Tag Archives: Washington University in Saint Louis

D-PLACE: an open access database of places, language, culture, and enviroment

In an attempt to be a bit more broad in my interpretation of the ‘society’ part of my commentary I’m including this July 8, 2016 news item on ScienceDaily (Note: A link has been removed),

An international team of researchers has developed a website at d-place.org to help answer long-standing questions about the forces that shaped human cultural diversity.

D-PLACE — the Database of Places, Language, Culture and Environment — is an expandable, open access database that brings together a dispersed body of information on the language, geography, culture and environment of more than 1,400 human societies. It comprises information mainly on pre-industrial societies that were described by ethnographers in the 19th and early 20th centuries.

A July 8, 2016 University of Toronto news release (also on EurekAlert), which originated the news item, expands on the theme,

“Human cultural diversity is expressed in numerous ways: from the foods we eat and the houses we build, to our religious practices and political organisation, to who we marry and the types of games we teach our children,” said Kathryn Kirby, a postdoctoral fellow in the Departments of Ecology & Evolutionary Biology and Geography at the University of Toronto and lead author of the study. “Cultural practices vary across space and time, but the factors and processes that drive cultural change and shape patterns of diversity remain largely unknown.

“D-PLACE will enable a whole new generation of scholars to answer these long-standing questions about the forces that have shaped human cultural diversity.”

Co-author Fiona Jordan, senior lecturer in anthropology at the University of Bristol and one of the project leads said, “Comparative research is critical for understanding the processes behind cultural diversity. Over a century of anthropological research around the globe has given us a rich resource for understanding the diversity of humanity – but bringing different resources and datasets together has been a huge challenge in the past.

“We’ve drawn on the emerging big data sets from ecology, and combined these with cultural and linguistic data so researchers can visualise diversity at a glance, and download data to analyse in their own projects.”

D-PLACE allows users to search by cultural practice (e.g., monogamy vs. polygamy), environmental variable (e.g. elevation, mean annual temperature), language family (e.g. Indo-European, Austronesian), or region (e.g. Siberia). The search results can be displayed on a map, a language tree or in a table, and can also be downloaded for further analysis.

It aims to enable researchers to investigate the extent to which patterns in cultural diversity are shaped by different forces, including shared history, demographics, migration/diffusion, cultural innovations, and environmental and ecological conditions.

D-PLACE was developed by an international team of scientists interested in cross-cultural research. It includes researchers from Max Planck Institute for the Science of Human history in Jena Germany, University of Auckland, Colorado State University, University of Toronto, University of Bristol, Yale, Human Relations Area Files, Washington University in Saint Louis, University of Michigan, American Museum of Natural History, and City University of New York.

The diverse team included: linguists; anthropologists; biogeographers; data scientists; ethnobiologists; and evolutionary ecologists, who employ a variety of research methods including field-based primary data collection; compilation of cross-cultural data sources; and analyses of existing cross-cultural datasets.

“The team’s diversity is reflected in D-PLACE, which is designed to appeal to a broad user base,” said Kirby. “Envisioned users range from members of the public world-wide interested in comparing their cultural practices with those of other groups, to cross-cultural researchers interested in pushing the boundaries of existing research into the drivers of cultural change.”

Here’s a link to and a citation for the paper,

D-PLACE: A Global Database of Cultural, Linguistic and Environmental Diversity by Kathryn R. Kirby, Russell D. Gray, Simon J. Greenhill, Fiona M. Jordan, Stephanie Gomes-Ng, Hans-Jörg Bibiko, Damián E. Blasi, Carlos A. Botero, Claire Bowern, Carol R. Ember, Dan Leehr, Bobbi S. Low, Joe McCarter, William Divale, Michael C. Gavin.  PLOS ONE, 2016; 11 (7): e0158391 DOI: 10.1371/journal.pone.0158391 Published July 8, 2016.

This paper is open access.

You can find D-PLACE here.

