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A composite window into human history

Better integration of ancient DNA studies with archaeology promises deeper insights.

DNA testing alone of ancient human remains can’t resolve questions about past societies.

It’s time for geneticists and archaeologists to collaborate more fully in the face of ever greater advancements in ancient DNA research, according to SMU archaeologist David J. Meltzer and his colleagues in a recent article in the scientific journal Science.

The authors write in “A composite window into human history” that over the past decade, DNA testing of ancient human remains has become a valuable tool for studying and understanding past human population histories.

Most notably, for example, is how sequencing of ancient genomes resolved the dispute over our species’ evolutionary relationship with Neanderthals, the authors point out.

Even so, the authors caution that collaboration with archaeologists is key for scientific accuracy as well as navigating ethical implications.

Archaeologists know from the study of artifacts that it isn’t always the case that people who share material culture traits were likewise part of the same biological population.

“One can have similar traits without relatedness, and relatedness without similarity in traits,” say the authors in the article.

At the same time, where there is biological relatedness, cultural relatedness can’t be assumed, nor can language groups indicate that biological populations, material assemblages or even social units are related.

“Geneticists are often keen to use ancient DNA to understand the causes and mechanisms of demographic and cultural change,” the authors write. “But archaeologists long ago abandoned the idea that migrations or encounters between populations are a necessary or sufficient explanation of cultural change.”

The authors make the point that understanding population movements requires broad investigation of many factors, including environmental and social contexts, timing and logistics, how new resources and landscapes were managed, and the transfer of cultural knowledge.

“Hence, it requires evidence for archaeology, paleoecology and other fields to supplement and complement ancient DNA data,” the authors write. “And that entails effective collaboration, one that goes beyond archaeologists serving as passive sample providers.”

Meltzer is Henderson-Morrison Professor of Prehistory in the SMU Department of Anthropology in Dedman College. As a scientist who studies how people first came to inhabit North America, Meltzer in 2009 was elected a member of the National Academy of Sciences in recognition for his achievements in original scientific research. In 2013 he was elected to the American Academy of Arts and Sciences.

Co-authors on the perspective piece with Meltzer were Niels N. Johannsen, Aarhus University, Denmark; Greger Larson, University of Oxford; and Marc Vader Linden, University College London.

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The New York Times: Something Strange in Usain Bolt’s Stride

Bolt is the fastest sprinter ever in spite of — or because of? — an uneven stride that upends conventional wisdom.

The New York Times reporter Jeré Longman covered the research of SMU biomechanics expert Peter Weyand and his colleagues Andrew Udofa and Laurence Ryan for a story about Usain Bolt’s apparent asymmetrical running stride.

The article, “Something Strange in Usain Bolt’s Stride,” published July 20, 2017.

The researchers in the SMU Locomotor Performance Laboratory reported in June that world champion sprinter Usain Bolt may have an asymmetrical running gait. While not noticeable to the naked eye, Bolt’s potential asymmetry emerged after the researchers dissected race video to assess his pattern of ground-force application — literally how hard and fast each foot hits the ground. To do so they measured the “impulse” for each foot.

Biomechanics researcher Udofa presented the findings at the 35th International Conference on Biomechanics in Sport in Cologne, Germany. His presentation, “Ground Reaction Forces During Competitive Track Events: A Motion Based Assessment Method,” was delivered June 18.

The analysis thus far suggests that Bolt’s mechanics may vary between his left leg to his right. The existence of an unexpected and potentially significant asymmetry in the fastest human runner ever would help scientists better understand the basis of maximal running speeds. Running experts generally assume asymmetry impairs performance and slows runners down.

Udofa has said the observations raise the immediate scientific question of whether a lack of symmetry represents a personal mechanical optimization that makes Bolt the fastest sprinter ever or exists for reasons yet to be identified.

Weyand, who is Glenn Simmons Professor of Applied Physiology and professor of biomechanics in the Department of Applied Physiology & Wellness in SMU’s Annette Caldwell Simmons School of Education & Human Development, is director of the Locomotor Lab.

