Store-bought tomatoes taste horrifically disgusting — err, bland. Now scientists have discovered a version of a gene that helps give tomatoes their flavor is actually missing in about 93 percent of modern, domesticated varieties. The discovery may help bring flavor back to tomatoes you can pick up in the produce section.

“How many times do you hear someone say that tomatoes from the store just don’t quite measure up to heirloom varieties?” Clifford Weil, program director of the National Science Foundation’s Plant Genome Research Program that supported the work, asked in a press announcement. “This study gets to why that might be the case and shows that better tasting tomatoes appear to be on their way back.”

Domestication Doom

An international team of researchers collected genomic information from 725 cultivated and wild tomatoes and assembled them into a pan-genome — a genome that captures the genetic information of all the varieties. Then they compared the pan-genome to the genome of a domesticated tomato called Heinz 1706. Until now, this tomato genome has served as the representative example of all tomato genomes.

The side-by-side comparison showed that the Heinz 1706 reference genome was missing nearly 5,000 genes that the other tomato varieties have. Many of these lost genes also equipped the plants with defenses against pathogens.

Tomatoes lost these genes through good old-fashioned breeding — not via genetic modifications — when breeders selected for traits that made tomatoes robust.

“During the domestication and improvement of the tomato, people mostly focused on traits that would increase production, like fruit size and shelf-life,” Zhangjun Fei, a plant geneticist at Cornell University in Ithaca, New York, who led the new research, said in a statement. “Some genes involved in other important fruit quality traits and stress tolerance were lost during this process.”

The identification of the previously unknown genes could help breeders create better tomatoes. “These new genes could enable plant breeders to develop elite varieties of tomatoes that have genetic resistance to diseases that we currently address by treating the plants with pesticides or other cost-intensive and environmentally unfriendly measures,” James Giovannoni, a molecular biologist at Cornell and USDA scientist, who co-led the work with Fei, said in a statement.

Taste Turnaround

The analysis also revealed a rare form of a gene that imparts tomato flavor to the fruit is missing in most modern, domesticated tomatoes. Yet, more than 90 percent of wild tomatoes have the flavor-punching version of the gene, the researchers report today in the journal Nature Genetics. Their analysis also shows that this flavor gene, called TomLoxC, uses carotenoids — the pigments that make tomatoes red — to make tomatoes tasty.

But there’s also good news for tomato-ravenous Americans, who each eat an average of nearly 100 pounds of the vegetables every year. The flavor gene is making a comeback. The rare version of TomLoxCused used to only be present in about 2 percent of tomato varieties. But in recent years, as breeders have begun to focus more on flavor, more and more modern tomato varieties have the gene. Nowadays, about 7 percent of tomatoes have it, meaning breeders have started selecting for it, Giovannoni explained, a trend that will hopefully keep growing.

The short article previews provided by Facebook can make users think they know more than they actually do about an issue, according to new research published in Research & Politics.

“Social media are so different from traditional types of media. In decades past, audiences had to choose to turn on the TV or open a newspaper to receive political information. Today, we receive that information inadvertently while scrolling through our Facebook and Twitter feeds. What’s more, that information can come from our friends and family members. I find these new dynamics fascinating,” said study author Nicolas Anspach, an assistant professor of political science at York College of Pennsylvania.

In the study, a group of 320 participants read an article from The Washington Post about the safety of genetically modified foods. Another group of 319 participants read a mock Facebook News Feed containing four article previews, where one preview was about genetically modified foods. A third group of 351 participants, which was used as a control, did not read anything.

To test their knowledge of the subject, the participants were then asked six factual questions about genetically modified foods. To test their confidence, they were also asked to estimate the number of questions they believed they answered correctly.

Participants who read the full article answered the most questions correctly, while those who read the News Feed correctly answered only one question more often than the control group on average. But participants who read the News Feed were more likely to overestimate their knowledge, especially among those motivated to experience strong emotions.

