This paper provide a model of the slime mold’s network construction algorithm.

“When [Physarum] grows on a nutrient-rich substratum, it covers the surface as a coherent layer (like a pancake). If nutrition becomes limited, it forms fenestrae and finally transforms into a network of interconnected veins that enclose the entire cytoplasmic volume (see the figure). Each vein is a gel-like tube covered by a cell membrane and contains a core of fluid cytoplasm. By rhythmic contraction of its cytoskeleton, cytoplasm is continually pumped through these veins, and this continuous mixing seems to be the reason why all nuclei proceed synchronously through the cell division cycle. The network architecture is highly dynamic. Veins change in thickness, they may form and vanish again, and the plasmodium as a whole can crawl over its substratum, moving over centimeters in a couple of hours. Plasmodia usually do not dissociate. If food sources are spatially separated, such as oat flakes scattered over a wet surface, the plasmodial veins attempt to connect these food sources along the shortest possible pathways, even finding optimized paths through a maze (2). How this optimization is performed in terms of molecular mechanisms remains a challenging question.”

[The model is] “based on feedback loops between the thickness of each tube and internal protoplasmic flow (18–22) in which high rates of streaming stimulate an increase in tube diameter, whereas tubes tend to decline at low flow rates (23). The initial shape of a plasmodium is represented by a randomly meshed lattice with a relatively fine spacing … The edges represent plasmodial tubes in which protoplasm flows, and nodes are junctions between tubes.”

(commentary)

Atsushi Tero, Seiji Takagi, Tetsu Saigusa, Kentaro Ito, Dan P. Bebber, Mark D. Fricker, Kenji Yumiki, Ryo Kobayashi, and Toshiyuki Nakagaki. Rules for Biologically Inspired Adaptive Network Design. Science 327 (5964), 439. (22 January 2010)

Drazen Prelec. A Bayesian Truth Serum for Subjective Data. Science 15 October 2004: Vol. 306. no. 5695, pp. 462 – 466. DOI: 10.1126/science.1102081

Here’s an example that demonstrates the crux of the method. The question is, “Is Picasso your favorite visual artist?” — assume that Picasso lovers are a minority. We want to develop an incentive system that gives Picasso lovers an incentive to answer truthfully that Picasso is their favorite, even though they are in the minority:

People who, for example, rate Picasso as their favorite should — and
usually do … — give higher estimates of the percentage of the population who shares
that opinion, because their own feelings are an informative `sample of one’ …. It
follows, then, that Picasso lovers — who have reason to believe that their best estimate of
Picasso popularity is high compared to others’ estimates — should conclude that the true
popularity of Picasso is underestimated by the population. Hence, one’s true opinion is
also the opinion that has the best chance of being surprisingly common.

Based off this idea, the method rewards people for giving “surprisingly common” answers. Each person is asked not only for their own answer, but also to predict the frequency of each answer in the population. The following equation is used to calculate the reward to give each person (equation 2, “score for respondent r” in the paper, page 5 of the PDF linked above):

log ((the actual frequency of this guy’s answer in the poll)/(the geometric mean of the predicted frequency of this guy’s answer in the poll))
+
alpha * sum over all answers (the actual frequency of this answer in the poll * log((this guy’s prediction of the frequency of this answer in the poll)/(the actual frequency of this answer in the poll)))

where alpha is a parameter between 0 and 1.

The first term in the reward rewards people for giving “surprisingly common” answers. The second term rewards people for giving accurate predictions of the frequency of answers.

The paper goes on to show that, given this reward function, truth-telling is a Nash equilibrium, and furthermore that for sufficiently small alpha, this equilibrium Pareto-dominates expected scores in other equilibria. It also discusses things that can go wrong, and what to do about them.

I’m a fan of it because it is an open-access journal featuring a “tiered system” and more.  From their website:

The Frontiers Journal Series is not just another journal. It is a new approach to scientific publishing. As service to scientists, it is driven by researchers for researchers but it also serves the interests of the general public. Frontiers disseminates research in a tiered system that begins with original articles submitted to Specialty Journals. It evaluates research truly democratically and objectively based on the reading activity of the scientific communities and the public. And it drives the most outstanding and relevant research up to the next tier journals, the Field Journals.