While it might not seem like that there would be a close link between anthropology and physics in the 19th and early 20th centuries, that information can be mined for more contemporary applications. For example, someone who wants to make a case for a more diverse scientific community may want to develop a social science approach to the discussion. The situation in my June 16, 2016 post titled: Science literacy, science advice, the US Supreme Court, and Britain’s House of Commons, could  be extended into a discussion and educational process using data from D-Place and other sources to make the point,

Science literacy may not be just for the public, it would seem that US Supreme Court judges may not have a basic understanding of how science works. David Bruggeman’s March 24, 2016 posting (on his Pasco Phronesis blog) describes a then current case before the Supreme Court (Justice Antonin Scalia has since died), Note: Links have been removed,

It’s a case concerning aspects of the University of Texas admissions process for undergraduates and the case is seen as a possible means of restricting race-based considerations for admission.  While I think the arguments in the case will likely revolve around factors far removed from science and or technology, there were comments raised by two Justices that struck a nerve with many scientists and engineers.

Both Justice Antonin Scalia and Chief Justice John Roberts raised questions about the validity of having diversity where science and scientists are concerned [emphasis mine].  Justice Scalia seemed to imply that diversity wasn’t esential for the University of Texas as most African-American scientists didn’t come from schools at the level of the University of Texas (considered the best university in Texas).  Chief Justice Roberts was a bit more plain about not understanding the benefits of diversity.  He stated, “What unique perspective does a black student bring to a class in physics?”

To that end, Dr. S. James Gates, theoretical physicist at the University of Maryland, and member of the President’s Council of Advisers on Science and Technology (and commercial actor) has an editorial in the March 25 [2016] issue of Science explaining that the value of having diversity in science does not accrue *just* to those who are underrepresented.

Dr. Gates relates his personal experience as a researcher and teacher of how people’s background inform their practice of science, and that two different people may use the same scientific method, but think about the problem differently.

I’m guessing that both Scalia and Roberts and possibly others believe that science is the discovery and accumulation of facts. In this worldview science facts such as gravity are waiting for discovery and formulation into a ‘law’. They do not recognize that most science is a collection of beliefs and may be influenced by personal beliefs. For example, we believe we’ve proved the existence of the Higgs boson but no one associated with the research has ever stated unequivocally that it exists.

More generally, with D-PLACE and the recently announced Trans-Atlantic Platform (see my July 15, 2016 post about it), it seems Canada’s humanities and social sciences communities are taking strides toward greater international collaboration and a more profound investment in digital scholarship.

Can the future influence the past? The answer is: mostly yes

The principles of quantum mechanics mystify me which, as it turns out, is the perfect place to start with the work featured in a Feb. 9, 2015 news item on ScienceDaily,

We’re so used to murder mysteries that we don’t even notice how mystery authors play with time. Typically the murder occurs well before the midpoint of the book, but there is an information blackout at that point and the reader learns what happened then only on the last page.

If the last page were ripped out of the book, physicist Kater Murch, PhD, said, would the reader be better off guessing what happened by reading only up to the fatal incident or by reading the entire book?

The answer, so obvious in the case of the murder mystery, is less so in world of quantum mechanics, where indeterminacy is fundamental rather than contrived for our reading pleasure.

A Feb. 13, 2015 Washington University at St. Louis (WUSTL) news release by Diana Lutz, which originated the news item, describes the research,

Even if you know everything quantum mechanics can tell you about a quantum particle, said Murch, an assistant professor of physics in Arts & Sciences at Washington University in St. Louis, you cannot predict with certainty the outcome of a simple experiment to measure its state. All quantum mechanics can offer are statistical probabilities for the possible results.

The orthodox view is that this indeterminacy is not a defect of the theory, but rather a fact of nature. The particle’s state is not merely unknown, but truly undefined before it is measured. The act of measurement itself that forces the particle to collapse to a definite state.

It’s as if what we did today, changed what we did yesterday. And as this analogy suggests, the experimental results have spooky implications for  time and causality—at least in microscopic world to which quantum mechanics applies.

Until recently physicists could explore the quantum mechanical properties of single particles only through thought experiments, because any attempt to observe them directly caused them to shed their mysterious quantum properties.

But in the 1980s and 1990s physicists invented devices that allowed them to measure these fragile quantum systems so gently that they don’t immediately collapse to a definite state.

The device Murch uses to explore quantum space is a simple superconducting circuit that enters quantum space when it is cooled to near absolute zero. Murch’s team uses the bottom two energy levels of this qubit, the ground state and an excited state, as their model quantum system. Between these two states, there are an infinite number of quantum states that are superpositions, or combinations, of the ground and excited states.

The quantum state of the circuit is detected by putting it inside a microwave box. A few microwave photons are sent into the box, where their quantum fields interact with the superconducting circuit. So when the photons exit the box they bear information about the quantum system.