“Social media can inform audiences, even the little article previews that appear in Facebook’s News Feed. However, with this learning comes a false confidence; some individuals (particularly those motivated by their gut reactions) think they learn more the issue than they actually do,” Anspach said.

“This overconfidence might translate to increased political participation, but concern remains over whether social media provide enough information for voters to make fully informed choices.”

“In our experiment, we used factual information to test learning. But it’s important to recognize there is a lot of garbage shared via social media. Before we get too excited about social media’s ability to inform audiences, we should also consider its potential to misinform,” Anspach explained.

In a similar study, Anspach and his colleagues found that people are more likely to believe misinformed social media comments over factual information embedded in article previews.

“I suspect future research will consider factors such as age or digital literacy to better understand how audiences react to facts and misinformation differently,” Anspach said.

The study, “A little bit of knowledge: Facebook’s News Feed and self-perceptions of knowledge“, was authored by Nicolas M. Anspach, Jay T. Jennings, and Kevin Arceneaux.

Coca-Cola has poured millions of dollars into scientific research at universities. But if the beverage giant doesn’t like what scientists find, the company has the power to make sure that their research never sees the light of day.

That’s according to an analysis published in the Journal of Public Health Policy that explains how Coca-Cola uses contract agreements to influence the public health research it financially supports.

The paper explains that Coca-Cola uses carefully-constructed contracts to ensure that the company gets early access to research findings, as well as the ability to terminate studies for any reason. Researchers say this gives the beverage company the ability to squash unfavorable research findings, such as studies that connect the consumption of sugar-sweetened beverages to obesity.

The study’s authors are affiliated with the University of Cambridge, London School of Hygiene and Tropical Medicine, University of Bocconi, and U.S. Right to Know, a nonprofit organization that advocates for greater transparency in the food system. They based their report on Coca-Cola research contracts obtained through numerous Freedom of Information requests, which uncovered over 87,000 pages of documents. In the stack, the study’s authors found five Coca-Cola research agreements with four universities: Louisiana State University, University of South Carolina, University of Toronto and the University of Washington.

Much of the research Coca-Cola supports is related to nutrition and physical activity.

While their analysis focused on Coca-Cola, the researchers say that these types of contracts aren’t unique in the world of corporate-sponsored science. As the U.S. government spends less on research, corporate sponsors are kicking in — but not always for the common good. POM, Monsanto and PepsiCo have sponsored health studies related to their products. But by revealing how just one company can influence and even kill studies without reason, the study’s authors make the case for greater transparency in corporate-sponsored scientific research.

The Fine Print

In parsing the fine print of these contracts, researchers found that Coca-Cola is entitled to review studies before they’re published, can provide comments on the research, and has the right to terminate research projects at any time, without reason. Contractual provisions also ensured that Coca-Cola maintained intellectual property rights connected to the research.

Although the researchers didn’t uncover concrete examples of Coca-Cola concealing research findings that could be harmful to the company, the researchers say it’s telling that these restrictive contractual clauses exist in the first place.

“Coca-Cola is writing into some of its research agreements the ability to influence — and even kill — its research projects. This is very significant,” said study author Gary Ruskin, who is also co-director of U.S. Right to Know, in an email. “One of the tenets of the scientific method is that the outcomes of experiments are not predetermined. But in some cases, Coca-Cola had the power to predetermine scientific outcomes, in that it could kill the studies if they turned out badly for Coca-Cola and its profits. That’s not science. It’s public relations.”

The study’s authors uncovered email exchanges showing scientists and university officials discussing Coca-Cola contract agreements.

In one such email, a scientist expressed uncertainty over a study termination and expressed concerns over intellectual property ownership. In another email exchange, a scientist at another university remarked that their contract was “very restrictive for an unrestricted grant.”

Corporate Interests

It’s not the first time the public is hearing about Coca-Cola’s questionable involvement in scientific research. A few years ago, Coca-Cola disbanded its Global Energy Balance Network, a group led by scientists and created by Coca-Cola. The group was criticized by the public health community for promoting the idea that lack of exercise, not poor diet, was primarily responsible for the obesity epidemic.