I’m a big fan of the variety of specialty journals they have:

• Aging Neuroscience
• Behavioral Neuroscience
• Cellular Neuroscience
• Computational Neuroscience
• Enteric Neuroscience
• Evolutionary Neuroscience
• Human Neuroscience
• Integrative Neuroscience
• Molecular Neuroscience
• Neural Circuits
• Neuroanatomy
• Neuroenergetics
• Neuroengineering
• Neurogenesis
• Neurogenomics
• Neuroinformatics
• Neuromethods
• Neuropharamacology
• Neuroprosthetics
• Neurorobotics
• Synaptic Neuroscience
• Systems Neuroscience

Just last night, I watched the tense but amazing film The Hurt Locker (don’t let the name disuade you, see the phenomenal Metacritic rating), which is about a bomb disposal squad during the recent Iraq War. There is one particularly stirring scene with a suicide bomber who claims that he was forced to wear a vest with explosives and doesn’t want to go through with it. The difficulty in the limited time before the bomb explosion revolves around whether to actually trust the man and the challenge of trusting someone when neither party speaks the other’s language. You can certainly at least understand (putting aside the ethics of war itself) why governments are interested in detecting nonverbal trust cues.

Details about the IARPA call for proposals are after the jump.

IARPA is soliciting submissions on the following areas aimed at
addressing the challenges of defining, understanding, and ultimately
detecting valid, reliable signatures of trust in humans:

1.) Different kinds of trust and what, if any, kinds of
neurophysiological signals might be associated with them. IARPA seeks
to understand the different manifestations that trust may take (i.e.
swift trust, conditional trust, unconditional trust, etc.) as well as
the different neurophysiological processes associated with one or more
of these kinds of trust.

2.) New models of neural systems and patterns of neural activation
related to different kinds of trust and associated neurophysiological
signatures of those activation patterns. IARPA seeks to understand the
degree to which the neural-bases of trust(s) may assist in detecting
peripheral signals of trust and trustworthiness under different
conditions.

3.) Potentially novel preconscious signals or combinations of signals
- neural, endocrine, physiological, behavioral, etc. – that may be
indicative of trust or trustworthiness among people in different
contexts. IARPA seeks to elucidate signals and neurobiological
processes that humans may use for assessing trust, but which are not
yet – or are currently poorly – understood.

4.) New sensor technologies or combinations of technologies that can
assist in detecting subtle but valid and reliable changes in
neurophysiological states that may be indicative of trust among
humans. IARPA seeks to explore the feasibility of using technology to
amplify systems that humans have evolved to preconsciously assess
trust in others.

5.) Novel, ecologically-valid, but ethical “trust-based” protocols
designed to assess the validity and reliability of potential trust
signals among two or more humans. IARPA seeks to develop new, more
sophisticated processes for understanding near real-time human
preconscious assessment of trust in near real-world circumstances.

-John O’Leary

…brainwashing their youth

• Vergoz et al, 2007, Science
• commentary

…and/or mysteriously disappearing from the face of the earth

• Colony Collapse Disorder

Keeping an eye on species poised to take over the world,
Davie

People with Williams syndrome, a genetic disorder, have “trouble with space and numbers” but “a love of company and conversation combined, often awkwardly, with a poor understanding of social dynamics and a lack of social inhibition”. Elsewhere, I believe that Williams syndrome patients have been described as feeling as though everyone is their friend.

The genetic cause of Williams syndrome is known.

The article also goes into the theory that human intelligence and language evolved to deal with large social groups, especially such complexities as deception, and posits that Williams syndrome allows us to dissociate some aspects of social intelligence from others, and from other aspects of intelligence.

Through its innovative structure, WNYC’s RADIO LAB (www.radiolab.org) blends storytelling, interviews with top scientists, music and innovative sound design to explore big ideas such as Morality, Space, Identity.

The hosts are Jad Abumrad, one of public radio’s youngest producers, and Robert Krulwich, veteran broadcast journalist for ABC with a sub-speciality in science. Together they create a “two guys chatting in a bar” feel, making complex scientific ideas accessible and exciting.

The series launches in NYC on WNYC on Friday, May 18, but will be available to anyone, anywhere as a podcast starting May 22. Podcasts and on-demand streaming can be found at www.radiolab.org.

An afternoon of video games with a Harvard sleep expert. A first-hand look at the psychological power of the doctor’s white coat. A lesson on the dire effects of sleep deprivation, through the eyes of a new mother.