An expert on human locomotion and the mechanics of running, Weyand has been widely interviewed about the running controversy surrounding double-amputee South African sprinter Oscar Pistorius. Weyand co-led a team of scientists who are experts in biomechanics and physiology in conducting experiments on Pistorius and the mechanics of his racing ability.

For his most recently published research, Weyand was part of a team that developed a concise approach to understanding the mechanics of human running. The research has immediate application for running performance, injury prevention, rehab and the individualized design of running shoes, orthotics and prostheses. The work integrates classic physics and human anatomy to link the motion of individual runners to their patterns of force application on the ground — during jogging, sprinting and at all speeds in between.

They described the two-mass model earlier this year in the Journal of Experimental Biology in their article, “A general relationship links gait mechanics and running ground reaction forces.” It’s available at bitly, http://bit.ly/2jKUCSq.

The New York Times subscribers or readers with remaining limited free access can read the full story.

EXCERPT:

By Jeré Longman
The New York Times

DALLAS — Usain Bolt of Jamaica appeared on a video screen in a white singlet and black tights, sprinting in slow motion through the final half of a 100-meter race. Each stride covered nine feet, his upper body moving up and down almost imperceptibly, his feet striking the track and rising so rapidly that his heels did not touch the ground.

Bolt is the fastest sprinter in history, the world-record holder at 100 and 200 meters and the only person to win both events at three Olympics. Yet as he approaches his 31st birthday and retirement this summer, scientists are still trying to fully understand how Bolt achieved his unprecedented speed.

Last month, researchers here at Southern Methodist University, among the leading experts on the biomechanics of sprinting, said they found something unexpected during video examination of Bolt’s stride: His right leg appears to strike the track with about 13 percent more peak force than his left leg. And with each stride, his left leg remains on the ground about 14 percent longer than his right leg.

This runs counter to conventional wisdom, based on limited science, that an uneven stride tends to slow a runner down.

So the research team at S.M.U.’s Locomotor Performance Laboratory is considering a number of questions as Bolt prepares for what he said would be his final performances at a major international competition — the 100 meters and 4×100-meter relay next month at the world track and field championships in London.

Among those questions: Does evenness of stride matter for speed? Did Bolt optimize this irregularity to become the fastest human? Or, with a more balanced stride during his prime, could he have run even faster than 9.58 seconds at 100 meters and 19.19 seconds at 200 meters?

“That’s the million-dollar question,” said Peter Weyand, director of the S.M.U. lab.

The S.M.U. study of Bolt, led by Andrew Udofa, a doctoral researcher, is not yet complete. And the effect of asymmetrical strides on speed is still not well understood. But rather than being detrimental for Bolt, the consequences of an uneven stride may actually be beneficial, Weyand said.

It could be that Bolt has naturally settled into his stride to accommodate the effects of scoliosis. The condition curved his spine to the right and made his right leg half an inch shorter than his left, according to his autobiography.

Initial findings from the study were presented last month at an international conference on biomechanics in Cologne, Germany. Most elite sprinters have relatively even strides, but not all. The extent of Bolt’s variability appears to be unusual, Weyand said.

“Our working idea is that he’s probably optimized his speed, and that asymmetry reflects that,” Weyand said. “In other words, correcting his asymmetry would not speed him up and might even slow him down. If he were to run symmetrically, it could be an unnatural gait for him.”

Antti Mero, an exercise physiologist at the University of Jyvaskyla in Finland, who has researched Bolt’s fastest races, said he was intrigued by the S.M.U. findings.

The New York Times subscribers or readers with remaining limited free access can read the full story.

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People ForWords team named semifinalist in national XPrize competition

SMU’s puzzle-solving smartphone app selected as one of eight to move to next round in $7M Barbara Bush Foundation Adult Literacy XPRIZE competition

For Corey Clark, deputy director for research in the SMU Guildhall game development program, adult literacy became a personal challenge the moment he learned of its scope. “There are about 600,000 adults in Dallas who have less than a third-grade reading level,” he says. “If we could help 10 percent of those people, that’s 60,000 people who could learn to read proficiently. That makes a difference in a lot of people’s lives.”

