I write about cities and infrastructures as living systems in First do no harm over at Streets.MN
Recently in biology Category
From KurzweilAI: ‘Rain Man’-like brains mapped with network analysis:
"Agenesis of the corpus callosum can arise if individuals are born missing DNA from chromosome 16 and often leads to autism.
Scientists have long puzzled over what the link is between this disorder and the autistic brain, said co-senior author of the paper Elliott Sherr, MD, PhD, professor of neurology and genetics especially since not all people with this malformation develop autism.
Doctors believe this is because the brain has a rich capacity for rewiring in alternative ways.
Pursuing this question, Mukherjee and Sherr turned to MRI and the mathematical technique of network analysis, which has long supported fields like civil engineering, helping urban planners optimize the timing of traffic lights to speed traffic. This is the first time network analysis has been applied to brain mapping for a genetic cause of autism.
The brain offers a significantly complicated challenge for analysis because, unlike the streets of a given city, the brain has hundreds of billions of neurons, many of which make tens of thousands of connections to each other, making its level of connectivity highly complex."
Jessica Schoner @ Network Distance on: StarTrib on Gender and Driving, and the Oh-so-timely Death of "Woman Driver" Jokes
"Given all these external forces that influence travel needs and choices, my conclusion is that there is likely no inherent physiological difference causing the difference in travel behavior; or if a biological difference exists, it is marginal and unmeasurable relative to these larger forces. These social, economic, and cultural forces shape the stereotypes of male and female drivers that we are so familiar with."
I agree culture is important. I disagree that physiological differences don't have effects. In particular, I think culture has a large biological component (culture and biology are mutually co-evolving systems). Risk taking has clear biological elements to it, and obviously drives a lot of traffic safety issues.
"Professor Nilli Lavie from UCL Institute of Cognitive Neuroscience, who led the study, explains: ‘An example of where this is relevant in the real world is when people are following directions on a sat nav [GPS receiver] while driving.
‘Our research would suggest that focusing on remembering the directions we’ve just seen on the screen means that we’re more likely to fail to observe other hazards around us on the road, for example an approaching motorbike or a pedestrian on a crossing, even though we may be ‘looking’ at where we’re going.’"
Reason: Lessons From the United Fruit Company - Reason.com discusses the new book by Rich Cohen, The Fish That Ate The Whale: The Life And Times Of America’s Banana King.:
"There is the efficiency. Zemurray got started in the banana business by figuring out how to distribute ‘ripes,’ the freckled bananas that were thrown away as useless discards before Zemurray figured out the logistics of fast-moving rail distribution."[United Fruit was also one of the early investors in RCA, as they held key radio patents, which were crucial for banana distribution.]
Tim Lee @ Ars: Four signs America’s broadband policy is failing
[He discovers networks with high fixed costs are not inherently competitive]
Bryan Caplan @ Econlog: A Signaling Theory of Suboptimal Telecommuting, :
"A fascinating senior paper by Georgetown undergraduate Alexander Clark suggests that the answer is yes. Clark's story: Workers physically commute for signaling reasons. Employers can monitor your productivity better when you actually come to the office. Workers who telecommute put themselves on the slow track to success - if they can even get hired in the first place. To bolster this thesis, Clark analyzes the American Time Use Survey using the employer learning-statistical discrimination (EL-SD) framework. He finds that the labor market does indeed take longer to reward telecommuters for their hard-to-observe abilities. "[Not only does telecommuting signal sloth, there is at least one survey cited which shows telecommuters don't work as many hours per day.]
I know from reading your blog that you are a bit keen on anthropomorphized transportation. This week I stumbled upon an old cartoon celebrating the 50th anniversary of the Wuppertal Schwebebahn from 1951. The "Laughing Schwebebahn" is not only smiling, but it also has wings. It's from Das Beste von der Schwebebahn in 50 Jahren (http://www.worldcat.org/title/beste-von-der-schwebebahn-in-50-jahren/oclc/8757312).
See wikipedia for more.
I am guessing this category (anthropomorphic monorails) is smaller than others, but please send in any other examples.
The picture is sort of difficult to see, but a bird family seems to think this traffic light (Franklin and Seymour) is a good nest site. This is not an unknown phenomenon. I would think the lights going on and off 24 hours a day would be annoying, but the rent is cheep.