The paper’s authors say the findings call into question the company’s motivations for funding health research. They are calling on Coca-Cola and other corporate backers of scientific research to publish lists of terminated studies. Ruskin said that journals should require scientists to share any research agreements with corporate funders and make them accessible.

In a statement from the company, Coca-Cola said “we agree research transparency and integrity are important,” but did not comment on specifics for this story. 
The super energetic gamma rays originated thousands of light-years away, and scientists still aren't exactly sure what generated them.

This image of the Crab Nebula in x-rays shows the pulsar clearly spinning at the nebula’s center.
NASA/CXC/ASU/J. Hester et al.

Astronomers using the Tibet AS-gamma Experiment have discovered the highest-energy light ever measured from an astrophysical source. Photons streaming from the Crab Nebula were recently measured at energies well over 100 tera-electronvolts (TeV). That’s a trillion electron volts, or some 10 times the maximum energy that the Large Hadron Collider sees when it slams particles together.

Scientists think the key is a pulsar lurking deep inside the heart of the Crab Nebula, the dense, rapidly spinning core left when a star exploded in a supernova almost a thousand years ago. Actually, since the nebula is located over 6,500 light-years away, the explosion occurred about 7,500 years ago, but the light from that explosion didn’t reach Earth until 1054 CE, when it exploded in our night skies as a bright new star, spotted by astronomers around the globe.

The supernova’s light faded after just weeks, but since then, the detritus has grown and spread, and it now glows wonderfully in the night sky at nearly every wavelength. It crackles in low-energy radio waves, blasts out high-energy gamma and x-rays, and shines at visible wavelengths in between.

But this ultra-high-energy light is new even for the Crab Nebula. Researchers from China and Japan published their findings in Physical Review Letters on July 29.

Record breaker

It’s difficult for high-energy photons like gamma rays to actually make it past Earth’s atmosphere. Instead, when gamma rays slam into air particles, they usually scatter into a shower of other particles. But astronomers have learned to search for these showers, usually with arrays spanning miles, since by the time these showers reach the ground, they may be spread out over a large area. Tibet AS-gamma combines 597 detectors scattered across 65,700 square meters on the surface. About 8 feet under this array sit 64 concrete barrels filled with water that serve as complementary detectors.

The larger array on the ground lets scientists trace the direction and energy of a high-energy event. The water detectors complement these observations by tracking the specific signature of such events. This allows researchers to distinguish gamma-rays from high-energy cosmic rays, which can produce similar showers of particles, even though cosmic rays are made of particles like protons and electrons, instead of photons.

Researchers collected data from both detectors in tandem from February 2014 until May 2017, and found a total of 24 events greater than 100 TeV that they could trace to the Crab Nebula. Some of the events reached a whopping 450 TeV. Separating the gamma ray events from the cosmic ray events isn’t a perfect science, so the researchers estimate that five or six of their observations were actually background cosmic rays. But the rest should be real, a sign of the powerhouse that lurks inside the Crab Nebula.

Star light, star bright

Very high-energy particles wouldn’t be good for humans if they actually struck us, but since they splinter into a cascade of other particles, there’s no danger from the Crab Nebula’s radiation on Earth.

It’s not totally clear how the Crab Nebula manages to charge up these gamma rays to such high energies. The pulsar at the nebula’s heart spins and sends out a powerful stellar wind, as well as generating powerful magnetic fields, which can accelerate these particles to high speeds, increasing their energy.

It’s not clear whether there’s a maximum energy scientists can expect. The new observations hint at the next challenge: finding petaelectronvolt gamma rays, those with 1,000 TeV worth of energy.

Tibet AS-gamma will keep looking. But considering it takes a few years to analyze the massive amounts of data the array collects, it’s possible such a signal has already been recorded, and is simply waiting to be sifted out of the noise.

