Aulden Foltz – The Stanford Daily https://stanforddaily.com Breaking news from the Farm since 1892 Tue, 10 Oct 2017 06:06:24 +0000 en-US hourly 1 https://wordpress.org/?v=6.4.3 https://stanforddaily.com/wp-content/uploads/2019/03/cropped-DailyIcon-CardinalRed.png?w=32 Aulden Foltz – The Stanford Daily https://stanforddaily.com 32 32 204779320 Classy Classes: Stanford Online course teaches danger of nuclear terrorism https://stanforddaily.com/2017/10/09/classy-classes-stanford-online-course-teaches-danger-of-nuclear-terrorism/ https://stanforddaily.com/2017/10/09/classy-classes-stanford-online-course-teaches-danger-of-nuclear-terrorism/#respond Tue, 10 Oct 2017 06:06:24 +0000 https://stanforddaily.com/?p=1130839 On Oct. 17, Stanford Online will release a new massive open online course (MOOC) entitled “The Threat of Nuclear Terrorism” to educate the public on the dangers of nuclear weapons.

The post Classy Classes: Stanford Online course teaches danger of nuclear terrorism appeared first on The Stanford Daily.

]]>
On Oct. 17, Stanford Online will release a new massive open online course (MOOC) entitled “The Threat of Nuclear Terrorism” to educate the public on the dangers of nuclear weapons. The MOOC is a part of the William J. Perry Project, an initiative founded by William J. Perry, a professor emeritus at Stanford’s Freeman Spogli Institute for International Studies and former U.S. Secretary of Defense.

The new class features 12 course staff ranging from former Los Alamos physicists to former career covert CIA operations officers. According to the course website, the interdisciplinary class hopes to attract a variety of students and asks for no prerequisites other than “curiosity and a passion for learning.” Robin Perry, director of the Perry Project, said through its used of a mixed staff, the MOOC’s creators hope to stress that there are many ways to contribute to nuclear reform— even in fields that seem wholly unrelated — so that students can learn how to take action in ways that suit their strengths and interests.

This class isn’t the first MOOC developed by the Perry Project. Last year, the group released “Living At the Nuclear Brink: Yesterday and Today,” a 10-week online adaptation of Perry’s Stanford lecture course.

“We wanted to reach more than the few-hundred people that could attend a Stanford class and worked with the [Vice Provost for Teaching and Learning] to create an online course that could be openly available to a much broader public,” Robin Perry said.

Classy Classes: Stanford Online course teaches danger of nuclear terrorism
A new MOOC focuses on nuclear technology and its threats (Courtesy of Lisa Perry).

The online platform also allows people to participate internationally. The class is free, so all a potential student needs is a computer and an Internet connection.

“This is a problem that isn’t going to be solved by the United States alone without working internationally to understand what the issues are,” Robin Perry said.

In addition to shortening the course time to five weeks and focusing it more on the topic of nuclear terrorism, the Perry Project worked with Stanford students to cater to an online platform. David Perry, education director of the Perry Project, said the course’s biggest change is a shift from a lecture to a discussion-based setup. In 10-minute segments, Professor William Perry will discuss a topic with one to three other experts. Some segments also feature Stanford students sitting in and asking questions.

“We tried to make a more classroom feel,” David Perry said. “You’re a student watching this online, but here are students, almost like a model for you, asking questions that you might have.”

Federico Derby ’19, an undergraduate student at Stanford who helped develop the new course, said that because nuclear politics and threat have been so heavily in the news lately, the class has several features to keep students up to date with curt events, including a “Nukes in the News” section and a live feed of Professor Perry’s Twitter account. Through these features, the course team hopes to add topicality to the class and give students updated information even though the content of the class itself cannot be altered to respond to the most current news.

Lisa Perry, digital communication director of the Perry Project, said the project is now working on its next course. Although this course is not yet named, it aims to cover possible ways nations could get into a nuclear war by accident.

“The point is not to just scare people,” Lisa Perry said. “It’s to give people real, tangible knowledge … to analyze what are the problems, where are the gaps in our security and what can be done to fill in those gaps and work to make not just the U.S. safer but the whole world safer from this risk.”

 

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Classy Classes: Stanford Online course teaches danger of nuclear terrorism appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2017/10/09/classy-classes-stanford-online-course-teaches-danger-of-nuclear-terrorism/feed/ 0 1130839
Researchers develop controllable gene therapy, make rats glow https://stanforddaily.com/2017/03/06/researchers-develop-controllable-gene-therapy-make-rats-glow/ https://stanforddaily.com/2017/03/06/researchers-develop-controllable-gene-therapy-make-rats-glow/#respond Mon, 06 Mar 2017 08:05:11 +0000 https://stanforddaily.com/?p=1124440 Researchers at Stanford have made mice glow using a new gene therapy technique, showing that the process can work on living animals. It has a variety of applications to many central problems in biology and medicine, including immunology and cancer research.

The post Researchers develop controllable gene therapy, make rats glow appeared first on The Stanford Daily.

]]>
Researchers at Stanford have made mice glow using a new gene therapy technique, showing that the process can work on living animals.

Researchers develop controllable gene therapy, make rats glow
(Courtesy of Linda Cicero).

Named charge-altering releasable transporters (CARTs), the new technique allows researchers to control how much of a desired protein is expressed inside a cell, and how long the gene therapy lasts. It has a variety of applications to many central problems in biology and medicine, including immunology and cancer research.

Previous gene therapy techniques have relied on permanently changing the DNA within a cell. Colin McKinlay, a third-year Ph.D. student in chemistry and co-lead author on the paper, explains that CARTs take advantage of messenger RNA (mRNA) rather than DNA to give researchers greater control over the process.

“By introducing mRNA into the cells, you can basically tell those cells to produce any given protein,” McKinlay said. “It’s more of a temporary effect and you have a lot more control over doing that.”

However, mRNA molecules are too large to enter the cell on their own. CARTs are able to latch onto the mRNA, cross the cell membrane, release the mRNA into the cell and quickly degrade into small molecules called metabolites naturally recognizable by the cell. After that, the cell takes over, translating the mRNA into the desired proteins.

“It’s kind of like the cell already has all of the ingredients,” McKinlay said. “We’re just providing the recipe, and the cell then puts all the pieces together.”

One possible application of the new gene therapy technique is creating new types of vaccinations. Typical vaccination techniques involve introducing a dead or weakened antigen, bacteria and foreign substances such as viruses into the cell, which the body then uses to create antibodies. CARTs could allow researchers to temporarily introduce specific proteins from the antigens into cells in order to specify targets for the immune system that are less sensitive to antigen mutation.

CARTs also have the potential to be used as a research tool. As transient polycations, CARTs allow proteins to be introduced and manufactured by the cell in controlled quantities and for a controlled amount of time, making them a valuable resource for studying signaling cascades and other biological phenomena.

The team behind CARTs primarily consists of Wender and Waymouth Group researchers, and also draws on collaborators across Stanford. As the team begins to test the potential applications of CARTs, more researchers are expected to come on board.

In their recent paper on bioluminescent proteins in mice, researchers worked with Christopher Contag, a professor of pediatrics at Stanford, to show that the technique can work in vivo in animal models, bringing the team a step closer to using it in humans.

“We couldn’t have done it if we were stuck just within the confines of the chemistry department,” said Jessica Vargas ’16, a former Ph.D. student in the Wender Lab and a co-lead author on the paper. “The work in general is a true testament to Stanford’s collaborative spirit.”

 

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Researchers develop controllable gene therapy, make rats glow appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2017/03/06/researchers-develop-controllable-gene-therapy-make-rats-glow/feed/ 0 1124440
Bacterial discovery raises questions on plant evolution https://stanforddaily.com/2017/02/13/bacterial-discovery-raises-questions-on-plant-evolution/ https://stanforddaily.com/2017/02/13/bacterial-discovery-raises-questions-on-plant-evolution/#respond Mon, 13 Feb 2017 21:45:10 +0000 https://stanforddaily.com/?p=1122919 Researchers at the Welander Lab discovered bacteria that produce a fatty molecule thought only to exist in flowering plants.