Via Tyler Cowan, Foxnews: Disney's ‘NextGen’ plan is expected cut wait times for rides and more:
"Details of the plan emerged in February 2011 when Walt Disney Parks and Resorts Chairman Tom Staggs announced some major changes at an investors' conference.
“Guests will be able to reserve times for their favorite attractions and character interactions…secure seats at our shows and spectaculars…make dining reservations…and pre-book many other favorite guest experiences -- all before even leaving their house," Staggs said.
Since then, Disney has remained quiet about the project -- even its existence.
“I can’t confirm nor deny it,” said Disney representative Marilyn Waters when FoxNews.com asked her about the NextGen project."
A gravity-ish model of the brain - KurzweilAI reports: A statistical model of the network of connections between brain regions :
"Researchers at the University of Cambridge have developed a simple mathematical model of the brain which provides a remarkably complete statistical account of the complex web of connections between various brain regions.
The brain shares a pattern of connections that is similar to other complex networks such as social networks and the Web. However, until now, it was not known what rules were involved in the formation of the human brain network.
The scientists, from the Behavioral and Clinical Neuroscience Institute in the University of Cambridge Department of Psychiatry, and the National Institute of Mental Health in the U.S., discovered that the network can be modeled as a result of just two different competing factors: a distance penalty based on the cost of maintaining long-range connections between various brain regions, and a second term modeling the preference for links between regions sharing similar input."
The wiring of the brain recapitulates the real external physical networks on which we travel (or our perception of it). If people are learning a map (e.g London taxicab drivers learning The Knowledge), they reshape their brain. The newish technical term for this set of internal brain connections is the Connectome. It would make some sense for this wiring to be topologically similar to the actual topology that is being reflected (i.e. one thinks there would be some parsimony in finding the shortest path on a physical network if it were actually the shortest path in the brain).
I realize (and wikipedia tells me so) that classical Recapitulation Theory (Ontogeny Recapitulates Phylogeny "in developing from embryo to adult, animals go through stages resembling or representing successive stages in the evolution of their remote ancestors" ) is disproven.
What I am hypothesizing is different that there is a non-random (statistically significant) resemblance between brain wiring and the physical relationships of the external world.
Now to test. How to test?
KurzweilAI reports: Complex wiring of the nervous system may rely on a just a handful of genes and proteins and researchers are working on mapping the internals of the brain.
"The needs of the many outweigh the needs of the few (or the one)." - Surak
"The needs of the one outweigh the needs of the many." - Kirk
Case A. An individual releases toxic substances into the unowned environmental commons where it is breathed in by many members of the community for the individual's benefit and to some community-members' cost. This is pollution.
Case B. The community releases toxic substances into an individual where it is ingested by the individual for the community's benefit and to some individuals' cost. This is immunization.
Is A bad and B good?
A produces in economic terms a "negative externality", an unwanted side-effect on third-parties. (Strictly speaking, pollution may also produce positive externalities, e.g. some agriculture may benefit from a change in the chemical composition of the air, or change in temperature, etc., these are often thought to be relatively small compared to the downsides)
B produces a "positive externality" (a good side-effect on third parties) [e.g. Herd immunity is whereby the immunity of a significant portion of the population protects others from disease, as it limits the ability of viruses to spread.]
So long as most individuals benefit from immunization, people seem to let it slide. But there have been a number of immunization attempts that were not generally successful, where the downsides may have outweighed the upside, the 1976 Swine Flu immunization is an example, where the flu killed 1 person, and the immunization killed 25 (of course, the story is quite complicated, and those who were immunized in 1976 were less likely to get ill in the 2009 outbreak, so it may have been net positive in the long run).
Pollution exists and is known to cause harm. Most people think all else equal, pollution is bad for society. There is debate on how much to regulate or price pollution, as well as the magnitude of the harm caused from individual pollutants. In the US, air pollution in general is down, though decreasing some pollutants may increase other pollutants (e.g. processes that reduce the size of pollutants may reduce the amount of large particulates but increase the number of small, less easily measured, particulates).
It is known that vaccines have side effects, it is not known in advance which unlucky individual will be the recipient of those side effects.
If you are a communitarian, A is unacceptable, B is acceptable. If you are an individualist, A is acceptable and B should be voluntary.
An individualist may willingly submit to immunization, but only if their personal benefit outweighs their personal cost, not strictly for herd immunity of for the benefit of others (unless those are things that they get salutary benefits from, either from a feeling of moral righteousness or from rising in status do to the perceptions of others). They believe society does not have the right to forcibly vaccinate individuals, or coerce individuals into vaccination in exchange for mandatory services (e.g. public education).