This challenge is at the heart of a partnership between Southern Methodist University and Literacy Instruction for Texas (LIFT), and their work has been recognized with a semifinalist position in the $7 million Barbara Bush Foundation Adult Literacy XPRIZE presented by Dollar General Literacy Foundation competition.

The team, People ForWords, includes collaborators from SMU Guildhall, SMU Simmons School of Education and Human Development, and LIFT. People ForWords is one of eight teams chosen for the semifinals out of 109 entrants, and the only Texas team to make the cut.

In this global competition, teams develop mobile applications, compatible with smart phone devices, that have the potential to increase literacy skills among adult learners. The solutions discovered through the applications will help reveal and overcome roadblocks in improving adult literacy through providing access, retention, and a scalable product to the public.

As development lead of People ForWords, Clark recruited a cadre of Guildhall-trained artists, programmers and producers via the program’s alumni career portal. The development team came together in March 2016. By October, they had created a beta version of Codex: The Lost Words of Atlantis.

As participants in a globe-trotting adventure, English-language learners play as enterprising archaeologists and work to decipher the forgotten language of a lost civilization. As the players solve the puzzles of the Atlantean runes, audible prompts for each letter and sound help them learn the look and feel of written English<, developing and strengthening their own reading skills. Developed for English- and Spanish-speaking adults, but safe for all ages, the game also provides history lessons as it visits real locations around the world. Needs of adult literacy learners very different from other gamers
Codex: The Lost Words of Atlantis supports English literacy learners in both English and Spanish. Egypt is the first destination in a planned five-region journey across the globe; in future versions, People ForWords plans to develop additional regions with new gameplay, new characters, and new literacy skills.

An important step in the game design process came with playtesting at LIFT Academy and Dallas’ Jubilee Park community center — where the designers could reach their game’s target audience. They quickly figured out that the needs of adult literacy learners were very different from those of other gamers.

“This was the first time some participants had used a desktop computer,” Clark says. “How do you make a game that’s fun and interactive, yet simple and intuitive enough to be a first experience with technology?”

To find out, Clark collected and analyzed data on game elements such as how long players stuck with a task, how many times they repeated moves, how quickly they progressed, and whether performing the game actions translated into the desired learning outcomes. “First, games have to be fun,” he says. “From story to characters, you want to engage people enough to play over and over again. And this happens to be the exact same process that reinforces learning.”

And as Clark points out, at its core, every game is about learning. “Whether it’s a map, a system or a skill, you learn something new with every move you make,” he says. “And games are safe environments to do that, because they allow you to fail in ways that aren’t overwhelming. They let you keep trying until you succeed.”

Illiteracy plays a factor in poverty
In North Texas, the XPRIZE is more than a competition. According to LIFT, one in five adults in North Texas cannot read, a key factor in poverty. Dallas has the fourth highest concentration of poverty in the nation, with a 41 percent increase from 2000 to 2014.

“This is a dedicated effort by our team to tackle the growing issue of low literacy and poverty in our communities,” according to a People ForWords statement. “Each organization involved in the collaboration brings their expertise to the competition: knowledge in education, adult literacy, and game development. Together these skills have allowed our team to build a functional, fun application that helps improve adult literacy through sharpening reading and writing skills.”

“The faculty at SMU Guildhall bridge the gap between serious academic research and commercial video games,” says Guildhall Director Gary Brubaker. “This environment has allowed our research and development team to yield a product for the XPRIZE adult literacy competition that brings together the creative, entertaining nature of games with the impactful literacy lessons being taught.”

Research plays a large role at SMU Guildhall. Not only are large-scale research endeavors such as the XPRIZE taking place year-round, but research is also incorporated into the curriculum. Independent studies such as student theses explore a vast range of interests within video game development and its global implications and uses. Both current students and alumni are able to put their analytical and research skills to good use by participating as funded research assistants on a myriad of Guildhall’s “games for good” projects.

“Our students greatly benefit from breaking ground with new gaming technologies and expanding their usage into other fields,” said Elizabeth Stringer, Deputy Director of Academics at SMU Guildhall. “Many of our graduates continue to use their game development skills to aid society and further causes for which they are passionate.”

