Circular Arguments and a Complex World

Mika Aaltonen

Mika Aaltonen of the BIT Research Centre at the Helsinki University of Technology in Finland argues that at the very fundamental level, human beings are storytelling animals, this premise may seem obvious but arises not because we like fairytales and fables but because of the way we perceive cause and effect. By learning from this revelation it might be possible to understand life stories, consciousness, biological systems, climate economic and business models, and countless physical processes that do not follow the simplistic beginning-middle-end narrative model of cause and effect.

Writing today in the International Journal of Management Concepts and Philosophy (2007, 2, 183-193), Aaltonen explains that our current view of causality is seriously limited because of our intrinsic need to frame a sequence of events as a kind of narrative even when such a storytelling approach does not fit with observations. The concept of time is usually used to connect information explain feedback loops and to provide a logical chronology for causes and their effects. However, things are not so simple in the real world.

Firstly, the way we perceive time is different from culture to culture and across human history and comes with its own baggage. For instance, some cultures have no concept of time at all, others see time as a river along which we flow looking to the future while others imagine our walking backwards away from past events. Modern physics too has destroyed any simplistic interpretation of time in relativity, gravitational theory, and quantum mechanics, in which time becomes not a steady stream from alpha to omega but a framework in which are embedded probability waves, matter, and energy.

Secondly, stretching back as far as Aristotle, and perhaps beyond, there were notions of cause not simply being a one thing must follow another scenario. This is not to suggest that there is anything mystical going on, but just that when we lay down strategies and plans these are often engineered again and again from a top-down position, like the re-working of a fairytale or fable. New characters and happenings may be incorporated but the gist of the process is simply to begin with a “Once upon a time…” and to end with an “…and they all lived happily ever after.” This is not the way things really are.

Aaltonen suggests that the discovery of complexity theory in science and the concept of chaotic and nonlinear behaviour show that cause and effect are much more complicated. However, if we can re-engineer the old philosophical tools we might better understand modern problems and find solutions to them. He suggests that there are three drivers, or forces, of causality – final cause, sensitivity to initial conditions, and circular cause.

“More than imagining and presenting the future as an extrapolation of the present, we should be looking for approaches that allow us to see and influence the future by responding to and influencing what is emerging,” Aaltonen told Sciencebase. This is the first force of causality, the sensitivity to initial conditions. The challenge and the inspiration for sense-making and strategic decision-making, he adds, lie in identifying and influencing the initial conditions of a system as they are emerging. We must prepare ourselves for coming change by identifying the initial conditions so we can shape the future to our advantage. We need foresight in other words!

In addition, circular causality can be used to model causal patterns. Activities on the very small scale do give rise to behaviour we can observe on the large scale. “The general term used for this phenomenon is ’emergence’,” explains Aaltonen, “Consciousness is an emergent property of the brain (and the rest of the body), inflation is an emergent property of an economic system, and meaning is an emergent property of language. Emergent properties are not, however, merely effects, there is multi-way communication.” He points out that phenomena on the large scale (macro level) can affect activity on the small scale (micro-level). “Causality,” he adds, “does not simply work from micro-causes to macro-effects. There is also a top-down process at work which means that causality in complex systems is circular.”

He suggests that if something outside an organism is seen as a final cause, a goal or objective, then voluntary behaviour embeds the organism in the environment. “People’s goal-seeking activities become sensitive to final conditions,” he explains. Small variations in the way a larger environment responds can and should dramatically influence how we ourselves respond to those changes. “This way, final cause becomes a target formed from continuous reflection,” he adds.

Understanding the interplay between these three causal forces is key to planning. It is ironic, he says, that we seem to place a natural emphasis on stories as efficient tools for understanding the world, given that strong stories of the past and the future themselves focus our attention and goals and so are reductive in nature, essentially bringing nothing new to the table.