Susan Kain in the New York Times has a pro-Introvert article: The Rise of the New Groupthink: "SOLITUDE is out of fashion. Our companies, our schools and our culture are in thrall to an idea I call the New Groupthink, which holds that creativity and achievement come from an oddly gregarious place. Most of us now work in teams, in offices without walls, for managers who prize people skills above all. Lone geniuses are out. Collaboration is in. "
In contrast, there are many who believe that cities, the machines that enables those inter-personal interactions, are the source of creativity. This is epitomized by recent books by Ed Glaeser and Ryan Avent.
We can make a simple table:
|Introvert||Optimal amount of stimulation if quite space,
|Hermit alone in thoughts,
|Extrovert||Too many attractions,
Connects rather than creates
|Unsatisfied, No one to riff with|
This is a gross oversimplification of personality and environments, and the text in the boxes is probably unfair to extroverts, who I am sure have created something in the history of humanity. It does however suggest both the risks of cities on being too stimulative (not enough time for thought), and the country (i.e. the antithesis of the city), which may be insufficiently stimulative and leave too much time for thought and not enough for testing of ideas.
Several really good ideas have come from the country though, and not just agricultural implements. My favorite story is that of Philo Farnsworth, one of the individuals credited with inventing the television. As wikipedia says: "A farm boy, his inspiration for scanning an image as series of lines came from the back-and-forth motion used to plow a field." We would not have had television as soon, or possibly in the same form, but for agricultural plowing strategies.
The key is to ensure the city has quite spaces, and the country has connecting places, both of which societies create, although one can argue whether the quantities and qualities are optimal for various things.
See also my old post: Does creativity whither with age?.
From David King:
So what is exciting for the future? Flying helicopters with your mind, of course! Clever researchers at the University of Minnesota have developed software that allows the user to fly around the Minnesota campus by thinking hard while wearing a special hat. Here is the paper, and video is at this io9.com link. Let's see more views of the future with mind control, autonomous cars and other technologies that fundamentally change the things we do (so we can do different things) instead of marginal improvements of what we already do. After all, we're still waiting for the telecommuting revolution to kick in.
Robin Hanson on how long distance travel was critical in human evolution ... Travel Made Humans. Well worth reading. Transportation is the mother of us all.
More from the annals of animal transportation: Geekosystem reports on ants building rafts: Mere Water Will Not Extinguish Fire Ants : ""
"Researchers at the Georgia Institute of Technology have done perhaps the only serious engineering study that involves dumping a bunch of fire ants in water and watching what happens. Engineering professor David Hu and grad student Nathan J. Mlot were interested in reports they had heard of South American fire ants forming massive rafts out of themselves and clumping together during flooding, and after gathering up fire ants by the roadside in Georgia, they put the anecdotes to the test.“They’ll gather up all the eggs in the colony and will make their way up through the underground network of tunnels, and when the flood waters rise above the ground, they’ll link up together in these massive rafts,” Mlot said."
From NYT: Using Crowds, and GPS, to Chart Roadkill
While Mr. Ringen's friends goad him with nicknames like "Doctor Roadkill," he is not alone in his peculiar pursuit. Hundreds of volunteers collect and upload roadkill data to the California Roadkill Observation System, a mapping Web site built by researchers at the University of California, Davis, to better understand where and why cars strike animals.
(Are these guys like trainspotters?).
A UGA press release Study identifies critical "traffic engineer" of the nervous system
Athens, Ga. - A new University of Georgia study published in the journal Nature has identified a critical enzyme that keeps traffic flowing in the right direction in the nervous system, and the finding could eventually lead to new treatments for conditions such as Alzheimer's and Parkinson's disease.
"There was no medical or any other applied science drive for this project; it was purely curiosity about how transport inside cells works," said study co-author Jacek Gaertig, professor in the cellular biology department in the UGA Franklin College of Arts and Sciences. "But it looks like we have identified an important enzyme that acts in the nervous system."
He explained that cells contain a network of tubes known as microtubules that are made of protein and serve as tracks for the shuttling of materials from one part of the cell to another. The traffic signs on this microtubule network are chemical additions such as acetylation marks. Microtubules in parts of neurons in the brain that send signals, for example, are loaded with acetylation marks. Microtubules in parts of neurons that receive signals, on the other hand, have few.