Testing of the eight semifinalists’ literacy software begins in mid-July with 12,000 adults who read English at a third grade level or lower. Selection of up to five finalists will depend on results of post-game testing to evaluate literacy gains among test subjects. Finalists will be named in May 2018, and the winner will be selected in 2019. — Kathleen Tibbetts, SMU

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SMU and LIFT team named one of eight semifinalists for $7M Barbara Bush Foundation Adult Literacy XPrize

SMU’s “Codex: Lost Words of Atlantis” adult literacy video game is puzzle-solving smartphone game app to help adults develop literacy skills

The SMU and Literacy Instruction for Texas (LIFT) team was named today one of eight semifinalists in the $7 million Barbara Bush Foundation Adult Literacy XPRIZE presented by Dollar General Literacy Foundation.

The XPRIZE is a global competition that challenges teams to develop mobile applications designed to increase literacy skills in adult learners.

SMU participants include education experts from SMU’s Simmons School of Education and Human Development, along with video game developers from SMU Guildhall — a graduate school video game development program. They are working with literacy experts from LIFT to design an engaging, puzzle-solving smartphone app to help adults develop literacy skills. Students from LIFT help test the game.

The SMU and LIFT team, People ForWords, is one of 109 teams who entered the competition in 2016. The team developed “Codex: Lost Words of Atlantis.”

In the game, players become archeologists hunting for relics from the imagined once-great civilization of Atlantis. By deciphering the forgotten language of Atlantis, players develop and strengthen their own reading skills. The game targets English- and Spanish-speaking adults.

Students at LIFT, a North Texas nonprofit adult literacy provider, have tested and provided key insights for the game during its development. According to LIFT, one in five adults in North Texas cannot read, a key factor in poverty. Dallas has the fourth highest concentration of poverty in the nation, with a 41 percent increase from 2000 to 2014. LIFT is one of the largest and most widely respected adult basic education programs in Texas and offers adult basic literacy, GED preparation and English as a Second Language programs with the goal of workforce empowerment.

Testing of the eight semi-finalists’ literacy software begins in mid-July with 12,000 adults who read English at a third grade level or lower. Selection of up to five finalists will depend on results of post-game testing to evaluate literacy gains among test subjects. Finalists will be named in May of 2018 and the winner will be named in 2019. — Nancy George, SMU

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Better than Star Wars: Chemistry discovery yields 3-D table-top objects crafted from light

Photoswitch chemistry allows construction of light shapes into structures that have volume and are viewable from 360 degrees, making them useful for biomedical imaging, teaching, engineering, TV, movies, video games and more

A scientist’s dream of 3-D projections like those he saw years ago in a Star Wars movie has led to new technology for making animated 3-D table-top objects by structuring light.

The new technology uses photoswitch molecules to bring to life 3-D light structures that are viewable from 360 degrees, says chemist Alexander Lippert, Southern Methodist University, Dallas, who led the research.

The economical method for shaping light into an infinite number of volumetric objects would be useful in a variety of fields, from biomedical imaging, education and engineering, to TV, movies, video games and more.

“Our idea was to use chemistry and special photoswitch molecules to make a 3-D display that delivers a 360-degree view,” said Lippert, an assistant professor in the SMU Department of Chemistry. “It’s not a hologram, it’s really three-dimensionally structured light.”

Key to the technology is a molecule that switches between non-fluorescent and fluorescent in reaction to the presence or absence of ultraviolet light.

The new technology is not a hologram, and differs from 3-D movies or 3-D computer design. Those are flat displays that use binocular disparity or linear perspective to make objects appear three-dimensional when in fact they only have height and width and lack a true volume profile.

“When you see a 3-D movie, for example, it’s tricking your brain to see 3-D by presenting two different images to each eye,” Lippert said. “Our display is not tricking your brain — we’ve used chemistry to structure light in three actual dimensions, so no tricks, just a real three-dimensional light structure. We call it a 3-D digital light photoactivatable dye display, or 3-D Light Pad for short, and it’s much more like what we see in real life.”