Crucially, these “weak,” off-resonance measurements do not disturb the qubit, unlike “strong” measurements with photons that are resonant with the energy difference between the two states, which knock the circuit into one or the other state.

In Physical Review Letters, Murch describes a quantum guessing game played with the qubit.

“We start each run by putting the qubit in a superposition of the two states,” he said. “Then we do a strong measurement but hide the result, continuing to follow the system with weak measurements.”

They then try to guess the hidden result, which is their version of the missing page of the murder mystery.

“Calculating forward, using the Born equation that expresses the probability of finding the system in a particular state, your odds of guessing right are only 50-50,” Murch said. “But you can also calculate backward using something called an effect matrix. Just take all the equations and flip them around. They still work and you can just run the trajectory backward.

“So there’s a backward-going trajectory and a forward-going trajectory and if we look at them both together and weight the information in both equally, we get something we call a hindsight prediction, or “retrodiction.”

The shattering thing about the retrodiction is that it is 90 percent accurate. When the physicists check it against the stored measurement of the system’s earlier state it is right nine times out of 10.

Going from a 50% accuracy rate to 90% is quite amazing and according to the news release, this has many implications,

The quantum guessing game suggests ways to make both quantum computing and the quantum control of open systems, such as chemical reactions, more robust. But it also has implications for much deeper problems in physics.

For one thing, it suggests that in the quantum world time runs both backward and forward whereas in the classical world it only runs forward.

“I always thought the measurement would resolve the time symmetry in quantum mechanics,” Murch said. “If we measure a particle in a superposition of states and it collapses into one of two states, well, that sounds like a process that goes forward in time.”

But in the quantum guessing experiment, time symmetry has returned. The improved odds imply the measured quantum state somehow incorporates information from the future as well as the past. And that implies that time, notoriously an arrow in the classical world, is a double-headed arrow in the quantum world.

“It’s not clear why in the real world, the world made up of many particles, time only goes forward and entropy always increases,” Murch said. “But many people are working on that problem and I expect it will be solved in a few years,” he said.

In a world where time is symmetric, however, is there such a thing as cause and effect? To find out, Murch proposes to run a qubit experiment that would set up feedback loops (which are chains of cause and effect) and try to run them both forward and backward.

“It takes 20 or 30 minutes to run one of these experiments,” Murch said, “several weeks to process it, and a year to scratch our heads to see if we’re crazy or not.”

“At the end of the day,” he said, “I take solace in the fact that we have a real experiment and real data that we plot on real curves.”

Here are links to and citations for the Physical Review paper and an earlier version of the paper,

 Prediction and retrodiction for a continuously monitored superconducting qubit by D. Tan, S. Weber, I. Siddiqi, K. Mølmer, K. W. Murch. arXiv.org > quant-ph > arXiv:1409.0510 (Submitted on 1 Sep 2014 (v1), last revised 10 Nov 2014 (this version, v2))

I last mentioned Kater Murch and his work in a July 31, 2014 post titled: Paths of desire: quantum style.

Paths of desire: quantum style

Shortcuts are also called paths of desire (and other terms too) by those who loathe them. It turns that humans and other animals are not the only ones who use shortcuts. From a July 30, 2014 news item on ScienceDaily,

Groundskeepers and landscapers hate them, but there is no fighting them. Called desire paths, social trails or goat tracks, they are the unofficial shortcuts people create between two locations when the purpose-built path doesn’t take them where they want to go.

There’s a similar concept in classical physics called the “path of least action.” If you throw a softball to a friend, the ball traces a parabola through space. It doesn’t follow a serpentine path or loop the loop because those paths have higher “actions” than the true path.

A July 30, 2014 Washington University in St. Louis (Missouri, US) news release (also on EurekAlert) by Diana Lutz, which originated the news item, describes the issues associated with undertaking this research,

Quantum particles can exist in a superposition of states, yet as soon as quantum particles are “touched” by the outside world, they lose this quantum strangeness and collapse to a classically permitted state. Because of this evasiveness, it wasn’t possible until recently to observe them in their quantum state.

But in the past 20 years, physicists have devised devices that isolate quantum systems from the environment and allow them to be probed so gently that they don’t immediately collapse. With these devices, scientists can at long last follow quantum systems into quantum territory, or state space.