What was once a conspiracy theory is now the subject of congressional debate, peer-reviewed studies, and now a Harvard experiment. Harvard scientists will attempt to replicate the climate-cooling effect of volcanic eruptions with a world-first solar geoengineering experiment. The university announced this month that it has created an external advisory panel to examine the potential ethical, environmental and geopolitical impacts of this geoengineering project, which has been developed by the university’s researchers.

According to Nature Magazine, Louise Bedsworth, executive director of the California Strategic Growth Council, a state agency that promotes sustainability and economic prosperity, will lead the Harvard advisory panel, the university said on 29 July. The other seven members include Earth-science researchers and specialists in environmental and climate law and policy.

What was once a conspiracy theory will soon be a reality—any day now.

Known as the Stratospheric Controlled Perturbation Experiment (SCoPEx), the experiment will spray calcium carbonate particles high above the earth to mimic the effects of volcanic ash blocking out the sun to produce a cooling effect.

The experiment was announced in Nature magazine last year, who was one of few outlets to look into this unprecedented step toward geoengineering the planet.

If all goes as planned, the Harvard team will be the first in the world to move solar geoengineering out of the lab and into the stratosphere, with a project called the Stratospheric Controlled Perturbation Experiment (SCoPEx). The first phase — a US$3-million test involving two flights of a steerable balloon 20 kilometres above the southwest United States — could launch as early as the first half of 2019. Once in place, the experiment would release small plumes of calcium carbonate, each of around 100 grams, roughly equivalent to the amount found in an average bottle of off-the-shelf antacid. The balloon would then turn around to observe how the particles disperse.

Naturally, the experiment is concerning to many people, including environmental groups, who, according to Nature, say such efforts are a dangerous distraction from addressing the only permanent solution to climate change: reducing greenhouse-gas emissions.

The idea of injecting particles into the atmosphere to cool the earth also seems outright futile considering what scientists are trying to mimic—volcanic eruptions. If we look at the second largest eruption of the 20th century, Mount Pinatubo, which erupted in the Philippines in 1991, it injected 20 million tons of sulfur dioxide aerosols into the stratosphere. Scientists from the USGS estimated that this 20 million tons only lowered the temperature of the planet by about 1°F (0.5°C) and this only lasted a year because the particles eventually fell to back to Earth.

The Harvard team, led by scientists Frank Keutsch and David Keith, has been working on the SCoPEx project for several years but they haven’t always been in total agreement. In fact, as Nature reported, Keutsch—who is not a climate scientist—previously thought the idea to be “totally insane.” But he’s since changed his mind. As Nature reports:

When he saw Keith talk about the SCoPEx idea at a conference after starting at Harvard in 2015, he says his initial reaction was that the idea was “totally insane”. Then he decided it was time to engage. “I asked myself, an atmospheric chemist, what can I do?” He joined forces with Keith and Anderson, and has since taken the lead on the experimental work.

Adding to the questionable nature of this experiment is the fact that it is largely funded by none other than Microsoft co-founder, Bill Gates. Gates is no stranger to funding controversial experiments as he’s publicly funded many of them including one that would implant devices into babies to automatically give them vaccines.

While the Harvard team’s experiment may sound like something out of a dystopian science fiction movie, the reality is that it has long been on the table of governments and think tanks from around the world. In fact, just last November, a study published in Environmental Research Letters, talked about doing the exact same thing—geoengineering and planes spraying particulates into the atmosphere to curb global warming.

Again, this is not some conspiracy theory. Watch him say all of this in the video below starting at the 12:05 marker.

Although we are hearing more and more talk about geoengineering, it has been around for a very long time and not just in the realm of conspiracy theories. In fact, scientists have already suggested that it could be going on right now, unintentionally.

Researchers with the National Oceanic and Atmospheric Administration (NOAA) are suggesting contrails from airplanes may be inadvertently geoengineering the skies.