The post Bacterial discovery raises questions on plant evolution appeared first on The Stanford Daily.

]]>
Researchers at the Welander Lab discovered bacteria that produce a fatty molecule thought only to exist in flowering plants, forcing scientists to re-evaluate the molecule as an indicator of past plant life and revealing new paths to synthesize these molecules.

The Welander Lab uses microbiology genomics to address questions in the geosciences. It deals with molecules called biomarkers, which are molecular degradation products that indicate the past presence of certain lifeforms.

Co-author of the study, Paula Welander, a geobiologist at Stanford’s School of Earth, Energy and Environmental Sciences, said that this breakthrough addresses open questions on genetic history.

“One of the big problems that we’ve had in this biomarker world is that we’re not always sure if we’ve detected all the potential organisms that could make a potential lipid,” Welander said. “How do you correlate the presence of this one molecule to an organism and what does that tell you if you see it being produced in an organism today?”

The biomarker in question is isoarborinol, a fatty molecule found only in flowering plants before this study. Previously, this biomarker produced incongruities when found in fossil records dating from before the evolution of flowering plants. The discovery of an isoarborinol-like molecule from bacteria explains some of these incongruities.

The project initially started as a study of sterol, a different biomarker thought to only be produced by eukaryotes. In an attempt to find prokaryotic sources of sterol, Welander lab researchers looked in genetic databases for organisms that produced cyclase proteins, which are involved in the first step of producing sterols. They discovered cyclase protein in a marine bacterium called Eudoraea adriatica and detected an unidentified molecule along with the sterols.

After the discovery, Welander consulted with her postdoctoral advisor, Roger Summons. Summons is a professor of geobiology at MIT who was on sabbatical at Stanford.

“Roger is a walking spectral library,” Welander said. “He’s studied these molecules for 20 to 30 years and he knows a lot… He’d never seen [this molecule]. He didn’t have a record of it.”

After collaborating with José-Luis Giner, an associate professor of chemistry at the State University of New York and a co-author of this paper, the team realized that the molecule belonged to a class of molecules called triterpenols. Theirs was the first triterpenol discovery in over 30 years.

The discovery of this molecule in bacteria and of the proteins that produce it introduce molecular mechanisms of production that differ from those in flowering plants. Connecting this molecular product with new proteins allows the Welander lab to study whether different organisms whose genes encode for the protein also produce isoarborinol-like molecules.

“By using the genes to identify these molecules, [we] can find novel things that we hadn’t been looking for before,” said Welander.

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Bacterial discovery raises questions on plant evolution appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2017/02/13/bacterial-discovery-raises-questions-on-plant-evolution/feed/ 0 1122919
Researchers test nanoparticle sensors in microscopic worms https://stanforddaily.com/2017/01/22/researchers-test-nanoparticle-sensors-in-microscopic-worms/ https://stanforddaily.com/2017/01/22/researchers-test-nanoparticle-sensors-in-microscopic-worms/#respond Mon, 23 Jan 2017 07:52:11 +0000 https://stanforddaily.com/?p=1121768 Stanford researchers are collaborating to create nanoparticles that emit light in response to a force stimulus. They hope to use these nanoparticles as sensors to study biological processes. Currently, they are testing these sensors in the digestive systems of 1 millimeter long worms called nematodes.

The post Researchers test nanoparticle sensors in microscopic worms appeared first on The Stanford Daily.

]]>
Stanford researchers are collaborating to create nanoparticles that emit light in response to a force stimulus. They hope to use these nanoparticles as sensors to study the miniscule, previously ignored forces governing many biological processes. Currently, they are testing these sensors in the digestive systems of millimeter-long worms called nematodes.

Alice Lay, a fourth-year Ph.D. candidate in applied physics in the Dionne Group, leads the project. Collaborating with her are associate professor in materials science and engineering Jennifer Dionne and professor of molecular and cellular physiology Miriam Goodman.

Their new sensors, when illuminated with near infrared light, emit visible light of a certain color and intensity depending on the forces being applied to them. These sensors are translating force into a color response, which can be collected and recorded with conventional cameras or microscopes.

“A lot of the time… instruments that are used to measure forces are very large [and] aren’t compatible for biospecimens,” Lay said. “Only recently have people been looking into scaling down the tools … If you combine advances in imaging and you have sensors that produce a stable optical response, it’s a lot easier to measure forces between and within cells.”

The first step to testing out these new tools in vivo is to look at digestion in nematodes.

“Digestion is one of the most primitive processes to visualize,” Dionne said. “Food is chewed, then swallowed, then further broken down before waste is excreted. Relatively strong forces are thought to be exerted by organs and cells at each step, so we should see a pretty vivid color change.”

Nematodes’ transparent bodies also allow the light emitted by the sensors to be easily recorded by a camera or microscope.

This collaboration between Lay, Dionne and Goodman came out of a meeting of the Stanford Neurosciences Institute. The organization brings together researchers from many different communities, including engineering, medicine, psychology and law, in order to better understand mental health and behavior. During one of the meetings, Goodman presented some of her work with nematodes while Lay presented on her lab’s work in nanotechnology.

“Miriam basically said, if you’re interested in understanding how neurons work, there are electrical signals to probe … but there are also mechanical forces which play a very important role,” Dionne said. “And Miriam pointed out that there aren’t many bio-compatible force sensors.”

Right now, the group’s sensors detect forces in the nanonewton to micronewton range, good for relatively large force processes such as digestion. But they hope also to develop nanoparticles that are sensitive in the piconewton to nanonewton phase, so as to study subcellular forces, such as the mechanical forces between neurons.

“I see this project as opening a door to a new way of thinking about how animals and tissues work,” Goodman said. “A lot of research in biology has focused on understanding chemical signals. … but there are also mechanical signals: forces that affect cells and tissues all over the body … and we really don’t know much about that at all.”

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Researchers test nanoparticle sensors in microscopic worms appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2017/01/22/researchers-test-nanoparticle-sensors-in-microscopic-worms/feed/ 0 1121768
Physicists propose new system for detecting neutrinos https://stanforddaily.com/2016/12/01/physicists-propose-new-system-for-detecting-neutrinos/ https://stanforddaily.com/2016/12/01/physicists-propose-new-system-for-detecting-neutrinos/#respond Thu, 01 Dec 2016 08:32:27 +0000 https://stanforddaily.com/?p=1120532 This system proposed by physicists, if proven effective, would not only reduce the cost of detecting neutrinos but also deepen our understanding of elementary particle physics.

The post Physicists propose new system for detecting neutrinos appeared first on The Stanford Daily.

]]>
Stanford professor of applied physics Peter Sturrock and other researchers released a paper this past month proposing a new system to detect neutrinos by monitoring radioactive decay rates. This system, if proven effective, would not only reduce the cost of detecting neutrinos from millions of dollars to thousands, but also deepen our understanding of elementary particle physics.

Purdue professor of physics and astronomy Ephraim Fischbach and astrophysicist Jeffrey Scargle of NASA’s Ames Research Center also collaborated on the paper.

Neutrinos, which are abundant, nearly massless elementary particles, are released as a byproduct of energy production in the sun’s deep interior. Not only can studying neutrinos help elucidate the behavior of the sun’s currently impenetrable interior, but studying the patterns of neutrino emission might possibly help to predict solar storms, which are intense bursts of radiation from the sun. These flares can cause damage and operational anomalies in man-made electronics.

Despite their abundance, however, neutrinos rarely interact with other particles, making them incredibly difficult to detect. Current methods are inefficient and involve building complicated, expensive detectors. One such detector, Super-Kamiokande, costs $100 million and requires 13 million gallons of ultra-pure water.