Kater Murch, PhD, an assistant professor of physics at Washington University in St. Louis, and collaborators Steven Weber and Irfan Siddiqui of the Quantum Nanoelectronics Laboratory at the University of California, Berkeley, have used a superconducting quantum device to continuously record the tremulous paths a quantum system took between a superposition of states to one of two classically permitted states.

Because even gentle probing makes each quantum trajectory noisy, Murch’s team repeated the experiment a million times and examined which paths were most common. The quantum equivalent of the classical “least action” path — or the quantum device’s path of desire — emerged from the resulting cobweb of many paths, just as pedestrian desire paths gradually emerge after new sod is laid.

The experiments, the first continuous measurements of the trajectories of a quantum system between two points, are described in the cover article of the July 31 [2014] issue of Nature.

“We are working with the simplest possible quantum system,” Murch said. “But the understanding of quantum interactions we are gaining might eventually be useful for the quantum control of biological and chemical systems.

“Chemistry at its most basic level is described by quantum mechanics,” he said. “In the past 20 years, chemists have developed a technique called quantum control, where shaped laser pulses are used to drive chemical reactions — that is, to drive them between two quantum states. The chemists control the quantum field from the laser, and that field controls the dynamics of a reaction,” he said.

“Eventually, we’ll be able to control the dynamics of chemical reactions with lasers instead of just mixing reactant 1 with reactant 2 and letting the reaction evolve on its own,” he said.

An artificial atom The device Murch uses to explore quantum space is a simple superconducting circuit. Because it has quantized energy levels, or states, like an atom, it is sometimes called an artificial atom. Murch’s team uses the bottom two energy levels, the ground state and an excited state, as their model quantum system.

Between these two states, there are an infinite number of quantum states that are superpositions, or combinations, of the ground and excited states. In the past, these states would have been invisible to physicists because attempts to measure them would have caused the system to immediately collapse.

But Murch’s device allows the system’s state to be probed many times before it becomes an effectively classical system. The quantum state of the circuit is detected by putting it inside a microwave box. A very small number of microwave photons are sent into the box where their quantum fields interact with the superconducting circuit.

The microwaves are so far off resonance with the circuit that they cannot drive it between its ground and its excited state. So instead of being absorbed, they leave the box bearing information about the quantum system in the form of a phase shift (the position of the troughs and peaks of the photons’ wavefunctions).

Although there is information about the quantum system in the exiting microwaves, it is only a small amount of information.

“Every time we nudge the system, something different happens,” Murch said. “That’s because the photons we use to measure the quantum system are quantum mechanical as well and exhibit quantum fluctuations. So it takes many of these measurements to distinguish the system’s signal from the quantum fluctuations of the photons probing it.” Or, as physicists put it, these are weak measurements.

Murch compares these experiments to soccer matches, which are ultimately experiments to determine which team is better. But because so few goals are scored in soccer, and these are often lucky shots, the less skilled team has a good chance of winning. Or as Murch might put it, one soccer match is such a weak measurement of a team’s skill that it can’t be used to draw a statistically reliable conclusion about which team is more skilled.

Each time a team scores a goal, it becomes somewhat more likely that that team is the better team, but the teams would have to play many games or play for a very long time to know for sure. These fluctuations are what make soccer matches so exciting.

Murch is in essence able to observe millions of these matches, and from all the matches where team B wins, he can determine the most likely way a game that ends with a victory for team B will develop.

Despite the difficulties, the team did establish a path of desire,

“Before we started this experiment,” Murch said, ” I asked everybody in the lab what they thought the most likely path between quantum states would be. I drew a couple of options on the board: a straight line, a convex curve, a concave curve, a squiggly line . . . I took a poll, and we all guessed different options. Here we were, a bunch of quantum experts, and we had absolutely no intuition about the most likely path.”

Andrew N. Jordan of the University of Rochester and his students Areeya Chantasri and Justin Dressel inspired the study by devising a theory to predict the likely path. Their theory predicted that a convex curve Murch had drawn on the white board would be the correct path.

“When we looked at the data, we saw that the theorists were right. Our very clever collaborators had devised a ‘principle of least action’ that works in the quantum case,” Murch said.

They had found the quantum system’s line of desire mathematically and by calculation before many microwave photons trampled out the path in Murch’s lab.