Chuck Long is a researcher with the Cooperative Institute for Research in Environmental Sciences (CIRES) at the NOAA Earth System Research Laboratory at the University of Colorado in Boulder. At the American Geophysical Union Fall Meeting in 2015, Long and his team released their paper, “Evidence of Clear-Sky Daylight Whitening: Are we already conducting geoengineering?” The analysis found that vapor from airplanes may be altering the climate through accidental geoengineering.

According to a new study, and not just because they’re excited about the possibility of food. Researchers found that dogs move their faces in direct response to the human gaze — usually producing so-called “puppy dog eyes” — even more than when they are presented with a treat.

“We can now be confident that the production of facial expressions made by dogs are dependent on the attention state of their audience and are not just a result of dogs being excited,” said co-author on the study Juliane Kaminski of the University of Portsmouth in a statement. She says this demonstrates that “dogs are sensitive to humans’ attention and that expressions are potentially active attempts to communicate, not simple emotional displays.”

This is certainly not the first study to find that animals are capable of producing facial expressions — most mammals can pull off something resembling a happy or sad face, but scientists generally assume that these are involuntary twitches rather than emotions. And we kind of know that too. When the family dog does that thing that looks exactly like smiling, we know that that’s just what happens when a dopey dog face pants after a good run.

But over the past few years, experts have slowly built the case that domesticated animals may actually use facial expressions to communicate with their human handlers. Using technology known as FACS (the Facial Action Coding System), researchers have catalogued facial expressions in macaques, dogs, and as of 2015, horses. We now know that humans have 27 distinct facial expressions, while chimpanzees can produce 13, horses can produce 17, and dogs can produce 16 (not bad, dogs). And, according to at least one study, horses can also read our facial expressions, and respond to angry faces differently than happy faces.

As for dogs, studies have inched toward the conclusion that dogs are smiling at us. One study found that dogs can be trained to identify human facial expressions even when presented with only part of a smiling or frowning face. Another found that dogs engage in the same social gazing behaviors as humans, scanning faces and eyes to determine intent and identify threats.

But until now, there was simply no evidence that dogs routinely make their own facial expressions in response to humans. So Kaminski and colleagues studied a small sample of 24 family dogs of various breeds, and filmed how each dog’s face responded as its owners faced it, offered it food, or looked away entirely. They then coded each facial expression with a modified dog version of FACS. They found that dogs produced more facial expressions when their owners were facing them than when they turned away or when food entered the picture.

There are many caveats to this study, including its small sample size and the looming question of whether these dogs produced facial expressions in response to human emotions or whether they have learned to make puppy dog eyes in response to the human gaze. But it is the closest scientists have come to demonstrating that your family pet is making faces at you.

“This study moves forward what we understand about dog cognition,” Kaminski said. “We now know dogs make more facial expressions when the human is paying attention.”

Ami Bhatt and her collaborators found that microbes in the human gut are making thousands of proteins so small that they've previously gone undetected.

Your body is a wonderland. A wonderland teeming with trillions of bacteria, that is. But it’s not as horrifying as it might sound. In fact, there’s mounting evidence that many aspects of our health are closely intertwined with the composition and hardiness of our microscopic compatriots, though exactly how is still mostly unclear.

Now, researchers at the Stanford University School of Medicine have discovered that these microbial hitchhikers — collectively known as the human microbiome — are churning out tens of thousands of proteins so small that they’ve gone unnoticed in previous studies. The proteins belong to more than 4,000 new biological families predicted to be involved in, among other processes, the warfare waged among different bacterial strains as they vie for primacy in coveted biological niches, the cell-to-cell communication between microbes and their unwitting hosts, and the critical day-to-day housekeeping duties that keep the bacteria happy and healthy.

Because they are so small — fewer than 50 amino acids in length — it’s likely the proteins fold into unique shapes that represent previously unidentified biological building blocks. If the shapes and functions of these proteins can be recreated in the lab, they could help researchers advance scientific understanding of how the microbiome affects human health and pave the way for new drug discovery.