At the heart of the SMU 3-D Light Pad technology is a “photoswitch” molecule, which can switch from colorless to fluorescent when shined with a beam of ultraviolet light.

The researchers discovered a chemical innovation for tuning the photoswitch molecule’s rate of thermal fading — its on-off switch — by adding to it the chemical amine base triethylamine.

Now the sky is the limit for the new SMU 3-D Light Pad technology, given the many possible uses, said Lippert, an expert in fluorescence and chemiluminescence — using chemistry to explore the interaction between light and matter.

For example, conference calls could feel more like face-to-face meetings with volumetric 3-D images projected onto chairs. Construction and manufacturing projects could benefit from rendering them first in 3-D to observe and discuss real-time spatial information. For the military, uses could include tactical 3-D replications of battlefields on land, in the air, under water or even in space.

Volumetric 3-D could also benefit the medical field.

“With real 3-D results of an MRI, radiologists could more readily recognize abnormalities such as cancer,” Lippert said. “I think it would have a significant impact on human health because an actual 3-D image can deliver more information.”

Unlike 3-D printing, volumetric 3-D structured light is easily animated and altered to accommodate a change in design. Also, multiple people can simultaneously view various sides of volumetric display, conceivably making amusement parks, advertising, 3-D movies and 3-D games more lifelike, visually compelling and entertaining.

Lippert and his team in The Lippert Research Group report on the new technology and the discovery that made it possible in the article “A volumetric three-dimensional digital light photoactivatable dye display,” published in the journal Nature Communications.

Some of the 3-D images generated with the new technology are viewable in this video.

Co-authors are Shreya K. Patel, lead author, and Jian Cao, both students in the SMU Department of Chemistry.

Genesis of an idea — cinematic inspiration
The idea to shape light into volumetric animated 3-D objects came from Lippert’s childhood fascination with the movie “Star Wars.” Specifically he was inspired when R2-D2 projects a hologram of Princess Leia. Lippert’s interest continued with the holodeck in “Star Trek: The Next Generation.”

“As a kid I kept trying to think of a way to invent this,” Lippert said. “Then once I got a background in chemistry molecules that interact with light, and an understanding of photoswitches, it finally dawned on me that I could take two beams of light and use chemistry to manipulate the emission of light.”

Key to the new technology was discovering how to turn the chemical photoswitch off and on instantly, and generating light emissions from the intersection of two different light beams in a solution of the photoactivatable dye, he said.

SMU graduate student in chemistry Jian Cao hypothesized the activated photoswitch would turn off quickly by adding the base. He was right.

“The chemical innovation was our discovery that by adding one drop of triethylamine, we could tune the rate of thermal fading so that it instantly goes from a pink solution to a clear solution,” Lippert said. “Without a base, the activation with UV light takes minutes to hours to fade back and turn off, which is a problem if you’re trying to make an image. We wanted the rate of reaction with UV light to be very fast, making it switch on. We also wanted the off-rate to be very fast so the image doesn’t bleed.”

SMU 3-D Light Pad
In choosing among various photoswitch dyes, the researchers settled on N-phenyl spirolactam rhodamines. That particular class of rhodamine dyes was first described in the late 1970s and made use of by Stanford University’s Nobel prize-winning W.E. Moerner.

The dye absorbs light within the visible region, making it appropriate to fluoresce light. Shining it with UV radiation, specifically, triggers a photochemical reaction and forces it to open up and become fluorescent.

Turning off the UV light beam shuts down fluorescence, diminishes light scattering, and makes the reaction reversible — ideal for creating an animated 3-D image that turns on and off.

“Adding triethylamine to switch it off and on quickly was a key chemical discovery that we made,” Lippert said.

To produce a viewable image they still needed a setup to structure the light.

Structuring light in a table-top display
The researchers started with a custom-built, table-top, quartz glass imaging chamber 50 millimeters by 50 millimeters by 50 millimeters to house the photoswitch and to capture light.

Inside they deployed a liquid solvent, dichloromethane, as the matrix in which to dissolve the N-phenyl spirolactam rhodamine, the solid, white crystalline photoswitch dye.