Here’s an illustrated quantum path of desire’s experimental data,

Caption: A path of desire emerging from many trajectories between two points in quantum state space. Credit: Murch Lab/WUSTL

Caption: A path of desire emerging from many trajectories between two points in quantum state space.
Credit: Murch Lab/WUSTL

The University of Rochester, a collaborating institution on this research, issued a July 30, 2014 news release (also on EurekAlert) featuring this poetic allusion from one of the theorists,

Jordan [Andrew N. Jordan, professor of physics at the University of Rochester] compares the experiment to watching butterflies make their way one by one from a cage to nearby trees. “Each butterfly’s path is like a single run of the experiment,” said Jordan. “They are all starting from the same cage, the initial state, and ending in one of the trees, each being a different end state.” By watching the quantum equivalent of a million butterflies make the journey from cage to tree, the researchers were in effect able to predict the most likely path a butterfly took by observing which tree it landed on (known as post-selection in quantum physics measurements), despite the presence of a wind, or any disturbance that affects how it flies (which is similar to the effect measuring has on the system).

The theorists provided this illustration of the theory,

Caption: Measurement data showing the comparison with the 'most likely' path (in red) between initial and final quantum states (black dots). The measurements are shown on a representation referred to as a Bloch sphere. Credit: Areeya Chantasri Courtesy: University of Rochester

Caption: Measurement data showing the comparison with the ‘most likely’ path (in red) between initial and final quantum states (black dots). The measurements are shown on a representation referred to as a Bloch sphere.
Credit: Areeya Chantasri Courtesy: University of Rochester

The research study can be found here,

Mapping the optimal route between two quantum states by S. J. Weber, A. Chantasri, J. Dressel, A. N. Jordan, K. W. Murch & I. Siddiqi. Nature 511, 570–573 (31 July 2014) doi:10.1038/nature13559 Published online 30 July 2014

This paper is behind a paywall but there is a free preview via ReadCube Access.

Light-harvesting antennas from laboratory constructs that are like ‘sun sponges’

As we know, plants are the best at harvesting energy from the sun but there are some scientists at Washington University in Saint Louis (Missouri, US) who claim they’ve developed a complex that’s better. From an Aug. 21, 2013 news item on Nanowerk,

In diagrams it looks like a confection of self-curling ribbon with bits of bling hung off the ribbon here and there. In fact it is a carefully designed ring of proteins with attached pigments that self-assembles into a structure that soaks up sunlight.

The scientists who made it call it a testbed, or platform for rapid prototyping of light-harvesting antennas–structures found in plants and photosynthesizing bacteria–that take the first step in converting sunlight into usable energy. The antennas consist of protein scaffolding that holds pigment molecules in ideal positions to capture and transfer the sun’s energy. The number and variety of the pigment molecules determines how much of the sun’s energy the antennas can grab and dump into an energy trap.

The Aug. 21, 2013 Washington University in Saint Louis news release by Diana Lutz, which originated the news item, provides more detail,

In the August 6, 2013 online edition of Chemical Science, a new publication of the Royal Society of Chemistry, the scientists describe two prototype antennas they’ve built on their testbed. One incorporated synthetic dyes called Oregon Green and Rhodamine Red and the other combined Oregon Green and a synthetic version of the bacterial pigment bacteriochlorophyll that absorbs light in the near-infrared region of the spectrum.

Both designs soak up more of the sun’s spectrum than native antennas in purple bacteria that provided the inspiration and some components for the testbed. The prototypes were also far easier to assemble than synthetic antennas made entirely from scratch. In this sense they offer the best of both worlds, combining human synthetic ingenuity with the repertoire of robust chemical machinery selected by evolution.

One day a two-part system (consisting of an antenna and a second unit called a reaction center) might serve as a miniature power outlet into which photochemical modules could be plugged. The sun’s energy could then be used directly to split water, generate electricity, or build molecular-scale devices.

The news release goes on to discuss the pigments used in the project and the complex’s self-assembly.

For those who want all the detail, here’s a link to and a citation for the published paper,

Integration of multiple chromophores with native photosynthetic antennas to enhance solar energy capture and delivery by Michelle A. Harris, Pamela S. Parkes-Loach, Joseph W. Springer, Jianbing Jiang, Elizabeth C. Martin, Pu Qian, Jieying Jiao, Dariusz M. Niedzwiedzki, Christine Kirmaier, John D. Olsen, David F. Bocian, Dewey Holten, C. Neil Hunter, Jonathan S. Lindsey and Paul A. Loach.  Chem. Sci., 2013, Advance Article DOI: 10.1039/C3SC51518D First published online 06 Aug 2013

I believe this is behind a paywall.