Although the new system of detecting neutrinos proposed by the paper has broad applications to many fields in physics and solar science, the system started with a problem in a completely different field. Fischbach was working on a difficult integral problem when he developed a new test for randomness.

Fischbach then applied this test to study nuclear decay, only to discover that nuclear decay was not random, but rather influenced by unknown signals.

With Sturrock and Scargle on board, the team was then able to analyze nuclear decay data and study what was causing this non-random variation. They found that these unknown signals seemed to correspond with the data from Super-Kamiokande and other neutrino detection facilities.

However, the team must compile more evidence before they can determine for sure that the signals they are seeing correspond to interacting neutrinos.

“We cannot prove that what we are seeing are neutrinos,” Fischbach said. “But what we can do is use the fact that we are seeing funny kinds of signals that look very much like the signals from Super-Kamiokande to infer that we are, in fact, seeing neutrinos.”

If the team can prove that these variations of decay rate are due to neutrinos, it is likely to change a lot about the way people think of physics.

“If the effects that we’re seeing are really due to neutrinos then they are interacting with matter in an entirely new way,” Fischbach said. “You cannot explain this phenomenon if they are attributed to neutrinos in any conventional way, so some new piece of physics must be out there.”

If these decay rate variations cannot be attributed to neutrinos, the discovery of non-stochastic, non-constant decay rates still raises the question of what forces are causing the variations.

“It’s also possible that we’re seeing the effects of other kinds of matter, so called dark matter, and a lot of things out there that can produce effects that look like neutrinos,” Fischbach said. “Since our lives depend on assuming radioactive decay rates are constant [i.e. carbon dating, medical applications], if they’re not, there will be a lot of changes in the way we [think of] things.”

 

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Physicists propose new system for detecting neutrinos appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2016/12/01/physicists-propose-new-system-for-detecting-neutrinos/feed/ 0 1120532
Researchers identify spontaneous order in water droplets https://stanforddaily.com/2016/10/30/researchers-identify-spontaneous-order-in-water-droplets/ https://stanforddaily.com/2016/10/30/researchers-identify-spontaneous-order-in-water-droplets/#respond Mon, 31 Oct 2016 05:54:12 +0000 https://stanforddaily.com/?p=1118896 Researchers at Stanford’s Tang Lab recently released a paper investigating the spontaneous emergence of order in water oil droplets squeezed through a funnel.

The post Researchers identify spontaneous order in water droplets appeared first on The Stanford Daily.

]]>
Researchers at Stanford’s Tang Lab recently released a paper investigating the spontaneous emergence of order in oil-filmed water droplets squeezed through a funnel. This finding has many potential applications, including modeling microscopic crystals and developing more efficient sample testing methods.

Research from the Tang Lab found order in a process previously considered random, which has implications for future experimental methods (Courtesy of Ella Maru Studio).
Research from the Tang Lab found order in a process previously considered random, which has implications for future experimental methods (Courtesy of Ella Maru Studio).

Tang Lab first noticed the spontaneous order among water oil droplets when they looked at the research project of Ryan Swodoba ’14, one of their undergraduate lab members. Swodoba started working in Tang Lab the summer after his sophomore year as a material science and engineering major. He was working with microscopic droplets of water, around 50 picoliters in volume, surrounded by a thin layer of oil.

Tang Lab studies the potential for the droplets to be used as mini test tubes to hold different samples. Swodoba was trying to figure out how quickly he could flow these droplets through a funnel without them breaking apart.

“It was really the groundwork [Swodoba] built up that led to later discovery that was picked up by Ya, who joined our lab a little later,” said Sindy Tang, assistant professor in the department of mechanical engineering.

Several years later, Ya Gai, a Ph.D. student in aerospace, aeronautical and astronautical engineering, re-visited the strange behavior of these droplets when they were extruded from the funnel at slower speeds.

“The droplets move like batches,” Gaid said. “And the location and the timing of this … seems to be very organized. We expect them to be stochastic and unpredictable, but it appears to us they are very ordered.”

In order to try to understand why the droplets were acting this way, Tang Lab collaborated with Wei Cai, an associate professor of mechanical engineering. Cai looked at the droplets from a solid mechanics view and discovered that they might be a good model for understanding the dynamics of microscopic crystals.

“It will be a model for a solid crystal, and what happens when we try to squeeze these solid crystals through this extrusion process going from a wider [space] into something that’s like a nanowire,” Tang said. “We realized there’s actually a very easy analogy between the experimental results we found and the solid mechanics that have been know for many years.”

Another possible application of this research is to improve the use of water oil droplets as a method for testing many samples as efficiently as possible. According to Tang, the benefit of traditional 96-well plates is that the position of the well will tell you what reaction is inside. Conversely, one of the current disadvantages of the water droplet sampling technique is the inability to predict the exact order that the samples will run.

“With these drops … once you make them, they flow around and mix, so you lose track of which drop contains what,” Tang said. “[But] with this order we can possibly predict where the drops will go and basically allow us to retrieve the spatial encoding that we have lost with this droplet system.”

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Researchers identify spontaneous order in water droplets appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2016/10/30/researchers-identify-spontaneous-order-in-water-droplets/feed/ 0 1118896
Archaeology dig uncovers marble figurines https://stanforddaily.com/2016/10/10/archaeology-dig-uncovers-marble-figurines/ https://stanforddaily.com/2016/10/10/archaeology-dig-uncovers-marble-figurines/#respond Tue, 11 Oct 2016 06:19:51 +0000 https://stanforddaily.com/?p=1117846 This past summer, archaeologists from the Çatalhöyük Research Project unearthed two marble figurines, considered one of the most significant finds in the project’s 23-year history.

The post Archaeology dig uncovers marble figurines appeared first on The Stanford Daily.

]]>
This past summer, archaeologists from the Çatalhöyük Research Project unearthed two marble figurines, considered one of the most significant finds in the project’s 23-year history.

Stanford archaeologists found an intriguing goddess figurine in a dig in Turkey (Courtesy of Jason Quinlan)
Stanford archaeologists helped uncover an intriguing goddess figurine in a dig in Turkey (Courtesy of Jason Quinlan)

The project involved several universities and professionals around the world, with more than 100 people working on-site every summer. The discovery of the figurines immediately attracted the attention of the project’s different teams and specialists.

“We found a lot of other beautiful… strange and wonderful things,” said Ian Hodder, professor of anthropology and classics at Stanford and head of the research project. “But just as a piece of art… I think the figurines are the most beautiful [objects] we found.”

Çatalhöyük is a large Neolithic settlement in present-day Turkey. It was occupied from approximately 7500 to 5700 B.C. These figurines were found by a Polish team in one of the upper layers of Çatalhöyük, representing a time period close to the end of occupation (around 6300 to 6000 B.C.).

“I remember that day I was working down the trench on a wall painting and… in a half and hour, pretty much everyone knew about [the figurines],” said Gesualdo Busacca, a Stanford Ph.D. student in archaeology who has been a part of the project for the past three years. “Everybody was curious and went to see where it was dug.”

“It was just very exciting,” Hodder said. “And I then called all the different specialists that needed to come study it: the figurine team, the photographer, the planner, the person that makes the maps and so on… So very quickly this Neolithic house was full of about 20 people all studying or looking at this object.”

The well-preserved craftsmanship and subject of these figurines distinguish them from most of the other figurines found in Çatalhöyük, which are often clay depictions of animals. The newly-found figurines are made of marble, a much rarer material.

These types of figurines, in the past, were thought to depict “mother goddesses.” However, the figurines of women found in Çatalhöyük were very rarely associated with children.

“A possibility is that the figurine does not actually represent a goddess but [rather] an elderly female person [who] had achieved some high status,” Busacca said. “Which may be indicated by the fact that the figure is very fat, so it’s a person that is not doing physical labor.”