Radio Lab, WNYC, New York Public Radio®’s highly-acclaimed show about wonder, discovery, and big ideas, is back!

Season 3 launches nationally on WNYC on Friday, May 18, and will air on over 100 public radio stations around the country throughout the spring and summer. Program descriptions below.

This season, co-hosts Jad Abumrad and Robert Krulwich tackle five new fascinating topics: Placebo, Sleep, Zoos, Memory and Forgetting and Mortality. They begin with seemingly simple questions — Could the best medicine be no medicine at all? Is there such a thing as a good cage? Is love a more powerful force than memory? – that serve as a launch pad into the unknown. Embarking on a curiosity spree, they unearth the implications of the latest scientific findings, stumble into surprising stories, and traverse philosophy, history, and culture, checking in all along the way with the scientists doing the real work.

SCHEDULE: RADIO LAB – Season 3
May 18 – June 15
Special 5-Week Season of Radio Lab
Fridays: 2pm on WNYC AM 820 / 3pm on 93.9 FM
Sundays: 6pm on 93.9 FM
Via live webstream and on-demand at www.wnyc.org

June 11 – 15
Encore of all five episodes
Daily: 2pm on WNYC AM 820 / 3pm on 93.9 FM
Via live webstream and on-demand at www.wnyc.org

PROGAM DESCRIPTIONS – in order of broadcast

Placebo
Could the best medicine be no medicine at all? The hour begins with a skeptical Kwakiutl Indian trained in shamanistic healing. He knows that his ritual healing is just a trick and yet he wonders: why does it work? With new research demonstrating the startling power of the placebo effect, Radio Lab examines the chemical consequences of belief and imagination. Jad Abumrad tours a hospital with his father, Dr. Abumrad, and witnesses the power of the white coat. After visiting 18th century France to witness the first double-blind placebo test, the show ends with reporter Gregory Warner’s visit to a Christian faith healer in a lakeside tent revival in New York’s Adirondack Mountains.

Sleep
Every creature does it – from giant hump back whales all the way down to fruit flies – and yet science still can’t answer the basic questions: Why do sleep? What is it for? In Radio Lab’s search for the answer we visit Harvard sleep researcher Dr. Robert Stickgold to play video games before dropping in on MIT’s Dr. Matt Wilson as he peers into the brains of slumbering rats. We hear from a mother who is sleep deprived and learn from UPENN’s Dr. Alan Pack about the toxicity of sleep deprivation. Our last stop in the hour is with Dr. Guilio Tononi for a theory on what slow wave sleep might be doing for our brains that is so important, we literally cannot live without it.

Zoos
In a cruel trick of evolution, humans can stand just three feet from a ferocious wild animal and still be perfectly safe. Is there such thing as a good cage? Neuroscientists are looking into the brains of caged animals to see the effects. But how far are we willing to go to do what is best for the animals in our care? NPR science desk reporter Nell Boyce takes us to Toledo, OH for a carcass feeding and reporter Jocelyn Ford goes one step further to a live animal feeding at a rural zoo in China. We end the hour with the story of one man’s promise to a big cat at the Bronx zoo — which took him to all they way to Belize to fulfill — to create the world’s first jaguar preserve.

Memory and Forgetting
According to the latest research, recall is an unstable and profoundly unreliable process. It’s easy come, easy go as we learn how true memories can be obliterated and false ones added. And Oliver Sacks joins us to tell the story of an amnesiac whose love for his wife and music transcend his 7-second memory.

Mortality
Is death a fact of life or a disease that can be cured (as some scientists claim)? When Dr. Leonard Hayflick discovered in 1962 a phenomena known as the ‘Hayflick Limit’ — that cells have a natural limit to their reproduction — the study of longevity was born. We hear from Dr. Cynthia Kenyon, whose tinkering with worm DNA brings her face-to-face with a grim reaper gene. We filter the modern search for the fountain of youth through personal stories of witnessing death…the death of a cell, the death of a loved one…and the aging of a society.

WNYC, New York Public Radio, is New York’s premier public radio station, comprising WNYC 93.9 FM and WNYC AM 820. As America’s most listened-to public radio stations, reaching more than one million listeners every week, WNYC FM and AM extend New York City’s cultural riches to the entire country and air the best national offerings from affiliate networks National Public Radio, Public Radio International and American Public Media. WNYC 93.9 FM broadcasts a wide range of daily news, talk, cultural and classical music programming, while WNYC AM 820 maintains a stronger focus on breaking news and international news reporting. For more information, visit www.wnyc.org.