“There is a need to integrate multiple views into strong and dominant stories and into sensemaking in order to add sensitivity to our understanding of the changes occurring in our world,” he argues. Moreover, strong stories actually drive us towards unobtainable goals in almost every walk of life whereas the essential properties of final cause, sensitivity to initial conditions and circular cause and their interplay demonstrate that causal relationships are shifting shapes in a nonlinear world. “If we are to understand the environments we live in, we require approaches that are reflexive, self-critical and nonlinear,” Aaltonen adds. That sentiment applies equally to stifling poverty and responding to climate change, managing a business or carrying out a scientific experiment.

Alchemical Happenings

ChemWeb Logo

As regular Sciencebase readers will know, I write a regular chemistry news round-up for ChemWeb under the plome-de-nume of The Alchemist. This is the latest incarnation of a column I first wrote for the original ChemWeb.com almost a decade ago. ChemWeb is now owned by chemical industry search engine chemindustry.com, which is fast developing the site into an indispensable resource for anyone working in the chemical sciences.

Anyway, here is a summary of the latest Alchemist chemistry news headlines.

This week, iron and chemical education skills are rewarded, while analytical and synthetic efforts finally pay off after almost four decades or work on a natural insecticide with the first total synthesis of the neem tree extract azadirachtin. The Alchemist also discovers that diamonds really are almost forever and nanoscopic polymer capsules can facilitate one-pot cascading biotransformations. Finally, a new range of fluorinated contrast agents for medical imaging could make cancer diagnostics stick and computational developments on actinide compounds could revolutionize our understanding of the chemistry of radioactive materials. That synthetic odyssey undertaken by Steve Ley and colleagues at Cambridge University to synthesise azadirachtin will feature in more detail here in a forthcoming post.

Two Slits Are Better Than One

Sciencebase Exclusive – Careful experimentation and theoretical analysis of a double-slit experiment have finally quashed a controversy in fundamental physics — the complementarity-uncertainty debate.

Ever since the catflap to the quantum world was opened up to us and Schrödinger’s feline friend was idiomatically let out of the bag, to mix a metaphor or two, there have been more questions and controversies raised than conundrums solved in the world of the very, very small. How can something be both particle and wave, for instance? What allows particles of matter to tunnel through solid objects? And, how is the interference pattern destroyed in a double-slit experiment when measurements are performed on the path traversed by a particle?

What is a double slit experiment, you ask? Well, traditionally, Young’s double-slit experiment consists of shining a light through two narrow, closely spaced slits and observing the results on a screen placed beyond the slits.

Intuitively, you might think that the result would simply be two bright lines, aligned with the slits, representing where the light passes through the slits and hits the card. However, this is not seen in practice, instead, the light is diffracted by the slits and produces fringes corresponding to wave-like interference pattern. The fringes of light and dark regions correspond to where either the light waves constructively (add) and destructively (subtract) from each other. Two peaks in the light wave meet to make a brighter fringe whereas a dark fringe is formed when a peak and a trough coincide. This result seemingly settles a three-century conundrum about whether light is particle or wave, showing apparently that it is a wave.

However, a similar experiment carried out with beams of electrons or atoms fired through the slits produces a very similar interference pattern. How could that be? Particles are solid objects, surely? Well, the double-slit experiment shows that they are not. They produce an interference pattern, which suggests that the particles behave as waves.

The double-slit experiments work perfectly well and reveals interference patterns with light, electrons, and beams of other particles, but only if the experimenter does not try to find out through which slit a particular wave-particle passed before hitting the screen. Try to fire particles through the slits one at a time and as illustratd in the 5-minute video below, you will still see an interference pattern. It is as if each particle passes through both slits simultaneously, each slit individually and together and neither slit all at the same time; behaving some as waves…

As if this were not complicated enough, physicists reasoned that if they could discover which slit the individual particle really goes through each time in this experiment, they could solve the problem. So, they put a measuring device next to one slot and observed what happens as particles are fired through the slits one at a time. Astoundingly, the interference pattern disappears, simply having a measuring device present to observe the route taken by the particles somehow disturbs their wave-like nature and they revert to being tiny, solid objects and produce just two bands on the screen as if they were tiny marbles rather than wave. How could the particles know they were being watched.