One of the most interesting characteristics about these figurines is their context. While figurines are usually found in rubble piles — many are accidentally conserved from the clay being burned in a fire — these figurines seem to have been intentionally placed face-up under a platform.

In early Çatalhöyük, it was customary for people to bury their dead underneath the floor. By the time period in which these figurines were made, the trend of burial in Çatalhöyük had started to evolve towards more proper cemeteries. Therefore, the dead were buried in external houses as opposed to within the house.

These figures, however, were found under a platform that archaeologists would have expected to find burials. They were also found with two objects: a piece of volcanic glass commonly used for making tool and a piece of galena, a lead ore.

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Archaeology dig uncovers marble figurines appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2016/10/10/archaeology-dig-uncovers-marble-figurines/feed/ 0 1117846
Physicists develop multi-pass microscopy https://stanforddaily.com/2016/10/03/physicists-develop-multi-pass-microscopy/ https://stanforddaily.com/2016/10/03/physicists-develop-multi-pass-microscopy/#respond Tue, 04 Oct 2016 05:14:27 +0000 https://stanforddaily.com/?p=1117558 Physicists develop microscope technique for clearer images and less damage.

The post Physicists develop multi-pass microscopy appeared first on The Stanford Daily.

]]>
Physicists at Stanford have developed a technique called multi-pass microscopy to obtain clearer images while reducing the damage inflicted on the sample. They outline their new technique in a paper titled “Multi-pass microscopy,” recently published in “Nature Communications.”

Normal light microscopes have light pass through the sample only once. The Mark Kasevich Research Group uses mirrors to reflect light back and forth across the specimen before finally being collected at a fixed number of passes.

By passing the same photons of light multiple times across the specimen, these researchers are able to improve the signal to noise ratio of the resulting image. This improves the quality of the image without using more light, which would damage the specimens.

“We try to get as much information as we can with as few interactions as we need to do,” said Thomas Juffmann, a postdoctoral research fellow and co-author of the paper. “Because an interaction always creates damage, always takes time, and so forth.”

One disadvantage of this new technique is the complexity involved with its set-up, since the microscope requires additional mirrors in order to reflect the light back and forth.

“We need basically twice as much equipment,” Juffmann said. “But what’s worse than that is that the alignment gets much harder because we need to make sure a spot on the sample… is re-imaged to exactly that spot many many times.”

Currently, the greatest difficulty with the technique is finding a way to collect the light at the end.

“How do you get the light out of your microscope because you have to have a mirror on each end so the light is kind of stuck in there?” said co-author Brannon Klopfer, a graduate student in the Kasevich group. “The easiest way of doing that is to have… a partially reflective mirror, and then you just collect this leaked out light.”

This both causes light to leak during the multi-pass process and reduces the amount of light that is used to create the final image. The Kasevich group hopes to develop a technique that reduces the light wasted in order to increase the amount captured in the end.

They also hope to eventually expand their research to electron microscopes, where the potential of damage poses a greater problem.

“You use electron microscopy when you wish to look at really small things, smaller than the wavelength of light, and it works great,” Juffmann said. “You can see single atoms in it, but you cannot image DNA or cells or proteins [at atomic resolution] simply because you create too much damage. You basically [destroy] your sample before you get a good image, and that’s where our scheme could help.”

This research takes advantage of camera technology with extremely fast shutter speeds: Shutter speeds can be as fast as 0.1 billionths of a second. This allows researchers to capture the light after it has made a fixed number of passes through the specimen.

Juffmann also uses this camera technology for an art and science outreach project called SEEC, which creates videos of light spreading at the speed of light across plants, people and objects.

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Physicists develop multi-pass microscopy appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2016/10/03/physicists-develop-multi-pass-microscopy/feed/ 0 1117558
Q&A with Knight Fellow Jeneé Desmond-Harris https://stanforddaily.com/2016/05/27/qa-with-knight-fellow-jenee-desmond-harris/ https://stanforddaily.com/2016/05/27/qa-with-knight-fellow-jenee-desmond-harris/#respond Fri, 27 May 2016 09:09:53 +0000 https://stanforddaily.com/?p=1115811 Jenée Desmond-Harris is one of this year’s John S. Knight Journalism Fellows. Desmond-Harris is focusing on investigating the best practices for journalists covering race in America. A former staff writer at Vox and editor at The Root, she freelances for many publications, including the New York Times and MSNBC. The Daily talked with Desmond-Harris about her experiences with journalism and being a JSK fellow.

The post Q&A with Knight Fellow Jeneé Desmond-Harris appeared first on The Stanford Daily.

]]>
Jenée Desmond-Harris is one of this year’s John S. Knight Journalism Fellows. Desmond-Harris is focusing on investigating the best practices for journalists covering race in America. A former staff writer at Vox and editor at The Root, she freelances for many publications, including The New York Times and MSNBC. The Daily talked with Desmond-Harris about her experiences with journalism and being a JSK fellow.

The Stanford Daily (TSD): What does a typical day look like for you?

Jeneé Desmond-Harris (JDH): There really is no typical day in the JSK Fellowship. We have a program that includes a variety … So a day could look like anything from going to three classes, to being at the library reading, to having meetings all day, to listening to a guest speaker, to having a meeting with the fellowship staff.

TSD: How did you first become interested in journalism?

JDH: I was actually a lawyer. I practiced for about four years. And I always loved writing, and I was always really passionate about issues related to race in America. So I began freelancing on the side as a lawyer, and I loved it. I eventually got hired by The Root – that’s an African American news and commentary site – and I went from there to Vox in Washington D.C.

TSD: How did you find yourself being a JSK fellow?

JDH: So the fellowship is designed for people who want to address a question or issue relating to their area of journalism. As someone who’s always written about race, I did a lot of experimenting with different ways to bring academic insights to my audience and try to dispel myths. I really wanted to take the opportunity to take some time to be more thoughtful about what audiences needed, and how I and other journalists could deliver the best possible and richest content to them. This year has been an opportunity to do a lot of thinking and a lot of learning, and unfortunately as a working journalist that’s often something that you don’t have time for. So once I heard about all the resources available here, everything from the actual Stanford courses to the group of fellows, who are amazing and who can teach you so much because of the work they’ve done, I just thought it would be a really great way for me to enhance my career.

TSD: What’s the community like among the JSK fellows?

JDH: We’re all very, very close. We really have become a family. There’s 19 of us, several are international, and we’re all mid-career but have very different backgrounds. Everything from investigative reporters to broadcast reporters to illustrators to journalism innovators, but we’re all here for the same reason: Because we want to get better at what we do and we have a lot of curiosity and a lot of questions. We have a lot of time to spend together and just get to know each other, which is a huge luxury. I’m sure that we’re gonna keep our relationships going long after the fellowship is over.

TSD: What in your experience made you want to improve race reporting in America?

JDH: I don’t think it’s a problem as much as a challenge. I think race is not an area where a lot of people are expected to have expertise, like they are with some other beats. So many people who are covering race, myself included, we’re often figuring it out as we go along. And that means we don’t have a huge knowledge base to draw from, and so that knowledge can be really important for readers, our audiences … I really felt like I wanted to have a chance to gather all the expertise and insights that most reporters don’t generally have on a day-to-day basis. And I also wanted to create some best practices for people who are still out in the world and just want to do the best they can with the time they have.

TSD: Are you still writing for publication during your fellowship?

JDH: I’m primarily focused on just the fellowship this year, but I did just do a piece for The New York Times on Donald Trump and race in America. I actually worked with one of my sociology professors here, Tomás Jiménez … I really developed some great relationships, and I know I’ll continue to use professors that I met here as resources for my pieces.

TSD: What else do you like to do for fun outside of the fellowship?

