Homemade microscope reveals how a cancer-causing virus clings to our DNA

M. Mitchell Smith, PhD, (left) built the laser microscope even though his background is in molecular genetics, not microscope building. He is pictured with collaborators Margaret J. Grant and Dean H. Kedes, MD, PhD. many more images and a 3-D animation are available.

Using a homemade, high-tech microscope, scientists at the University of Virginia School of Medicine have revealed how a cancer-causing virus anchors itself to our DNA. That discovery could pave the way for doctors to cure incurable diseases by flushing out viruses, including HPV and Epstein-Barr, that now permanently embed themselves in our cells.

"The reason we can't get rid of these [viruses] is because we can't figure out a way to get their DNA out of the nucleus, out of the cell," explained UVA researcher Dean H. Kedes, MD, PhD. "They depend on this 'tether' to remain anchored to the DNA within our cells, and to remain attached even as the cells divide. This tether is a key factor to disrupt in devising a cure."

Now that scientists can understand this vital infrastructure, they can work to disassemble it. "Without it," Kedes noted, "the virus is going to lose its hold in the body. ... Bad for the virus, but very good for the patient."

Homemade Microscope

The researchers used the microscope built by fellow investigator M. Mitchell Smith, PhD, to reveal the structure of the tether used by a virus called Kaposi's sarcoma-associated herpesvirus (KSHV). Until now, such tethers have largely eluded scientists because they are so diabolically small, defying even the most high-tech approaches to determining their form. "We're seeing things on the order of 8,000 times smaller than a human hair," said Smith, who built UVA's microscope piece-by-piece based on one pioneered in the Physics and Astronomy Department at the University of Maine.

Smith's microscope is nothing like the simple light microscope seen in every high school biology class. It's a stunning marriage of stainless steel and laser beams, looking much like an oversized sci-fi Erector set. It sits on a table that almost fills a small room.

"It's a set of lasers, a bunch of optics that focus and filter the lasers," Smith explained, gesturing to various components. "I'm trained as a molecular geneticist, not as an optical physicist ... so we worked on it for maybe three years. But it's continually a work in progress."

The device has already proved a game-changer, allowing him and Kedes to unveil the viral tether. The researchers -- in UVA's Department of Microbiology, Immunology and Cancer Biology -- used fluorescent antibodies to mark individual molecules on the tether and then recorded their location in space. They then combined the resulting images to create an outline of the shape, a bit like mapping a city from thousands of GPS signals.

To complete their 3D portrait, they combined their results with information drawn from other imaging techniques, such as X-ray crystallography. The result is the most complete portrait of the tether ever created. And that information likely will prove vital for cutting the rope on the virus' grappling hook.

The researchers envision using the approach for many other stubborn viruses, such as Epstein-Barr (the virus that causes infectious mononucleosis) and HPV (human papillomavirus). Further, they suspect that such viruses' tethers may share similarities with the one they revealed. "Now, for the first time," Kedes said, "it's OK to say, 'Let's focus on structures that are vital to the virus that before were below the limits of our standard methods of detection within infected cells.'"

Findings Published
The researchers have published their findings in the scientific journal PNAS, the Proceedings of the National Academy of Sciences. The research team consisted of Margaret J. Grant, Matthew S. Loftus, Aiola P. Stoja, Kedes and Smith.

Read more at Science Daily

Animal Advocates and Academics Seek Personhood Rights for Chimpanzees

When legal scholar Steven Wise first found Tommy, the male chimpanzee was living alone in a shed on a used trailer lot along Route 30 in Gloversville, New York. Believed to have been born in the early 1980s, Tommy was raised from infancy by David Sabo, proprietor of a circus troupe. When Sabo died in 2008, at least some of the chimps in his care, according to Wise, went to the owners of the trailer business.

Five years ago, Wise's Nonhuman Rights Project (NhRP) — a legal advocacy group for animals — filed a petition calling for, in part, Tommy's "immediate release from illegal detention." The petition further said: "Respondents are detaining Tommy in solitary confinement in a small, dank, cement cage in a cavernous dark shed ... ."

Based on the Animal Welfare Act (AWA), Tommy's owners appear to be in full compliance with federal law, which says that chimps, under certain conditions, can be housed alone and in cages. Nevertheless, Tommy's "confinement constitutes a profound harm that demands remedy by the courts," Gary Comstock, a professor of philosophy at North Carolina State University, told Seeker.

In February, Comstock and 16 other philosophers co-authored an amicus brief in support of an NhRP motion seeking habeas corpus relief for Tommy and another chimpanzee named Kiko. The New York State Court of Appeals is weighing whether or not to allow the suit to proceed. NhRP argues that chimpanzees like Tommy and Kiko should be recognized as a "person," since under current US law, one is either a person or a thing. Wise, president of the NhRP, explained that things "lack the capacity for any legal rights. Welfare protections do not alter this fact."