Next they projected patterns into the chamber to structure light in two dimensions. They used an off-the-shelf Digital Light Processing (DLP) projector purchased at Best Buy for beaming visible light.

The DLP projector, which reflects visible light via an array of microscopically tiny mirrors on a semiconductor chip, projected a beam of green light in the shape of a square. For UV light, the researchers shined a series of UV light bars from a specially made 385-nanometer Light-Emitting Diode projector from the opposite side.

Where the light intersected and mixed in the chamber, there was displayed a pattern of two-dimensional squares stacked across the chamber. Optimized filter sets eliminated blue background light and allowed only red light to pass.

To get a static 3-D image, they patterned the light in both directions, with a triangle from the UV and a green triangle from the visible, yielding a pyramid at the intersection, Lippert said.

From there, one of the first animated 3-D images the researchers created was the SMU mascot, Peruna, a racing mustang.

“For Peruna — real-time 3-D animation — SMU undergraduate student Shreya Patel found a way to beam a UV light bar and keep it steady, then project with the green light a movie of the mustang running,” Lippert said.

So long Renaissance
Today’s 3-D images date to the Italian Renaissance and its leading architect and engineer.

“Brunelleschi during his work on the Baptistery of St. John was the first to use the mathematical representation of linear perspective that we now call 3-D. This is how artists used visual tricks to make a 2-D picture look 3-D,” Lippert said. “Parallel lines converge at a vanishing point and give a strong sense of 3-D. It’s a useful trick but it’s striking we’re still using a 500-year-old technique to display 3-D information.”

The SMU 3-D Light Pad technology, patented in 2016, has a number of advantages over contemporary attempts by others to create a volumetric display but that haven’t emerged as commercially viable.

Some of those have been bulky or difficult to align, while others use expensive rare earth metals, or rely on high-powered lasers that are both expensive and somewhat dangerous.

The SMU 3-D Light Pad uses lower light powers, which are not only cheaper but safer. The matrix for the display is also economical, and there are no moving parts to fabricate, maintain or break down.

Lippert and his team fabricated the SMU 3-D Light Pad for under $5,000 through a grant from the SMU University Research Council.

“For a really modest investment we’ve done something that can compete with more expensive $100,000 systems,” Lippert said. “We think we can optimize this and get it down to a couple thousand dollars or even lower.”

Next Gen: SMU 3-D Light Pad 2.0
The resolution quality of a 2-D digital photograph is stated in pixels. The more pixels, the sharper and higher-quality the image. Similarly, 3-D objects are measured in voxels — a pixel but with volume. The current 3-D Light Pad can generate more than 183,000 voxels, and simply scaling the volume size should increase the number of voxels into the millions – equal to the number of mirrors in the DLP micromirror arrays.

For their display, the SMU researchers wanted the highest resolution possible, measured in terms of the minimum spacing between any two of the bars. They achieved 200 microns, which compares favorably to 100 microns for a standard TV display or 200 microns for a projector.

The goal now is to move away from a liquid vat of solvent for the display to a solid cube table display. Optical polymer, for example, would weigh about the same as a TV set. Lippert also toys with the idea of an aerosol display.

The researchers hope to expand from a monochrome red image to true color, based on mixing red, green and blue light. They are working to optimize the optics, graphics engine, lenses, projector technology and photoswitch molecules.

“I think it’s a very fascinating area. Everything we see — all the color we see — arises from the interaction of light with matter,” Lippert said. “The molecules in an object are absorbing a wavelength of light and we see all the rest that’s reflected. So when we see blue, it’s because the object is absorbing all the red light. What’s more, it is actually photoswitch molecules in our eyes that start the process of translating different wavelengths of light into the conscious experience of color. That’s the fundamental chemistry and it builds our entire visual world. Being immersed in chemistry every day — that’s the filter I’m seeing everything through.”

The SMU discovery and new technology, Lippert said, speak to the power of encouraging young children.

“They’re not going to solve all the world’s problems when they’re seven years old,” he said. “But ideas get seeded and if they get nurtured as children grow up they can achieve things we never thought possible.” — Margaret Allen, SMU