. We insist that our world is increasingly complex, yet we have created a communications culture that has decreased the time available for us to sit and think, uninterrupted. Teens growing up with always-on communication are primed to receive a quick message to which they are expected to give a rapid response. They may never know another way. Their experience raises a question for us all: are we leaving enough time to take one's time?

Are you talking about a permanent change?

It seems to be part of a larger trend in media culture for people not to know what they think until they get a sense of what everyone else thinks. But we learn about what everyone else thinks by reading highly polarised opinions that encourage choosing sides rather than thinking things through. You can give media culture a positive spin and say that people are more socially enmeshed, but it has a darker side: as a feeling emerges, people share the feeling to see if they have the feeling. And sometimes they don't have the feeling until they check if other people have it too. This kind of behaviour used to be associated with early adolescents, with their need for validation. Now always-on technology is turning it into a norm.
"A question for us all: are we leaving enough time to take one's time?"

Surely being socially enmeshed can also have a positive side?

The challenge for this generation is to think of sociality as more than the cyber-intimacy of sharing gossip and photographs and profiles. This is a paradoxical time. We have more information but take less time to think it through in its complexity. We're connecting globally but talking parochially.

Are you saying that people are missing the broader picture?

People are connecting one-on-one - they have their online social network or their cellphone with 250 people on speed dial - but do they feel part of a community? Do they feel responsibility to a set of shared political commitments? Do they feel a need to take responsibility for issues that would require that they act in concert rather than just connect? Recently, connectivity and statements of identity on places such as Facebook or MySpace have themselves become values. It is a concern when self-expression becomes more important than social action.

What kind of responsibility are they ducking?

Summer 2006 finds the world enmeshed in multiple wars and genocidal campaigns. It finds the world incapable of calling a halt to environmental destruction. Yet, with all of this, people seem above all to be fascinated by novel technologies. On college campuses there is less interest in asking questions about the state of the world than in refining one's presence on Facebook or MySpace. Technology pundits may talk in glowing terms about new forms of social life, but the jury is out on whether virtual self-expression will translate into collective action.

Explore the other features in New Scientist's guide to the social networking revolution:

This is your space – Discover how social networking evolved, how it works and how it is already revolutionising the way we live, socialise and work

The end of privacy? – You wouldn't tell a stranger on the bus about your sexual habits, so why do people reveal this stuff on websites available to everyone? Will their openness return to haunt them?

I saw the best minds of my generation destroyed by Google – A short story by Bruce Sterling

The internet could be so much better – Social networking websites like MySpace or YouTube owe everything to the genius of Ted Nelson, who invented hypertext in the 1960s

Give it a try – Feeling left out of the social networking revolution? There are many ways you can get involved, so take a look

From issue 2569 of New Scientist magazine, 20 September 2006, page 48-49
Profile

Sherry Turkle is Abby Rockefeller Mauzé Professor of the Social Studies of Science and Technology at the Massachusetts Institute of Technology. Her books include The Second Self: Computers and the human spirit (MIT Press, 2005) and Life on the Screen: Identity in the age of the internet (Touchstone, 1997). Her next, Evocative Objects: Things we think with, will be published in April 2007. She is also completing a book on robots and the human spirit.

EvoMUSART

Evonet Wiki : EvoMUSART looks like it would be a fun place to submit a paper to. Let's see if I can tweak one of my assignments this semester to become a submission.

Richard Dawkins on TED Talks

Richard Dawkins on TED Talks

By posting a link to a video, I'm stretching the meaning of "Readings" for this blog.

An entertaining 22 minute video on why the universe is queerer than we *can* suppose. As an evolutionary biologist, Dawkins thinks that we have been naturally selected to function well in the middle world, where things are approximately a few magnitudes larger or smaller than we are. Our experience and expertise is limited to a narrow band of objects and sense data, because those have been the most useful to human survival.

All this makes me think of that age-old quandary - that 'we' are approximately metre long units with these ideas, but are there smaller components within us (or larger conglomerations of units like us) that have a corresponding consciousness at a different level?

Sunday, September 17, 2006

Special Issue on the Evolution of Complexity

Special Issue on the Evolution of Complexity

Guest Editors:

Carlos Gershenson
Centrum Leo Apostel, Vrije Universiteit Brussel
Krijgskundestraat 33. B-1160, Brussels, Belgium
cgershen at vub.ac.be

Tom Lenaerts
SWITCH, Flanders Interuniversity Institute for Biotechnology
Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
tlenaert at vub.ac.be

Motivation

As a result of the quality of the Evolution of Complexity workshop at ALife X last June in Bloomington and the interest of the attendants; we announce a call for papers for a special issue on this theme for the Artificial Life journal.

The evolution of complexity is a central theme in Biology. Yet it is not without ambiguity. Complexity has been used to refer to different things. For instance, complexification has been interpreted as a process of diversification between evolving units or as a scaling process that is related to the idea of transitions between different levels of complexity. Other meanings of complexity have been introduced, both inside and outside of Biology. In most cases, though, the central concern is to understand what produces complexity.

The focus of this special issue will be on biological interpretations of complexity and on evolutionary and related dynamics as driving mechanisms for producing complexity. Questions to be addressed in the special issue include:

* How could complexity growth be measured or operationalised in natural and artificial living systems?
* How can existing data from nature be brought to bear on the study of this issue?
* What are the main hypotheses about complexity growth that can actually be tested today?
* Are the principles of natural selection as they are currently understood sufficient to explain the evolution of complexity in living systems?
* What are the environmental and other constraints of the evolution of complexity in living systems?
* What is the role of developmental mechanisms in the evolution of complexity in living systems?
* What are conditions could reduce evolved complexity in living systems?
* How factors allow the evolution of complexity in living systems to be manipulated and controlled?
* What models are most appropriate for understanding the evolution of complexity in living systems?