Acetylation marks were discovered in 1983, and researchers recently determined their role in regulating the binding of the motor proteins that shuttle materials along microtubules. What has been unclear for more than 25 years, however, was the cellular process by which these acetylation marks are formed. In other words, which enzyme decides where the traffic signs go?
Through a series of studies using the microscopic protozoan Tetrahymena, the nematode C. elegans, zebrafish and human cancer cells, Gaertig and his colleagues revealed that an a protein known as MEC-17 is the traffic engineer in charge of microtubule acetylation.
MEC-17 acts as an enzyme to catalyze the acetylation reaction on microtubules, and is involved in the sensation of touch in the nematode. Its depletion in zebrafish, which are commonly used as a model organism to study basic processes, results in neuromuscular defects. Importantly, several research groups have previously reported that the levels of acetylation marks on microtubules are altered in human neurodegenerative diseases such as Huntington's, Parkinson's and Alzheimer's.
Gaertig said that with the enzyme identified and its mechanism of action known, it is now possible for drug manufacturers to search for compounds that block or enhance its activity.
Interesting study (the downsides of accessibility):
How do Roads Spread AIDS in Africa? A Critique of the Received Policy Wisdom Date: 2009-11 By: Djemaï, Elodie URL: http://d.repec.org/n?u=RePEc:tse:wpaper:22243&r=ure This paper empirically analyzes the influence of road proximity on HIV-infection using geographical data on road infrastructure and the Demographic and Health Surveys collected in six African countries. Firstly we show that living in proximity to a major road increases the individual risk of infection. This observed relationship is found to be sensitive to the use of the road and to be robust after correcting for potential selection bias related to the non random placement of people. Secondly, our findings reveal that road infrastructure improves the level of HIV/AIDS-knowledge and facilitates access to condoms, providing no support to the hypothesis that HIV-infection is purely due to ignorance and misfortune. Thirdly, we find that the increased risk of infection is driven by a higher likelihood of engaging in casual sexual partnerships that more than offsets the effect of the increased use of condoms. Keywords: HIV/AIDS epidemic, spatial inequalities, risk taking JEL: I10
In New Scientist: Picking our brains: Why are some people smarter?
One important factor [in intelligence] seems to be how well our neurons can talk to each other. Martijn van den Heuvel, a neuroscientist at Utrecht University Medical Center in the Netherlands, found that smarter brains seem to have more efficient networks between neurons - in other words, it takes fewer steps to relay a message between different regions of the brain. That could explain about a third of the variation in a population's IQ, he says.
So can we extrapolate that ``smarter'' cities have more efficient networks (in a sense, higher accessibility)? This may be the source of agglomeration economies that give value to cities over random space, the ability to connect.
For your blog since you've been keeping up with the slugs predicting roadways, here is a story of a drop of oil that solves a maze. I'm not sure what happens if the slugs get their hands on the oil, but there seems to be some spurious lesson about intelligence from these stories. What a maze-solving oil drop tells us of intelligence (New Scientist)
Following up a recent post , more on the slime mold as network architect ... from Scientific American:
It is not clear to me who has precedence, UK or Japan based slime mold researchers, but interesting nonetheless.
From New Scientist: Designing highways the slime mould way
... Jeff Jones and Andrew Adamatzky, specialists in unconventional computing at the University of the West of England in Bristol, wondered if biology could provide an alternative to conventional road planning methods. To find out, they created templates of the UK using a sheet of agar on which they marked out the nine most populous cities, excluding London, with oat flakes. Then, in the place of London, the pair introduced a colony of P. polycephalum, which feeds by spawning tendrils to reach nutrients, and recorded the colony's feeding activity (see picture).
Most of the resulting "maps" mimicked the real inter-city road network, but some offered new routes. For instance, the motorway between Manchester and Glasgow passes along the west coast of the UK, but the slime mould preferred to travel east to Newcastle and then north to Glasgow ( /arxiv.org/abs/0912.3967 ). "This shows how a single-celled creature without any nervous system - and thus intelligence in the classical sense - can provide an efficient solution to a routing problem," says Jones.
Saturday, August 22, 2009
CANBERRA, Australia --
Traffic noise could be ruining the sex lives of urban frogs by drowning out the seductive croaks of amorous males, an Australian researcher said Friday.
Another explanation for the dearth of frogs? (see section 3.7, there has been other research on this).