People want more compensation, security for their genomic data

Genomic data donated by the public is valuable for the companies that collect it. But a recent survey finds that once people are aware of issues surrounding the use and security of genetic information, people are more concerned about how it might be used and expect to be better compensated for providing it.

Research co-authored by Ifeoma Ajunwa, assistant professor of labor relations, law and history at Cornell University, details the results of the first nationally representative survey to consider DNA collection from both nonprofit and for-profit settings.

Ajunwa and Forrest Briscoe, professor of management and organization at Pennsylvania State University, co-authored "Evolving Public Views on the Value of One's DNA and Expectations for Genomic Database Governance: Results from a National Survey," published March 11 in PLOS One. {module INSIDE STORY}

"A common theme in our findings is how people value control," Briscoe said. "They are more willing to provide data if they are told they will be able to select how it's used in the future - and if they can have it removed from the database later on. What they don't want is total loss of control once it's out there."

In their study, the authors provided 2,020 survey respondents with a three-minute video created from mainstream media coverage of genomic databases. Then they asked a series of questions about how governance policies - the ways data held by these companies is secured, used and regulated - would impact the respondents' willingness to provide data, as well as the payment they expect to receive.

After watching the video, nearly 12% of respondents said they would provide their data for free; more than 50% said they would provide it if compensated with payment and nearly 39% said they wouldn't provide it even if payment was available. This contrasted with results reported by academic research biobanks, which find consistently higher rates of willingness to donate DNA.

"When people were more informed, they were a lot more interested in requiring greater security for their data, and they were a little bit more hesitant to give it up," said Ajunwa.

The survey also asked how 12 specific policies would affect respondents' willingness to provide genomic data. The three policies that made them most likely to provide it were: the ability to request their data be deleted; assurance that their data wouldn't be sold or shared; and requiring specific permissions to reuse the data.

They were least likely to want to provide their data if the company sold access to pharmaceutical firms, provided data to the federal government or retained the data indefinitely.

"People need to know the full worth of their genetic data in order to make an informed consent," Ajunwa said. "How much is the data worth, what kinds of safeguarding are necessary, is it OK to have something in digital form and therefore more vulnerable? There are all of these outstanding questions to be answered."

UPenn researchers find new minor planets beyond Neptune

An updated catalog of trans-Neptunian objects, and the methods used to find them, could aid in future searches for undiscovered planets in the far reaches of the solar system

Using data from the Dark Energy Survey (DES), researchers have found more than 300 trans-Neptunian objects (TNOs), minor planets located in the far reaches of the solar system, including more than 100 new discoveries. Published in The Astrophysical Journal Supplement Series, the study also describes a new approach for finding similar types of objects and could aid future searches for the hypothetical Planet Nine and other undiscovered planets. The work was led by graduate student Pedro Bernardinelli and professors Gary Bernstein and Masao Sako. {module INSIDE STORY}

The goal of DES, which completed six years of data collection in January, is to understand the nature of dark energy by collecting high-precision images of the southern sky. While DES wasn't specifically designed with TNOs in mind, its breadth and depth of coverage made it particularly adept at finding new objects beyond Neptune. "The number of TNOs you can find depends on how much of the sky you look at and what's the faintest thing you can find," says Bernstein.

Because DES was designed to study galaxies and supernovas, the researchers had to develop a new way to track movement. Dedicated TNO surveys take measurements as frequently as every hour or two, which allows researchers to more easily track their movements. "Dedicated TNO surveys have a way of seeing the object move, and it's easy to track them down," says Bernardinelli. "One of the key things we did in this paper was figure out a way to recover those movements."

Using the first four years of DES data, Bernardinelli started with a dataset of 7 billion "dots," all of the possible objects detected by the software that were above the image's background levels. He then removed any objects that were present on multiple nights--things like stars, galaxies, and supernova--to build a "transient" list of 22 million objects before commencing a massive game of "connect the dots," looking for nearby pairs or triplets of detected objects to help determine where the object would appear on subsequent nights.