Paper Submission:

Submitted articles and letters should follow the submission guidelines of the Artificial Life Journal, available at http://mitpress.mit.edu/ALIFE. Authors should also include a cover letter describing briefly the relevance of their article to the specific topic of this call.

These articles and letters should NOT be submitted to the journal editor, but should be uploaded through the special issue website (single PDF files only, include cover letter as the first page of the paper).

Papers will be judged by members of the Program Committee on their relevance to the call for papers, originality, clarity of the presentation, and overall quality.

Important Dates:

Submission deadline: December 15th, 2006
Notification of acceptance: February 1st, 2007
Camera-ready papers due: March 1st, 2007

Programme Committee:

Chris Adami
Lee Altenberg
Mark Bedau
Hugues Bersini
John Bonner
Dominique Chu
Jim Crutchfield
Bruce Edmonds
Carlos Gershenson
Mario Giacobini
Franics Heylighen
Tom Lenaerts
Juan Julián Merelo
Barry McMullin
Chrystopher Nehaniv
Charles Ofria
Jorge Pacheco
Tom Ray
Jon Rowe
Stanley Salthe
Cosma Shalizi
Richard Watson
Larry Yeager

Replication Properties of Parity Cellular Automata

Replication Properties of Parity Cellular Automata.
doi:10.1142/S0218127402004632
International Journal of Bifurcation and Chaos [in Applied Sciences and Engineering], Vol. 12, No. 3 (2002) 477-494
PEDRO JULIÁN
LEON O. CHUA
Abstract: In this paper we analyze the replication properties of additive or parity Cellular Automata (CA). The objective of the paper is twofold. Firstly, to review and extend the existing results in the cases of one- and two-dimensional CA. Secondly, to report a general result that states the replication properties of an n-dimensional CA, whose evolution law depends on an arbitrary m number of neighbor cells.

Sujai's note: Should have cited this in Fractal Replication in Time Manipulated 1D Cellular Automata.

The View from Elsewhere: Perspectives on ALife Modelling

The View from Elsewhere: Perspectives on ALife Modelling (2002)
Michael Wheeler, Seth Bullock, Ezequiel Di Paolo, Jason Noble, Mark Bedau, Philip Husbands, Simon Kirby, Anil Seth, Artificial Life 8, to appear.
http://citeseer.ist.psu.edu/wheeler02view.html

Came across this when searching for Edinburgh and ALife. The eight panelists at the 6th European Conference on Artificial Life in Prague in 2001 express the following views:

Mark Bedau: ALife is a philosophical endeavour. Armchair simulations and armchair philosphy. May not find any underlying principles, hallmarks of complex life, though that's the goal. Philosophers should use simulation as a method.

Michael Wheeler: ALife is NOT a philosophical method. ALife models are NOT thought experiments. They are real enough experiments and real enough models, much as mathematical models in biology.

Seth Bullock: ALife simulations could be the bridge between theoretical and empirical/field biologists who find it hard to digest the mathematics. Models become a tool for communication. Suggests hastening the process of developing and deciding on formal, orthodox, well understood ways of communicating model specifications and results.

Anil Seth: Individual Based Models (IBMs) were seen as mediators between theoretical and empirical biology but 10 years hence, that's not always been the case. Because "IBMs are hard to develop, hard to communicate, and hard to understand. The abundance of free parameters runs the risk of WYWIWYG (what-you-want-is-what-you-get)". However, he thinks the same flexibility of ALife models encourages re-evaluating theoretical dogmas.

Jason Noble: ALife models have demonstrated how selective pressures could result in simple signalling systems in animals, but not shown much about how human language could have evolved out of such a system. Linguistics treats the former as given and is more interested in the latter. ALifers should concentrate on specific language evolution models.

Simon Kirby: ALife techniques important to lingustics because they could help checking claims of explanatory linguistics. Three adaptive systems - Learning a language involves the adaptation (within a lifetime) of internal representations of utterances; Languages adapt to the biases inherent in the learning mechanism over a historical time scale; The innate specification of learning biases adapts on a biological time-scale to make the languages that emerge from the cultural processes learnable by children.

Philip Husbands: Uses the analogy of the Ratio Club (Alan Turing, Ross Ashby, Grey Walter, Jack Good, Thomas Gold, Albert Uttley, Donald Mackay, Horace Barlow, DA Scholl, P Merton, Eliot Slater) to show how cross disciplinary collaborations between ALife and Biology are a must.

Ezequiel Di Paolo: Cybernetics' main tenet was that the mind is a manifestation of physics and should be studied using the methods of physics. Gestalt psychologists and neurophysiologists protested because its reductive atomism was not justified empirically. Which banner should ALife follow - a flag of convenience, a fruitful exploration of ideas, or as cybernetics, a discipline meant to do the job of other disciplines, only with a different, more abstract approach.

A summary of the reactions of the panelists noted that most saw ALife as an inter disciplinary collaboration, a space for people to try out new ideas/ techniques, that could then be incorporated into the parent discipline (biology, economics, etc). But some argued it's independent status, and argued for the strong ALife position - where the goal is to create novel forms of life.