Brief co-author David Peña-Guzmán of California State University, San Francisco, told Seeker: "I think most people resist the notion of personhood mainly because they are not aware that the only alternative to it is thinghood. If you ask most people whether animals are analogous to things such as chairs and desks, most will emphatically say 'no.' If you then ask them whether animals can have rights, many will say 'yes.' These two answers add up to personhood."

According to Wise and the philosophers, the fight over Tommy highlights a persistent yet urgent problem concerning US law that treats nonhuman animals as things despite growing scientific evidence and societal acceptance that they are intelligent, sensitive, and social beings that can even at times communicate their feelings to humans.

Brief co-author Kristin Andrews of York University, for example, told Seeker that another chimp named Bruno learned sign language at the University of Oklahoma during research on communication. When funding for the project ran out, he was sent to a biomedical facility. Researcher Mark Bodamer of the university project later visited the chimp. Andrews said, "Bruno, who hadn't signed while at the biomedical facility, started signing when he saw Mark. What did he say? Key out!"

Tommy, a chimpanzee, is seen in Unlocking the Cage, a film by Chris Hegedus and D.A. Pennebaker.

L. Syd Johnson of Michigan Technological University, who is another author of the brief, said there have been many times in human history where hierarchies of humans have been established, sometimes by skin color, sex, age, religion, and having or not having certain abilities.

"On the 'thing' side of the divide, at various times in history, slaves, women, and children have been regarded as things and not persons," Wise said. "It took a mighty social struggle to move each of these beings into the class of rights-bearers — persons."

He added, "A person need not have the full suite of human rights, either. Corporations are persons but cannot marry, for example. Personhood is a tremendously flexible concept in the law. No third option is needed."

The European Union, however, has a third option in place.

Brief co-author Andrew Fenton of Dalhousie University told Seeker that the Treaty on the Functioning of the European Union, otherwise known as the Lisbon Treaty, recognizes nonhuman animals as "sentient beings,” but the treaty does not offer nonhuman primates full protections. For example, a stipulation allows that if there were "an unexpected outbreak of a life-threatening or debilitating clinical condition in human beings," nonhuman great apes could be used in research.

Peña-Guzmán said that if a third term like "sentient beings" could give chimpanzees the same protections as the term "person," then it is not even necessary to have this other wording in the first place.

If the third term does not afford the same protections, then "it is not as good," he said.

He continued, "What matters to us, ultimately, is that chimpanzees be given the right to bodily liberty, independently of what term is used. In the US at this moment in history, the only category that does this is 'person.'"

Andrews and Wise told Seeker that a formal definition of a person,"in the US legal context, can be traced back to John W. Salmond's Jurisprudence, first published in 1907 and cited by the most widely used legal dictionary in the US, Black's Law Dictionary. Salmond mentions that persons are subjects of "legal rights or duties." A person is therefore a rights bearer, and one either bears rights or does not.

Implementing that seemingly simple concept turns out to be far more complicated than imagined.

Consider that an Opinion of the Court rejecting NhRP's claims about chimpanzees concluded: [U]nlike human beings, chimpanzees cannot bear any legal duties, submit to societal responsibilities, or be held legally accountable for their actions. In our view, it is this incapability to bear any legal responsibilities and societal duties that renders it inappropriate to confer upon chimpanzees the legal rights — such as the fundamental right to liberty protected by the writ of habeas corpus — that have been afforded to human beings."

Lawyer Steven Wise is seen in court in Unlocking the Cage, a film by Chris Hegedus and D.A. Pennebaker.

A writ of habeas corpus, what NhRP is seeking for Tommy, means to "produce the body" and is a court order to show valid reason for an individual's detention. In Tommy's case, that refers to his being locked up alone in metal cage.

Johnson said that in 1874, the American Society for the Prevention of Cruelty to Animals even filed a writ of habeas corpus on behalf of an abused child because the law at the time did not recognize children as persons, and there were no laws then against child abuse.

If the court's criteria for personhood were to hold on every level, some of the most vulnerable people — infants, the mentally ill, people with dementia — would be considered things, not persons.

NhRP brief co-author Tyler John of Rutgers University told Seeker that the New York court's legal argument "excludes basic legal protections for some humans who morally deserve these basic legal protections. It therefore must be mistaken."

"But," he added, "we should also note that on a proper understanding of civic responsibilities, many nonhuman animals can, in fact, bear civic responsibilities. None of us were taught to obey the law from an early age through abstract philosophical reflection; we learned it through modeling of good behavior and through the good things that happen when we obey rules. Chimpanzees and other social animals can learn to obey many civic duties in the same way."