With the 7 billion dots whittled down to a list of around 400 candidates that were seen over at least six nights of observation, the researchers then had to verify their results. "We have this list of candidates, and then we have to make sure that our candidates are actually real things," Bernardinelli says.

To filter their list of candidates down to actual TNOs, the researchers went back to the original dataset to see if they could find more images of the object in question. "Say we found something on six different nights," Bernstein says. "For TNOs that are there, we actually pointed at them for 25 different nights. That means there's images where that object should be, but it didn't make it through the first step of being called a dot."

Bernardinelli developed a way to stack multiple images to create a sharper view, which helped confirm whether a detected object was a real TNO. They also verified that their method was able to spot known TNOs in the areas of the sky being studied and that they were able to spot fake objects that were injected into the analysis. "The most difficult part was trying to make sure that we were finding what we were supposed to find," says Bernardinelli.

After many months of method-development and analysis, the researchers found 316 TNOs, including 245 discoveries made by DES and 139 new objects that were not previously published. With only 3,000 objects currently known, this DES catalog represents 10% of all known TNOs. Pluto, the best-known TNO, is 40 times farther away from the sun than Earth is, and the TNOs found using the DES data range from 30 to 90 times Earth's distance from the sun. Some of these objects are on extremely long-distance orbits that will carry them far beyond Pluto.

Now that DES is complete, the researchers are rerunning their analysis on the entire DES dataset, this time with a lower threshold for object detection at the first filtering stage. This means that there's an even greater potential for finding new TNOs, possibly as many as 500, based on the researchers' estimates, in the near future.

The method developed by Bernardinelli can also be used to search for TNOs in upcoming astronomy surveys, including the new Vera C. Rubin Observatory. This observatory will survey the entire southern sky and will be able to detect even fainter and more distant objects than DES. "Many of the programs we've developed can be easily applied to any other large datasets, such as what the Rubin Observatory will produce," says Bernardinelli.

This catalog of TNOs will also be a useful scientific tool for research about the solar system. Because DES collects a wide spectrum of data on each detected object, researchers can attempt to figure out where the TNO originated from, since objects that form more closely to the Sun have are expected to have different colors than those that originated in more distant and colder locations. And, by studying the orbits of these objects, researchers might be one step closer to finding Planet Nine, a hypothesized Neptune-sized planet that's thought to exist beyond Pluto.

"There are lots of ideas about giant planets that used to be in the solar system and aren't there anymore, or planets that are far away and massive but too faint for us to have noticed yet," says Bernstein. "Making the catalog is the fun discovery part. Then when you create this resource; you can compare what you did find to what somebody's theory said you should find."

Astronomers use slime mold supercomputer simulations to map dark matter holding universe together

The behavior of one of nature's humblest creatures is helping astronomers probe the largest structures in the universe.

The single-cell organism, known as slime mold (Physarum polycephalum), builds complex filamentary networks in search of food, finding near-optimal pathways to connect different locations. In shaping the universe, gravity builds a vast cobweb structure of filaments tying galaxies and clusters of galaxies together along faint bridges hundreds of millions of light-years long. There is an uncanny resemblance between the two networks: one crafted by biological evolution, and the other by the primordial force of gravity.

The cosmic web is the large-scale backbone of the cosmos, consisting primarily of the mysterious substance known as dark matter and laced with gas, upon which galaxies are built. Dark matter cannot be seen, but it makes up the bulk of the universe's material. The existence of a web-like structure to the universe was first hinted at in the 1985 Redshift Survey conducted at the Harvard-Smithsonian Center for Astrophysics. Since those studies, the grand scale of this filamentary structure has grown in subsequent sky surveys. The filaments form the boundaries between large voids in the universe. Astronomers have gotten creative in trying to trace the elusive cosmic web, the large-scale backbone of the cosmos. Researchers turned to slime mold, a single-cell organism found on Earth, to help them build a map of the filaments in the local universe (within 500 million light-years from Earth) and find the gas within them. The researchers designed a computer algorithm inspired by the organism's behavior and applied it to data containing the positions of 37,000 galaxies ({module INSIDE STORY}

But astronomers have had a difficult time finding these elusive strands because the gas is so dim it is hard to detect. Now a team of researchers has turned to slime mold to help them build a map of the filaments in the local universe (within 500 million light-years from Earth) and find the gas within them.