JDH: I’ve really enjoyed starting to ride a bike again. I think that’s been incredibly fun. This probably sounds nerdy and somewhat boring, but I love having the time to read everything I want to read, from books to just everything on the Internet. Also, exploring the Bay Area. I grew up here, so I’ve had the chance to get back into hiking and visiting the beaches. It’s just so beautiful here, so it’s been a great experience.

 

Contact Aulden Foltz at afoltz@stanford.edu.

The post Q&A with Knight Fellow Jeneé Desmond-Harris appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2016/05/27/qa-with-knight-fellow-jenee-desmond-harris/feed/ 0 1115811
Researchers examine emotional role in financial fraud https://stanforddaily.com/2016/05/15/researchers-examine-emotional-role-in-financial-fraud/ https://stanforddaily.com/2016/05/15/researchers-examine-emotional-role-in-financial-fraud/#comments Mon, 16 May 2016 05:52:07 +0000 https://stanforddaily.com/?p=1115129 Researchers at the Stanford Center on Longevity have found in a new report that the ways in which elderly people process high-arousal emotions, such as anger and excitement, is in part responsible for their heightened susceptibility to fraud.

“There’s evidence that [the elderly] are targeted, but to me that’s sort of like [wondering] why criminals rob banks,” said Laura Carstensen, professor of psychology and founding director of the Stanford Center on Longevity. “That’s where the money is.”

The post Researchers examine emotional role in financial fraud appeared first on The Stanford Daily.

]]>
Researchers at the Stanford Center on Longevity have found in a new report that the ways in which elderly people process high-arousal emotions, such as anger and excitement, is in part responsible for their heightened susceptibility to fraud.

“There’s evidence that [the elderly] are targeted, but to me that’s sort of like [wondering] why criminals rob banks,” said Laura Carstensen, professor of psychology and founding director of the Stanford Center on Longevity. “That’s where the money is.”

The study took advantage of the fact that emotion can be measured using two qualities: positivity and arousal. Positivity measures the distinction between happy and sad, while arousal measures how relaxed the person is. Arousal is often accompanied by increased heart and breathing rates.

The research focused on emotional arousal, splitting participants into three groups: high-arousal positive (excitement), high-arousal negative (anger) and low-arousal (neutral).

Participants would begin the experiment by playing a computer game during which they won and lost money based on predetermined experimental groupings. This game would be customized depending on which of the three groups the participants were placed. The excited group began the game by losing a lot of money but gradually gained money as the game continued. The angry group began by winning money but lost much of it throughout the game. The neutral group won and lost small amounts of money consistently throughout the game.

The participants then reported their degree of positivity and arousal. They were then shown a series of eight advertisements and asked to rank how much they believed the advertisement and their likelihood to purchase the associated product.

The study found that high-arousal emotion increased the intent to purchase in older, but not younger, adults. According to Carstensen, this was a surprising result.

“Originally, our hypothesis was that high-arousal positive states would make people more likely to buy something, and we’d see positive states in older people more than in younger people,” Carstensen said. “But we didn’t. We saw [that] both negative and positive states made older people more likely to be interested in the products that we presented to them.”

The research also found that, with younger adults but not older adults, the advertisements’ reported believability being could be used to predict likelihood of purchase. This trend carried through all three of the emotional groups and suggests that other factors are overshadowing perceived credibility for the elderly group in determining whether or not to purchase the product.

The researchers hope that these findings, along with a more comprehensive study of the factors contributing to fraud susceptibility, can help people make wise decisions when faced with financial fraud.

“I think we’d want to see if we can induce [susceptibility to fraud] and then override it,” said Ian H. Gotlib, the David Starr Jordan Professor of Psychology and chair of Stanford’s psychology department.

According to Gotlib, the next steps will be to look for procedural interventions that could calm down potential targets for fraud and reduce their anger.

Even though emotional arousal was not reported to affect purchase intention in younger adults, Carstensen highlighted the importance of keeping such factors in mind when faced with financial decisions.

“Don’t make financial decisions when you’re excited or you’re really afraid of something,” Carstensen said. “It’s always better when someones trying to sell you something to wait a day, sleep on it.”

 

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Researchers examine emotional role in financial fraud appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2016/05/15/researchers-examine-emotional-role-in-financial-fraud/feed/ 1 1115129
Researchers to revisit drug trials for major viruses https://stanforddaily.com/2016/04/15/researchers-to-revisit-drug-trials-for-major-viruses-cancer/ https://stanforddaily.com/2016/04/15/researchers-to-revisit-drug-trials-for-major-viruses-cancer/#respond Fri, 15 Apr 2016 08:22:55 +0000 https://stanforddaily.com/?p=1113647 Stanford scientists have relaunched research on a previously shelved category of drugs, known as broad-spectrum antiviral drugs, in the hope that it will reveal information about new strategies to fight both difficult-to-combat viruses such as dengue and ebola, along with cancer.

This research, published in Nature Chemical Biology, was headed by the two senior authors of the paper, assistant professor of genetics Michael Bassik and professor of chemistry Chaitan Khosla.

The post Researchers to revisit drug trials for major viruses appeared first on The Stanford Daily.

]]>
Stanford scientists have relaunched research on a previously shelved category of drugs, known as broad-spectrum antiviral drugs, in the hope that it will reveal information about new strategies to fight both difficult-to-combat viruses such as dengue and ebola, along with cancer.

This research, published in Nature Chemical Biology, was headed by the two senior authors of the paper, assistant professor of genetics Michael Bassik and professor of chemistry Chaitan Khosla.

The project itself is part of a larger initiative headed by associate professor of medicine Jeffrey Glenn. Glenn started the U19 Center for Excellence in Translational Research, which aims to identify new strategies to fight viruses. One technique is to develop drugs that target the host cell rather than the virus itself.

“Viruses are very good at mutating and changing their activities, and so often you get resistant viruses that come up very quickly,” Bassik said. “This new class of drugs…that target the host cell processes are much more likely to be applied to a wide range of viruses, and the viruses [are] much less likely to be able to mutate around that activity.”

The drug was originally a product of GlaxoSmithKline, a British pharmaceutical company. The company had performed a chemical screen to identify compounds that blocked viral replication, and one in particular, GSK983, proved very successful. After further studies, however, the company decided to halt research.

“They probably spent, without exaggeration, hundreds of millions of dollars researching this drug,” Bassik said. “But then they stopped working on it, and we still don’t know why that is.”

To study how the mechanisms behind the drug’s function, these researchers used two screening techniques: shRNA and CRISPR-Cas9. Both work by reducing or deleting expression of individual genes and assessing the resulting activity of the drug. shRNA reduces expression by up to 90 percent, while CRISPR-Cas9 effectively stops all expression. Using both techniques allows researchers to study which genes interact with the drug.

The researchers discovered that the drug operated by inhibiting the activity of dihydroorotate dehydrogenase (DHODH), a protein that appears early on in the pathway the cell uses to synthesize pyrimidines, which are simple building blocks of nucleic acids such as DNA and RNA. The virus, unable to use the cell’s hijacked nucleotide synthesis mechanisms to replicate itself, dies. However, the main problem with this drug is that cells can also gather the building blocks for nucleic acids from the blood.

Future research aims to halt the cell’s absorption of these building blocks from the blood, thus preventing both pathways from building RNA needed for viral replication.

“The idea is to block the two pathways together,” said Ayse Okesli, a postdoctoral research fellow in chemistry. “[to inhibit] uptake from the blood, in addition to synthesis from scratch. And then, hopefully, we will have a good strategy to go forward to work in humans.”

Okesli also comments on the applicability of this research to tackle other problems. One such problem is cancer research which, likewise, relies on DNA/RNA synthesis in order to propagate.

“It’s pretty real” said Okesli. “Academic projects don’t always apply to life this easily. This is a cool project that has a potential to change many people’s lives in the future.”

Correction: A previous version of this article spelled Ayse Okesli’s last name as “Okelsi.” Additionally, references to protein synthesis were changed to nucleotide synthesis and a clarification was added to distinguish shRNA and CRISPR-Cas9. The Daily regrets these errors. 