This loss of interference has been explained by several of the biggest names in twentieth century physics, among them Niels Bohr and Richard Feynman. They suggested that whenever the path is measured within the double-slit, the momentum of the wave-particle is uncontrollably and irreversibly disturbed. Think about it, it has to be affected by the observer somehow because the very act of observing involves some kind of sharing of information either via photons, charge, energy or matter. This process “washes out” the interference fringes.

Most physicists simply accept this as being precisely what happens. It is a little vague and some might say “handwaving” because it does not pin down the nature of this washing out nor say anything about how the momentum is disturbed by the transaction between observer and observed. More precisely, it is simply what happens because of the back-reaction resulting from the Heisenberg uncertainty relation that says we cannot know simultaneously both the energy and position of any quantum wave or particle with absolute precision. While that kind of folds the argument into a loop, Feynman famously pointed out that, ‘No one has ever thought of a way around the uncertainty principle.’

But, not everyone was happy with this. In 1991, Marlan Scully, Berthold-Georg Englert, and Herbert Walther (Nature 1991, 351, 111) suggested that a microscopic pointer could be used to carry out the observation in such a way that the very act of observation would not disturb the momentum of the particle and so bypass the uncontrollable and irreversible effects suggested by Bohr that leads to interference breakdown. However, Pippa Storey, Sze Tan, Matthew Collett, and Daniel Walls (Nature, 1994, 367, 626), countered this argument, demonstrating that no matter how small the observer nor how the measurements are made, momentum is affected and the interference pattern would disappear. A long and controversial debate has raged between the two scientific factions that back either the Scully or Walls teams.

A theoretical solution was posited by Howard Wiseman and colleagues in 2003 (Phys Rev A, 2003, 311, 285) and refined in 2004 (J. Opt. B: Quant. Semiclass. Opt. 2004, 6, S506-S517). Now, in a seminal paper published today in the New Journal of Physics, Aephraim Steinberg together with Wiseman and colleagues Mir, Lundeen, Mitchell, and Garretson have applied the theory in a novel double-slit setup. Their experimental results suggest that, as is the way with all things quantum, both camps are equally correct and equally wrong. Somehow, you can have your quantum cake and eat it.

They found that by using only weak measurements, they can directly observe the momentum transfer that causes interference breakdown but equally do so without disturbing the two-slit superposition. They effectively verify both the Scully and Walls views. In terms of the Scully position, the team shows that there is no change in the mean momentum, or the mean energy, whereas with respect to the Walls work, they show that the momentum is spread, as one would expect given the uncertainty inherent in the quantum world, according to Heisenberg’s principle.

Feynman always held that the double-slit setup was central to quantum theory, but would never be fully understood. This work by Wiseman and colleagues shows that the humble double-slit experiment can still throw up new quantum mysteries to baffle us.

Could World of Warcraft Fight Disease?

Corrupted blood

In September 2005, about 4 million World of Warcraft gamers saw a new and unexpected challenge in the game. Players exploring a new area within the game encountered an extremely virulent, highly contagious disease, known as Corrupted Blood, which had been introduced in an update on the 13th of that month. The disease quickly spread, like the Black Death, to the population centres of the fantasy world, killing many and causing social chaos. But, who, other than the gamers themselves should care about virtual deaths and digital disease?