They designed a computer algorithm, inspired by slime-mold behavior, and tested it against a supercomputer simulation of the growth of dark matter filaments in the universe. A computer algorithm is similar to a recipe that tells a supercomputer precisely what steps to take to solve a problem.

The researchers then applied the slime mold algorithm to data containing the locations of 37,000 galaxies mapped by the Sloan Digital Sky Survey at distances corresponding to 300 million light-years. The algorithm produced a three-dimensional map of the underlying cosmic web structure.

They then analyzed the ultraviolet light from 350 quasars (at much farther distances of billions of light-years) cataloged in the Hubble Spectroscopic Legacy Archive, which holds the data from NASA's Hubble Space Telescope's spectrographs. These distant cosmic flashlights are the brilliant black-hole-powered cores of active galaxies, whose light shines across space and through the foreground cosmic web. Imprinted on that light was the telltale absorption signature of otherwise undetected hydrogen gas that the team analyzed at specific points along the filaments. These target locations are far from the galaxies, which allowed the research team to link the gas to the universe's large-scale structure.

"It's really fascinating that one of the simplest forms of life actually enables insight into the very largest-scale structures in the universe," said lead researcher Joseph Burchett of the University of California (UC), Santa Cruz. "By using the slime-mold simulation to find the location of the cosmic web filaments, including those far from galaxies, we could then use the Hubble Space Telescope's archival data to detect and determine the density of the cool gas on the very outskirts of those invisible filaments. Scientists have detected signatures of this gas for several decades, and we have proven the theoretical expectation that this gas comprises the cosmic web."

The survey further validates research that denser regions of intergalactic gas are organized into filaments that the team found stretches over 10 million light-years from galaxies. (That distance is more than 100 times the diameter of our Milky Way galaxy.)

The researchers turned to slime mold simulations when they were searching for a way to visualize the theorized connection between the cosmic web structure and the cool gas detected in previous Hubble spectroscopic studies.

Then team member Oskar Elek, a computational media scientist at UC Santa Cruz, discovered online the work of Sage Jenson, a Berlin-based media artist. Among Jenson's works were mesmerizing artistic visualizations showing the growth of a slime mold's tentacle-like network of food-seeking structures. Jenson's art was based on outside scientific research, which detailed an algorithm for simulating the growth of slime mold.

The research team noted a striking similarity between how the slime mold builds complex filaments to capture new food, and how gravity, in shaping the universe, constructs the cosmic web strands between galaxies and galaxy clusters.

Based on the simulation, Elek developed a three-dimensional supercomputer model of the buildup of slime mold to estimate the location of the cosmic web's filamentary structure.

Although using a slime-mold-inspired simulation to pinpoint the universe's largest structures may sound bizarre at first, scientists have used supercomputer models of these humble microorganisms, as well as grown them in Petri dishes in a lab, to solve such complex problems as finding the most efficient traffic routes in large cities, solving mazes and pinpointing crowd evacuation routes. "These are hard problems to solve for a human, let alone a computer algorithm," Elek said.

"You can almost see, especially in the map of galaxies in the local universe from the Sloan data, where the filaments should be," Burchett explained. "The slime-mold model fits that intuition impressively. The structure that you know should be there is all of a sudden found by the computer algorithm. There was no other known method that was well suited to this problem for our research."

The researchers say that it is very difficult to design a reliable algorithm for finding the filaments in such a large survey of galaxies. "So it's quite amazing to see that the virtual slime mold gives you a very close approximation in just minutes," Elek explained. "You can literally watch it grow." Just for comparison, growing the organism in a petri dish takes days. Slime mold actually has a very special kind of intelligence for solving this one spatial task. After all, it's critical to its survival.