Contact Aulden Foltz at afoltz@stanford.edu.

The post Researchers to revisit drug trials for major viruses appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2016/04/15/researchers-to-revisit-drug-trials-for-major-viruses-cancer/feed/ 0 1113647
Glamorous Grad Students: James Russell https://stanforddaily.com/2016/03/01/glamorous-grad-students-james-russell/ https://stanforddaily.com/2016/03/01/glamorous-grad-students-james-russell/#respond Tue, 01 Mar 2016 08:26:59 +0000 https://stanforddaily.com/?p=1111826 James Russell is a third year PhD candidate in cellular and molecular biology researching cell wall patterning in diatom algae. He is also the founder of Empco Holdings, which grows and sells bioluminescent algae. For this edition of our weekly feature of graduate students, The Daily talked with Russell about his research and Empco.

The post Glamorous Grad Students: James Russell appeared first on The Stanford Daily.

]]>
James Russell is a third-year Ph.D. candidate in cellular and molecular biology researching cell wall patterning in diatom algae. He is also the founder of Empco Holdings, which grows and sells bioluminescent algae. For this edition of our weekly feature of graduate students, The Daily talked with Russell about his research and Empco.

The Stanford Daily (TSD): What areas of research are you doing here at Stanford?

(Courtesy of Jason Russell)
(Courtesy of James Russell)

James Russell (JR): Most of the things I have worked on have in one way or another involved different types of algae… In my research here, I work on diatoms, which produce these microscopic nanopattern cell walls out of glass — a really unique aspect in biology. Most organisms that create a cell wall do so out of long, complex sugars, and in the case of these algae, they’re taking one of the most abundant minerals in earth’s crust, silicon, and forming a cell wall out of glass. This of course is just innately interesting to study. Why is this microbe using glass when everything else is using sugars to make its cell walls?

What really attracts me to it are these these very reproducible nanoscale patterns… that they form in these cell walls. My research is concerned with what is governing the patterns that they make… I’m taking more of a molecular genetics approach and trying to understand on the gene level which genes are responsible for these patterns. And once these genes are identified, we can ask, what is the structure of the proteins that these genes encode? What I imagine is that there are some structural proteins that form scaffolds that resemble these structures. Those scaffolds are temporary until the cell wall is built, but given that they’re protein in nature, they can very easily be engineered, hypothetically, into any pattern.

TSD: And moving towards your business, Empco, how did that get started?

JR: It’s kind of an odd beginning. I was doing an internship when I was in high school… We were going through very wild examples of biology, and one of the things that came up were these bioluminescent algae… We decided to get ahold of these organisms and try some simple experiments… What we learned quickly is that actually obtaining a pure culture of these organisms was very difficult. There were very few sources to begin with. In addition, the sources that were out there were full of contamination, including with other algae, which was an issue with the experimentation. So I spent quite a bit of time [purifying the algae], and once I had these cultures, I was talking to a professor at UC Santa Barbara who runs a public outreach site about bioluminescent organisms. He offered to give my name out to people who were interested in acquiring these organisms.

TSD: What was your business like at the very beginning? Where were you growing this algae?

JR: I was providing these cultures kind of informally after this internship, and then as an undergraduate I established an actual website through which to sell this product. At that time, it was very much a home-based operation. As part a different project, I had been working on totally different types of algae and trying to understand their feasibility for different products, including biofuels. This was kind of a home project, and in the process I had acquired a lot of used lab equipment. So when I first established [Empco], I took that lab equipment and started using it in my home for this business. As it matured, it quickly grew too large and too weird to have in my apartment at Berkeley, and so I moved it to what was essentially a room with electricity and running water in the Berkeley area… I was there for a number of years, and then, when I came to Stanford, I found an actual office space in Menlo Park, where I now operate.

TSD: Are you planning on expanding the business in the future?

JR: I don’t have any immediate plans to expand it. I think it’s been a really fun business to manage part-time as a student… But the market for bioluminescent algae is niche, to say the least. Outside of random bouts of publicity that cause a spike in demand, I don’t see it growing stably much more. However, I’m open to whatever happens.

TSD: How does your research influence your business?

JR: Being able to establish pure cultures and have sterile technique are minimal skill sets for this kind of business. Also, being able to help customers with their projects: while a majority of customers have very simplistic needs in terms of advice, there are occasional customers who have very interesting proposals. One of the more interesting types of customers that I see are these artists. They envision very elaborate art setups, the center of which is this bioluminescent algae… I think after doing years of research, you just have a good sense technically of what’s possible… You’re able to think creatively about how to do these things so that they actually work.

This interview has been condensed and edited.

 

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Glamorous Grad Students: James Russell appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2016/03/01/glamorous-grad-students-james-russell/feed/ 0 1111826
Stanford researchers add to Neanderthal debate https://stanforddaily.com/2016/02/17/stanford-researchers-add-to-neanderthal-debate/ https://stanforddaily.com/2016/02/17/stanford-researchers-add-to-neanderthal-debate/#respond Wed, 17 Feb 2016 08:13:32 +0000 https://stanforddaily.com/?p=1110957 Two Stanford researchers are using mathematics to model the extinction of Neanderthals. Biology professor Marcus Feldman and applied physics Ph.D. student in William Gilpin collaborated with Kenichi Aoki of Meiji University to release a paper this past month using a measure of “culture” as the distinguishing factor between humans and Neanderthals.

The new paper took an interdisciplinary approach in order to explain why humans, not Neanderthals, became the prevalent species.

According to previously existing research, modern humans migrated to Europe around 45 thousand years ago. At the time, Neanderthals had already lived in Europe for hundreds of thousands of years and had established much larger populations than the migrating humans.

The post Stanford researchers add to Neanderthal debate appeared first on The Stanford Daily.

]]>
Two Stanford researchers are using mathematics to model the extinction of Neanderthals. Biology professor Marcus Feldman and Applied Physics Ph.D. student William Gilpin collaborated with Kenichi Aoki of Meiji University to release a paper this past month using a measure of “culture” as the distinguishing factor between humans and Neanderthals.

The new paper took an interdisciplinary approach in order to explain why humans, not Neanderthals, became the prevalent species.

According to previous research, modern humans migrated to Europe around 45 thousand years ago. At the time, Neanderthals had already lived in Europe for hundreds of thousands of years and had established much larger populations than the migrating humans.

In the past, there has been academic debate over whether humans and Neanderthals interacted. Research in the past few years, however, has revealed that modern day humans outside of Africa have approximately 1.5 to 2.1 percent Neanderthal DNA in their genome, meaning that there must have been interaction and coexistence. This raised the question of why humans surpassed Neanderthals. 

“Everybody’s hypothesis has been that we were probably smarter [than Neanderthals], in some respects,” said Shripad Tuljapurkar, a Stanford biology professor who commented on the research. “What this paper does is it actually attempts to get fairly precise about explaining what this smartness is.”

Feldman and Gilpin do not assume that humans had higher cognitive function than Neanderthals. Instead, they express the “smartness” of humans through what they call “culture.” Feldman and Gilpin use this term in a very specific way.

Drawing from paleobiological, archaeological and anatomical literature, Feldman and Gilpin highlight a number of skills humans developed before or at a greater complexity than the Neanderthals. They focus mainly on complex language and tool development. These skills, rather than cognitive function or artistic ability, would have directly affected human population size.

“Because of [human’s] advanced culture, their population is able to grow faster, the environment is able to support more of them, and the result is that the culture itself allows modern humans to overwhelm the Neanderthal,” Feldman said.

In the future, Feldman and Gilpin hope to add spatial effects to their models since human-Neanderthal interactions occurred over massive areas and timescales. Both the physical migration of humans and the spread of ideas and culture need to be taken into account.