Well, according to Eric Lofgren of Tufts University School of Medicine, in Boston and Nina Fefferman of Rutgers University, in Piscataway, we all should care because the virtual epidemic could provide a very useful model of how diseases spread, how individuals and groups respond to the presence of a killer disease, and what we might do to control an outbreak, of bird flu or a SARS-type disease, in the real world. Writing in the journal Lancet Infectious Diseases, the team explains how simulation models are very useful in studying the spread of disease, epidemiology. However, validating the models or tailoring them to particular human behaviour patterns is next to impossible. The World of Warcraft incident, known as the Corrupted Blood outbreak, on the other hand, “provided an excellent example of the potential of such systems.” They explain that while data from the Corrupted Blood outbreak were not gathered scientifically at the time and so represent a missed opportunity, there is the potential for deliberately engineering such gameplay into other virtual worlds. “Virtual outbreaks designed and implemented with public-health studies in mind have the potential to bridge the gap between traditional epidemiological studies on populations and large-scale computer simulations,” the researchers say, “these would involve both unprogrammed human behaviour and large numbers of test participants in a controlled environment where the disease parameters are known.”

The use of distributed networks to help solve scientific and medical problems is not new. many Internet users will have heard of the likes of [email protected] This system is essentially a program you install on your computer which uses idle time to search for signs of extra terrestrial life in downloaded astronomical data.

[email protected] is just one of a group of applications based on BOINC, the Berkeley Open Infrastructure for Network Computing. You can use your Windows, Mac, or Linux machine to help find cures for disease, study climate change, discover pulsars and solve various other problems in earth sciences, astronomy, physics, biology, medicine, mathematics and strategy games. You can find a full list of projects here.

A recent paper in the International Journal of Web and Grid Services (2007, 3, pp 354-368) reviewed the state of the art in such distributed applications the world over. According to Bertil Schmidt of the University of New South Wales, Australia, desktop grid computing, as these kinds of distributed applications are known technically, is a relatively new technology but can nevertheless provide massive computing power for a variety of applications. He points out that the cost is low for the researchers, given that once set loose in the wild, the running costs of the program are themselves distributed to the downloaders’ computer and the costs to the researchers are then only in terms of retrieving results from those machines as and when necessary and analysing the incoming data.

Schmidt explains how BOINC provides “a proven open-source infrastructure to set up such projects in a relatively short time” and surveys the scientific projects, e-science, that have adopted this strategy. “The power and mass appeal of desktop grid computing for implementing task-parallel problems have been demonstrated in projects such as [email protected],” Schmidt explains, pointing out that as of April 2007, the average performance of [email protected] was around 250 teraflops. A teraflops (sometimes teraFLOPS), is a million million floating point operations (or instructions) per second. The combined average performance of all BOINC-based projects was around 0.5 petaflops spread over more than 400 000 active CPUs, which is more powerful in total than IBM’s BlueGene/L, which peaks at 0.280 petaFLOPS. By comparison, the next generation supercomputer, Blue Gene/P, will run at 3000 teraflops, or 3 petaFLOPS, so this distributed power represents a vast resource for e-science and is as yet only very partially tapped.

Personally, I have the World Community Grid running on my computer. This application allows you to help out in the fight against Dengue fever, AIDS, and phase 2 of the human proteome folding project. At the time of writing, teh project has 318,888 members and is running on 715,025 devices amounting to a total of 107,837 years of computing time so far. You can view the latest stats here.

If you have a fast computer and are not running CPU or memory intensive applications, then you could do even more with any of those e-science projects, allowing the BOINC application to run even when your machine is not idle. You will not only accrue more “credits and kudos” on your chosen project but you could just solve one of the problems facing humanity.

Diamonds Almost Forever

Diamonds almost as old as the Earth itself have been found locked in ancient crystals of zircon from the Jack Hills region of Western Australia, according to scientists writing in Nature this week. The diamonds could provide unique insights into the early evolution of our planet’s crust.

Zircons are tough and resist heat and some samples have been shown to be several billion years old. As such, they retain vital clues about the Earth’s geological evolution, at least as far as the crust and mantle are concerned. Recent studies of these ancient crystals have suggested that the Earth may have cooled much faster than previously thought, with the continental crust and oceans forming some 4.4 billion years ago.