# # #

Kevin Lafferty, a parasitologist, has put forth the idea that a fairly ubiquitous parasite (infecting O(10%) of Americans, and up to 2/3 of people in places like Brazil) is responsible for some of the diversity of human culures (1). The parasite uses common housecats to increase its transmission to the next host in the life cycle, and has a subtle effect on human personality, with some studies claiming that it even causes neuroticism, and even schizophrenia. (One clinical report (2) claims that “subjects with latent toxoplasmosis had higher intelligence [and] lower guilt proneness.” Hmm!)

Anyway, Lafferty noted that toxoplasmosis varies in prevalence from world region to world region, and then tries to draw correlates between these prevalences and local cultures:

“Drivers of the geographical variation in the prevalence of this parasite include the effects of climate on the persistence of infectious stages in soil, the cultural practices of food preparation and cats as pets. Some variation in culture, therefore, may ultimately be related to how climate affects the distribution of T. gondii, though the results only explain a fraction of the variation in two of the four cultural dimensions, suggesting that if T. gondii does influence human culture, it is only one among many factors.”

I wonder how one could test this hypothesis? Look for recent immigrants from one culture to another, who have lower Toxoplasmosis incidence? (Preferably finding populations that go in opposite directions, as a control.) Track culture change vs. migration vs. climate change?

Unlikely, perhaps. But nice that people are still thinking big

– Ed

(1) Lafferty, K
Can the common brain parasite, Toxoplasma gondii, influence human culture?
Proceedings of the Royal Society B: Biological Sciences
doi:10.1098/rspb.2006.3641

Picked up by the popular press here

(2) Flegr J, Havlicek J.
Changes in the personality profile of young women with latent toxoplasmosis.
Folia Parasitol (Praha). 1999;46(1):22-8.

A study on network properties of the whole brain (functional connectivity data from fMRI)… interesting to see this type of work published in J. Neurosci. Building on previous fMRI/whole brain connectivity studies, the authors use a set of wavelet basis functions to estimate the correlations between different anatomical regions.

Also includes some analyses on resiliency of the system (via a metric like “largest connected cluster”) to random and targeted attack (ie. node deletion). It would be neat if they also did some analysis of common stroke damage. I would think that a stroke probably doesn’t qualify as a “targeted attack”, in the traditional sense, but, due to the predefined structure of the major circulatory structures (eg. circle of Willis), there are likely regions that are near the most commonly blocked arteries, etc. Perhaps someone with some medical qualifications could weigh in here?

There is also a nice discussion of why the human brain does not appear to be a scale-free network: That nodes do not seem to follow the “rich-get-richer” rule of preferential attachment. Evolutionarily recent structures like prefrontal seem to be among the hubs of the system and older structures like limbic regions do not dominate. Here’s a picture of the connectivity map from the paper:

Full abstract after the jump.

Small-world properties have been demonstrated for many complex networks. Here, we applied the discrete wavelet transform to functional magnetic resonance imaging (fMRI) time series, acquired from healthy volunteers in the resting state, to estimate frequency-dependent correlation matrices characterizing functional connectivity between 90 cortical and subcortical regions. After thresholding the wavelet correlation matrices to create undirected graphs of brain functional networks, we found a small-world topology of sparse connections most salient in the low-frequency interval 0.03–0.06 Hz. Global mean path length (2.49) was approximately equivalent to a comparable random network, whereas clustering (0.53) was two times greater; similar parameters have been reported for the network of anatomical connections in the macaque cortex. The human functional network was dominated by a neocortical core of highly connected hubs and had an exponentially truncated power law degree distribution. Hubs included recently evolved regions of the heteromodal association cortex, with long-distance connections to other regions, and more cliquishly connected regions of the unimodal association and primary cortices; paralimbic and limbic regions were topologically more peripheral. The network was more resilient to targeted attack on its hubs than a comparable scale-free network, but about equally resilient to random error. We conclude that correlated, low-frequency oscillations in human fMRI data have a small-world architecture that probably reflects underlying anatomical connectivity of the cortex. Because the major hubs of this network are critical for cognition, its slow dynamics could provide a physiological substrate for segregated and distributed information processing.