By borrowing mathematical techniques from classical systems in physics, Feldman and Gilpin were able to come up with a possible explanation for an otherwise unexplained phenomenon. Much of the flexibility of their research relies on the fact that each member of the research team comes from very different backgrounds in academia.

Feldman focuses his research on theoretical biology, while Gilpin has a background in classical physics. Their colleague, Aoki, works on a Japanese Science Foundation project called The Replacement of Neanderthals by Modern Humans, which funds archaeological, paleontological and anatomical projects.

“The nice thing about being a professor here at Stanford is how easy it is to do this kind of interdisciplinary research,” Feldman said. “We don’t build walls around departments.”  

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Stanford researchers add to Neanderthal debate appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2016/02/17/stanford-researchers-add-to-neanderthal-debate/feed/ 0 1110957
Stanford geologists refute coal development theory https://stanforddaily.com/2016/02/02/stanford-geologists-refute-coal-development-theory/ https://stanforddaily.com/2016/02/02/stanford-geologists-refute-coal-development-theory/#comments Tue, 02 Feb 2016 19:22:36 +0000 https://stanforddaily.com/?p=1110115 Two Stanford geologists are disputing the decade-old explanation of the large amount of coal accumulated during the Carboniferous Period. Associate Professor Kevin Boyce and Postdoctorate Research Fellow Matthew Nelsen, collaborated with scientists across the country to release a paper this past month where they propose a new understanding of coal development.

The previous hypothesis of coal accumulation focused on a temporal lag between the evolution of lignin production in woody plants and the evolution of lignin-degrading fungi to break down this new material. This would have resulted in the non-degraded lignin building up, depositing massive amounts of coal.

The post Stanford geologists refute coal development theory appeared first on The Stanford Daily.

]]>
Two Stanford geologists are disputing the decade-old explanation of the large amount of coal accumulated during the Carboniferous Period. Associate Professor Kevin Boyce and Postdoctorate Research Fellow Matthew Nelsen collaborated with scientists across the country to release a paper this past month in which they propose a new understanding of coal development.

The previous hypothesis of coal accumulation focused on a temporal lag between the evolution of lignin production in woody plants and the evolution of lignin-degrading fungi to break down this new material. This would have resulted in the non-degraded lignin building up, depositing massive amounts of coal.

“But [this explanation] can’t be true,” Boyce said.

The paper that Boyce and Nelsen collaborated on uses several lines of evidence in order to disprove the old hypothesis.

The most convincing evidence includes a fossil record of lignin-degrading fungi pre-dating the Carboniferous period. New research also reveals that the standard preparation of fossilized plants washes away much of the fossilized fungi and microbes, suggesting the current fungi fossil record to be an underestimate of what was actually present at the time.

The hypothesized 130-million-year evolutionary lag between the plants and the fungi would also have resulted in severe environmental consequences.

“Even if plants were less productive then, there’s probably a good three or so gigatons of lignin being produced per year,” Boyce said. “If you had 80 million years without lignin decay, you’d run out of CO2 in the atmosphere in a couple hundred years… we’d freeze the earth.”

Their paper also includes a graph displaying the accumulation of organic sediments over time. Rather than showing a steady increase over the Carboniferous Period, the graph has many spikes of accumulation, each of which lasts around 500,000 years.

“If that was fungi, what would they do? Evolve, un-evolve, and then evolve back?” Boyce said. “The actual record of accumulation doesn’t really work for it being a biotic cause. It looks much more grounded in abiotic processes.”

The new theory explains coal accumulation using weather and tectonic activity. The Carboniferous Period was not only warm, but also coincided with the separation of Pangaea. The spikes on the graph coincide with basins opening up and providing a place for plant material to be deposited before eroding away.

Boyce and Nelsen looked at the coal accumulation in Denver around 50 million years ago as a model to explain the 300-million-year-old phenomenon of Carboniferous accumulation.

“It was equivalently productive and wet, and a lot of coal formed because the incipient Rocky Mountains were there so there was a place to put all the coal,” Boyce said. “So the local rates of accumulation were similar to what was going on worldwide during the Carboniferous.”

According to Nelson, discontent with the evolutionary lag hypothesis has been around for some time before the publishing of this recent paper.

“I think there were some grumblings in the literature: people going after this but not anywhere near the level of detail that we did,” Nelsen said.

This raises the larger issue: If geologists had seen problems with the hypothesis, why had nothing been done to disprove it earlier?

According to Boyce, the unique collaborative circumstances hadn’t occurred in the past.

“You’re very often at the edge of what you know yourself and it’s very important to have the right collaborators looking at it from other directions,” Boyce said.

Further, Boyce cites a tendency in science to ignore, rather than go after, theories believed to be false.

“That becomes a real problem,” said Boyce, “because people using [geology] from outside the field aren’t going to recognize who was ignoring what… These things have actual consequences.”

 

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Stanford geologists refute coal development theory appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2016/02/02/stanford-geologists-refute-coal-development-theory/feed/ 4 1110115
Research reveals new information about how aquatic animals move https://stanforddaily.com/2015/11/12/research-reveals-new-information-about-how-aquatic-animals-move/ https://stanforddaily.com/2015/11/12/research-reveals-new-information-about-how-aquatic-animals-move/#respond Thu, 12 Nov 2015 08:51:57 +0000 https://stanforddaily.com/?p=1106822 Stanford engineering professor John Dabiri collaborated with scientists from across the country to shed light on the counterintuitive way aquatic creatures move. These new insights provide the foundations for bio-inspired underwater vehicles and methods for studying aquatic animal movement.

The post Research reveals new information about how aquatic animals move appeared first on The Stanford Daily.

]]>
Scientists have discovered that aquatic animals, unlike humans, create low pressure zones to pull themselves through the water. (Courtesy of Sean P. Colin)
Scientists have discovered that aquatic animals, unlike humans, create low pressure zones to pull themselves through the water. (Courtesy of Sean P. Colin)

Stanford engineering professor John Dabiri collaborated with scientists from across the country to shed light on the counterintuitive way aquatic creatures move. These new insights provide the foundations for bio-inspired underwater vehicles and methods for studying aquatic animal movement.

When humans move through water, we create high pressure zones and push off the water. However, Dabiri and his colleagues discovered that the aquatic animals they studied, jellyfish and lamprey, instead create low pressure zones to pull themselves through the water. According to Dabiri, these findings, contrary to the presumption that these animals would use methods of propulsion similar to humans, surprised even the researchers.

We just assumed it was something wrong with our measurement technique or our calculations,” Dabiri said, referencing the first time they saw the low pressure zones.

At the start of the experiment, Dabiri and his colleagues at the Marine Biological Laboratory ran into the problem of not being able to measure the pressures generated by the swimming animals.

“If I wanted to figure out your walking gait, for example, I might have you walk on a special plate that would measure the forces that you’re exerting on the ground,” Dabiri said. “We haven’t had the equivalent for a swimming or flying animal.”

To solve this, they used a technique called particle image velocimetry, which consists of putting glass beads coated with silver into the water tank and shining a laser through the tank. The silver reflects light from the laser, and by looking at how the beads move, scientists can then determine pressures at work pushing the beads in that way.

Particle image velocimetry has been used to study conventional engineering systems like airflow over a plane wing or water flow through pipes, said Dabiri, but the method has not previously been applied to the interactions of animals with their environments.

Dabiri plans to adapt this technique even further, creating a system small enough that a scuba diver could take the measurement tool on a dive. He explained that this will better our understanding of animal movement, since animals tend to move differently in the confined space of a laboratory than they do in the wild.

Dabiri also hopes to use his research to improve the design of underwater vehicles and maximize fuel efficiency. He suggests looking at jellyfish, lamprey and other aquatic animals in order to mimic how they use lower pressures to pull themselves through the water.

Dabiri joined Stanford’s faculty this past July and has high hopes for the University’s progress in his field.