Now, Martina Menneken and colleagues at the Westfaeische Wilhelms-Universitaet Muenster, in Germany, have investigated mineral inclusions within zircons and found that some of them contained small diamonds. The zircons have been dated using uranium and lead isotopes and found to be over four billion years old,” almost one billion years older than the previous oldest-known terrestrial diamonds, and present in material that crystallized within 300 million years of the formation of the Earth itself.

The authors suggest that these diamond inclusions formed under ultrahigh-pressure conditions, which implies that the Earth had a relatively thick continental crust and crust-mantle interaction at least 4.25 billion years ago. Diamonds are formed in the earths interior, where they are brought to the surface by volcanoes and it is known as one of the hardest materials on earth.

Azadirachtin Done

Azadirachtin structure

Steve Ley and his team (some 40 PhD students over the last two decades) have finally cracked the total synthesis of the natural insecticide azadirachtin. This hugely complex natural product extracted from the Indian neem tree put up quite a struggle from the year it was isolated (1968) till its structure was unequivocally elucidated (seventeen years later) till the publication of Ley’s paper in Angewandte Chemie outlining the 64-step strategy for making it from standard starting materials. Check out the Angewandte press site for a more detailed write-up and the paper itself for full details of the completion of these chemical odyssey.

Why Do We Yawn?

Yawning

No one knows why we yawn. There are lots of theories, some talk about it signalling tiredness or getting oxygen to the brain, others mention clearing out stale air from the lungs and reducing blood carbon dioxide levels. Most are baloney. But, one thing that is certain, yawns can be infectious. Catch sight of someone yawning, and nine times out of ten, you will yawn yourself within a few seconds. But, that still doesn’t really answer the question, why do we yawn? Is such an infectious yawn a message to others in the group that it’s time for bed? Probably not, otherwise why yawn first thing on getting out of bed? Either way researchers have found that people with autism spectrum disorder don’t tend to succumb to an infectious yawn.

Atsushi Senju of the Centre for Brain and Cognitive Development at Birkbeck, University of London has shown for the first time that children with some degree of autism are not susceptible to contagious yawning. Autism Spectrum Disorder is a developmental disability that severely affects social interaction and communication including empathy. Report published in the August issue of the Royal Society journal Biology Letters.

This would seem an obvious result given that contagious yawning is thought to share similar cognitive and neural mechanisms as empathy.

Senju and colleagues from the University of Tokyo showed videos of people yawning or making mouth movements to 24 children with autism spectrum disorder and to 25 non-ASD children. Both groups of children yawned the same number of times while watching the video of general mouth movements, but the non-ASD children yawned more when watching the video of people yawning.

“This is the first report that a neuropsychological or psychiatric condition can selectively impair contagious yawning, sparing spontaneous yawning,” explains Senju, “Our study confirms the prediction of ’empathy theory’, by demonstrating that individuals with autism, who show atypical developments in empathy, also show selective impairment in contagious yawning.”

None of this answers the question of why do we yawn in the first place? Apparently, yawning becomes contagious at around one to two years of age, although unborn fetuses also yawn (presumably not contagiously though!) and can be triggered in animals by stimulating the hypothalamus in the brain with injected dopamine, excitatory amino acids, nitric oxide, and neuropeptides. None of this really explains why we yawn. The empathy angle perhaps points to an ancient benefit in group behaviour, but what that benefit is, science does not yet know.

For more on simple experiments and the power of yawn, check out the neuroscience for kids page at Washington U.

By the way, did you notice while reading this whether you yawned? Hopefully, it was not merely boredom that did it…

Antibodies Online

antibodies-online launched in April 2006 and calls itself the marketplace for research antibodies providing scientists in Germany, Austria, and Switzerland with invaluable assistance in finding antibodies quickly and easily, a task that was once very time-consuming when predominantly paper-based catalogues were the only resource for searching available.