A paper describing the research findings was published Aug. 8 in Cell. Ami Bhatt, MD, PhD, assistant professor of medicine and of genetics, is the senior author. Postdoctoral scholar Hila Sberro, PhD, is the lead author.

‘A clear blind spot’

“It’s critically important to understand the interface between human cells and the microbiome,” Bhatt said. “How do they communicate? How do strains of bacteria protect themselves from other strains? These functions are likely to be found in very small proteins, which may be more likely than larger proteins to be secreted outside the cell.”

But the proteins’ miniscule size had made it difficult to identify and study them using traditional methods.

“We’ve been more likely to make an error than to guess correctly when trying to predict which bacterial DNA sequences contain these very small genes,” Bhatt said. “So until now, we’ve systematically ignored their existence. It’s been a clear blind spot.”

It might be intimidating for the uninitiated to think too deeply about the vast numbers of bacteria that live on and in each of us. They account for far more cells in and on the human body than actual human cells do. Yet these tiny passengers are rarely malicious. Instead, they help with our digestion, supplement our diet and generally keep us running at our peak. But in many cases, it’s been difficult to pick apart the molecular minutiae behind this partnership.

Bhatt and her colleagues wondered if answers might be found in the small proteins they knew were likely to wiggle through the nets cast by other studies focusing on the microbiome. Small proteins, they reasoned, are more likely than their larger cousins to slip through the cell membrane to ferry messages — or threats — to neighboring host or bacterial cells. But how to identify and study these tiny Houdinis?

“The bacterial genome is like a book with long strings of letters, only some of which encode the information necessary to make proteins,” Bhatt said. “Traditionally, we identify the presence of protein-coding genes within this book by searching for combinations of letters that indicate the ‘start’ and ‘stop’ signals that sandwich genes. This works well for larger proteins. But the smaller the protein, the more likely that this technique yields large numbers of false positives that muddy the results.”

A big surprise

To tackle the problem, Sberro decided to compare potential small-protein-coding genes among many different microbes and samples. Those that were identified repeatedly in several species and samples were more likely to be true positives, she thought. When she applied the analysis to large data sets, Sberro found not the hundreds of genes she and Bhatt had expected, but tens of thousands. The proteins predicted to be encoded by the genes could be sorted into more than 4,000 related groups, or families, likely to be involved in key biological processes such as intercellular communication and warfare, as well as maintenance tasks necessary to keep the bacteria healthy.

“Honestly, we didn’t know what to expect,” Bhatt said. “We didn’t have any intuition about this. The fact that she found thousands of new protein families definitely surprised us all.”

The researchers confirmed the genes encoded true proteins by showing they are transcribed into RNA and shuttled to the ribosome for translation — key steps in the protein-making pathway in all organisms. They are now working with collaborators to learn more about the proteins’ functions and to identify those that might be important to the bacteria fighting for space in our teeming intestinal carpet. Such proteins might serve as new antibiotics or drugs for human use, they believe.

“Small proteins can be synthesized rapidly and could be used by the bacteria as biological switches to toggle between functional states or to trigger specific reactions in other cells,” Bhatt said. “They are also easier to study and manipulate than larger proteins, which could facilitate drug development. We anticipate this to be a valuable new area of biology for study.”

Bhatt is a member of Stanford Bio-X, the Stanford Cancer Institute, the Stanford Maternal & Child Health Research Institute and a fellow of Stanford ChEM-H.

Other Stanford co-authors are graduate student Brayon Fremin; postdoctoral scholars Soumaya Zlitni, PhD, and Fredrik Edfors, PhD; and Michael Snyder, PhD, professor and chair of genetics.

Researchers from One Codex, the Joint Genome Institute of the Department of Energy, the Alexander Fleming Biomedical Sciences Research Center in Greece, and Lawrence Berkeley National Laboratory also contributed to the study.

The study was supported by the National Institutes of Health (grants HG000044, K08CA184420, P30CA124435, and 1Ro1AT010123201), the PhRMA Foundation, the U.S. Department of Energy and a Damon Runyon Clinical Investigator Award.