“I’m hoping — both in terms of the faculty interactions and the students — that we’ll continue to expand the envelope in terms of applying a physical approach to understanding biological systems,” Dabiri said. “It’s mainly been aquatic animals, but there’s other faculty thinking about bird flight or plant systems and others, and I think this whole umbrella area has an exciting future at Stanford.”

 

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Research reveals new information about how aquatic animals move appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2015/11/12/research-reveals-new-information-about-how-aquatic-animals-move/feed/ 0 1106822
Q&A with Stanford law professor Deborah Rhode on obesity and public policy https://stanforddaily.com/2015/11/05/qa-with-stanford-law-professor-deborah-rhode-on-obesity-and-public-policy/ https://stanforddaily.com/2015/11/05/qa-with-stanford-law-professor-deborah-rhode-on-obesity-and-public-policy/#comments Thu, 05 Nov 2015 23:37:45 +0000 https://stanforddaily.com/?p=1106344 Stanford law professor, Deborah Rhode’s paper titled, “Obesity and Public Policy: A Roadmap for Reform,” was recently published in the Virginia Journal of Social Policy & the Law. The Daily spoke with Rhode about her article and the next steps towards obesity reform.

The post Q&A with Stanford law professor Deborah Rhode on obesity and public policy appeared first on The Stanford Daily.

]]>
Stanford law professor Deborah Rhode’s paper, titled “Obesity and Public Policy: A Roadmap for Reform,” was recently published in the Virginia Journal of Social Policy & the Law. The article outlines the causes and consequences of the obesity epidemic, justifications for government intervention and policies that have been most effective thus far. As obesity rates rise, constituting 17 percent of children and one-third of adults, Rhode urges us to act now on what we know as far as the success and limitations of past reforms.

The Daily spoke with Rhode about her article and the next steps towards obesity reform.

The Stanford Daily (TSD): What made you interested in obesity prevention policies?

Deborah Rhode (DR): I had done a little bit of work for a book I wrote, “The Beauty Bias,” on weight discrimination, and that raised my interest. Then an opportunity came to develop a policy laboratory course at Stanford Law School on what Santa Clara County could do with respect to obesity prevention. In order to equip myself to teach the course, I felt I had to do a review of the field. And once I had done that, one thing led to another, and I decided to write it up as an article.

TSD: What have you observed to be the most effective measures for preventing obesity?

DR: The conventional wisdom is people need to exercise more and eat less, which is true. They also need to eat the right kind of food, and in order to nudge people in that direction, I think there are a variety of public policy initiatives that we can take advantage of. Taxing sugar-free soda would be an example of that. We also need to encourage fitness; there’s quite a bit of evidence that suggests that fitness is a better predictor of health than weight alone, except at the highest levels of morbid obesity.

We need to do more in terms of public policy to encourage kids from a very early age to be active and to engage in athletic activities and more to encourage adults to do the same. So everything from investing more money in physical education in the schools to better bike paths so that people can bike to work and encouraging employers to provide support for both healthy eating and fitness-related activities would be examples.

TSD: As far as education, is there a difference between how adults and children should be educated about obesity?

DR: As in every area of education, the instruction needs to be age-appropriate. And adults are likely to resent what [opponents call] the “nanny state” – people telling them what to do. But there are a variety of ways that we can inform individuals to help them make more healthy choices. Calorie counts in fast food restaurants are a good example of that because we know that even nutrition experts don’t make accurate assessments of what’s in fast food.

TSD: You mentioned the “nanny state,” but what other factors are holding back obesity reform?

DR: I think you have a very well-financed lobby on the other side – soft drink manufacturers, fast food manufacturers – who are really resistant to anything that might curtail consumption, which is part of the solution to the obesity problem.

TSD: What progress in obesity reform do you think we’ll see in the next 10 years?

DR: I think that the issue is now on the agenda in a way that it hasn’t been in the last quarter century. Part of this is due to the concerted efforts of health professionals, but certainly Michelle Obama’s initiative in focussing White House attention on this issue helped. And both state and federal government, as both employers and insurers, are extremely concerned with the prevention of obesity-related diseases. So I think you’ll see more public policy efforts in the next decade.

 

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Q&A with Stanford law professor Deborah Rhode on obesity and public policy appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2015/11/05/qa-with-stanford-law-professor-deborah-rhode-on-obesity-and-public-policy/feed/ 2 1106344
Course evaluations revamped after complaints about old system https://stanforddaily.com/2015/10/21/course-evaluations-revamped-after-complaints-about-old-system/ https://stanforddaily.com/2015/10/21/course-evaluations-revamped-after-complaints-about-old-system/#comments Thu, 22 Oct 2015 05:47:35 +0000 https://stanforddaily.com/?p=1105481 In response to widespread dissatisfaction with student course evaluations, the University will launch a new form at the end of fall quarter.

The post Course evaluations revamped after complaints about old system appeared first on The Stanford Daily.

]]>
In response to widespread dissatisfaction with student course evaluations, the University will launch a new evaluation form at the end of fall quarter.

These new evaluations are the product of a multi-year process led by the Course Evaluation Committee (CEC). While designing the new forms, this committee looked at many different sources, including past survey results, scholarly literature and comments from hundreds of undergraduates organized into focus groups at the Behavioral Lab at the Stanford Graduate School of Business.

The main purpose of the new forms is to improve teaching effectiveness, according to CEC Chairman Russell Berman. 

These shouldn’t be about a popularity contest: ‘do I like this professor personally?’” Berman said. “It’s ‘does the course work for students?’”

In the 2010-2011 course evaluations, 35 percent of students fell into “straight-line responding,” in which they provided the same answer for every question on the page. To counter this, the CEC designed the new evaluations not only to make this kind of response impossible, but also to decrease the boredom that causes such responses.

The survey was reduced from 36 discrete parts to 12. Faculty are also able to customize the form to their class by entering in specific course learning goals and up to six additional questions three of which are open-ended, and three of which are closed-ended.

Instead of following the old “Excellent, Very Good… Poor” method of response, the closed-ended questions will incorporate “construct-specific” answer choices that are specific to what the question is asking.

For example, the question “How organized was the course?” has the answer set of “Extremely organized, Very organized… Not organized at all.” These styles of answer sets, along with mixing answer sets on a question-to-question basis, have been shown through research to improve the quality of survey responses.

The new form will also incorporate the open-ended question “What would you like to say about this course to a student who is considering taking it in the future?” which will be made viewable to students considering the course.

This qualitative review of courses was designed to provide a more reliable alternative to websites such as RateMyProfessors.com. Unlike commercial websites, where anyone can write a review for any course, the reviews from Stanford’s course evaluations are guaranteed to be from Stanford students who have completed the course.

CEC member and professor of political science Jon Krosnick commented that these publicized qualitative responses not only give students valuable information to consideration while choosing courses, but also encourage them to fill out the evaluations.

“It’s kind of like paying it forward. You are going to give information based on your experience so that other students will benefit the way you did from exactly this information,” said Krosnick.

In fact, course evaluations at Stanford were invented by students. According to the CEC report, the history of course evaluations dates back to the late 1950s when a student publication called “The Scratch Sheet” published qualitative descriptions of courses. Only later did faculty take action to adopt these student-initiated evaluations into their teaching.

After years of research, the CEC hopes the new evaluations will improve both student impact on academic affairs and undergraduate teaching as a whole.

“We are very hopeful that students will say, ‘Wow, I had no idea. It’s really cool that the university cares and put this effort into it, and that they want to see our views on courses. It’s not going to take that long. I’m going to do it,’” Krosnick said.

 

Contact Aulden Foltz at afoltz ‘at’ stanford.edu.

The post Course evaluations revamped after complaints about old system appeared first on The Stanford Daily.

]]>
https://stanforddaily.com/2015/10/21/course-evaluations-revamped-after-complaints-about-old-system/feed/ 6 1105481