The company also acts as a kind of immunological broker allowing antibody distributors and producers to ply their trade online at low costs and no risks. The reason I mentioned it on ChemSpy.com is that the their site provides access to information on some 60,000 antibodies in a database, with that number growing every day. Such a resource could prove invaluable to many researchers working in silico let alone in vitro and in vivo. antibodies-online.com claims to be one of the largest vendor-independent platform for research antibodies in that region and plans to increase its product portfolio to more than 100,000 antibodies by Spring 2008, which could make it an even more useful resource.

Quantum Dots and Spin Pumps

Spin pumped quantum dotIt is not so long ago, that the first thing that sprang to mind when one read the phrase ‘quantum dot’ was the idea of some rather esoteric and complicated aspect of avant garde physics. This is still partly true, there is some rather complex experimental work underway underpinned by even more complex theoretical work investigating the bizarre properties of tiny devices that can trap a single electron in zero-dimensions.

Practical applications of quantum dots have emerged recently in sensor science but US and Brazilian researchers hope to exploit them in a new kind of electronics, known as spintronics where electron charge and quantum spin add an extra dimension to electronic operations and computation. Spin currents might also be used to allow quantum communications take place “in-chip” in devices so small that light propagation is not practical. Such developments will open up quantum dots that can increase processing speed, storage capacity, and functionality of conventional electronics, communication, and computations and technologies.

Eduardo Mucciolo of the Department of Physics at the University of Central Florida, Orlando and Caio Lewenkopf of the Department of Theoretical Physics at State University of Rio de Janeiro, Brazil, are investigating lateral semiconductor quantum dots. They believe that such devices could be used as pumps to produce spin polarised currents, by exploring quantum phase coherence phenomena. The effect, called pure spin pumping, is analogous to charging a battery in conventional electronics. Such a spin pump might provide the much-needed circuit element for spin-based electronics.

Writing in the International Journal of Nanotechnology (2007, 4, 482-495), Mucciolo and Lewenkopf describe a lateral semiconductor quantum dot. In these systems, electrons within a two-dimensional gas are trapped within small puddles by the application of a voltage; applied voltages control the shape and size of these puddles. Electrodes can be used to vary the width of the point contacts between the electron puddle and the 2D gas. Controlling these point contacts allows quantum dots to be “opened” and “closed”.

Controlling these point contacts allows them to “open” and “close” the quantum dots. This effect dates back to the early 1990s, points out Mucciolo. “Closing and opening the propagation through a constriction, the point contact, can be used to detect spin-polarized currents,” he explains, “This is how Susan Watson and colleagues at Middlebury College managed to see spin currents coming out of their quantum dot pump in 2003.”

“Recently, our spin pump proposal passed its first experimental test,” say the researchers, who now hope that other teams will take up the challenge and investigate the potential of spin pump quantum dots.

“The main idea behind the spin pumping mechanism was actually published for the first time in Physical Review Letters in a paper I co-authored with Claudio Chamon (Boston University) and Charles Marcus (Harvard University),” adds Mucciolo. The main development since that earlier work presented in the current paper with Lewenkopf is that now they have carried out a much more detailed analysis to demonstrate the precise details, this was entirely missing from the PRL paper, Mucciolo told us. “In the J Nanotech paper we also develop a general formalism that could serve as a basis for the theoretical investigation of several aspects of spin pumps which, albeit important, have not yet been considered in the literature,” Mucciolo adds.

Growing Nano Journals

The American Chemical Society is following up the success of its preliminary reports publication Nano Letters with a full-blown journal – ACS Nano. Penn State’s Paul Weiss will be Editor and the journal will publish monthly in print and online.

The inaugural issue features work from David Allara, Hongjie Dai, Prashant Kamat, and Frank Caruso, as well as a conversation with Nobel Laureate Heinrich Rohrer, and an editorial from Weiss. A news ection, NanoFocus, will also feature.

If you’re an institutional subscriber you can access Nano at no extra charge for the remainder of 2007 at www.acsnano.org.