Even if there are some legal duties that certain human and nonhuman animals cannot have, this does not by itself mean that we need new legal categories for these individuals, John continued.

He added, "Children and chimpanzees deserve the legal protection of their basic rights to liberty and bodily integrity regardless of whether they can bear legal duties, and under the law this amounts to personhood."

John further pointed out that if a very young child were to refuse a lifesaving medical procedure, guardians could override the decision. No one, on the other hand, may override a human adult's clear-headed decision to refuse such a procedure.

"But this does not mean that we need to classify young children as falling between persons and things," he said.

In a recent op-ed in The New York Times, NhRP brief co-author Jeff Sebo suggests that "a more inclusive view of personhood" might take into account the following features: conscious experience, emotionality, a sense of self or bonds of care, or interdependence.

He argues that Tommy and Kiko, "are conscious, emotional, intelligent, social beings whose lives are deeply entangled with our own, their current state of isolation notwithstanding. As a result, they count as persons on any view inclusive enough to meet contemporary standards of human rights."

If Sebo's criteria for personhood were upheld, though, chimpanzees would not be the only nonhuman animals that could pass this type of test. Common pets, such as dogs and cats, clearly would, too. It is easy for us to relate to these complex and social mammals that are somewhat like ourselves.

But biases likely affect the values we place on less similar animals like fish — and insects.

"I want to allow for the possibility that insects can have rights," Sebo, director of the animals studies master's degree program at New York University, told Seeker. "If insects are conscious, and if conscious beings can have rights, then insects can have rights, even if they have different rights than humans."

"Of course," he added, "others might disagree with me about this. Either way, we can start by accepting that Kiko and Tommy can have rights and then we can ask the other, more difficult questions that follow."

The NhRP argues that autonomy is a sufficient, but not a necessary, requirement for personhood. This could lead down a slippery slope over how we judge the inherent worth of other species and even other aspects of nature. Brief co-author Robert Jones of California State University, Chico, told Seeker that many ecosystem components, such as plants, clearly play essential roles in the web of life, "but lack so-called intrinsic value."

"However," he added, "those beings who possess subjective experiences that have an attractive or aversive quality — such as pain and suffering, pleasure and joy — have an interest in not having those experiences in the way that a boulder or blade of grass does not."

Wise said that as the common law continues to evolve, there may be other criteria beyond autonomy on which to base rights for nonhuman animals. For now, his organization's focus is on seeking legal rights and personhood for not only chimpanzees, but also elephants and orcas.

NhRP has already begun litigating on behalf of elephants Minnie, Beulah, and Karen at the Commerford Zoo in Goshen, Conn. The US Department of Agriculture has cited the zoo over 50 times for failing to adhere to minimum standards required under the Animal Welfare Act, according to NhRP, which reports that the zoo continues to use bullhooks — elephant-training tools with a metal hook at the end — on the pachyderms.

Minnie the elephant performing at Commerford Zoo, Goshen, Conn.

While prospects for the elephants remain unknown, NhRP has made strides in other litigation. In 2015, at the behest of the organization, Justice Barbara Jaffe became the first judge in history to issue a writ of habeas corpus on behalf of two chimpanzees, Hercules and Leo. The legal document was later amended to strike out the phrase "writ of habeas corpus." Court appeals failed to obtain "legal persons" status for the chimps.

The New Iberia Research Center (NIRC), where the chimps were born in 2006, had previously leased Hercules and Leo to Stony Brook University for a study on bipedal walking. After the litigation, Hercules and Leo were returned to NIRC in 2015.

According to the journal Science, on March 21 of this year, NIRC moved the primates to the Project Chimps sanctuary in Georgia. Wise has "serious concerns" about Project Chimps. For example, he said that "there is only one outdoor area for the chimps at the site." He told Science, though, “I’m glad to hear Hercules and Leo are getting out of New Iberia."

Wise hopes that the two males can be moved to another sanctuary, Save the Chimps, which is in Florida and has offered to house the primates at no extra cost to NIRC. Like the three elephants, it remains unknown for now what will ultimately happen to these two chimps.

Jaffe's issuance of the writ of habeas corpus, however, marks a legal milestone that was followed in 2016 by a similar judgment in Argentina granting "nonhuman person" status to a chimp named Cecilia. The chimp was ordered removed from a zoo and transferred to a sanctuary.

Approximately 2,000 chimpanzees are kept in captivity in the US alone. According to the World Animal Foundation, about 300 are in zoos, and the remaining 1,700 were bred for medical research. The situation seems monumental when other animals are factored in. There are 100 million animals held captive for entertainment and research purposes, based on Humane Society International estimates.

A recent survey conducted by the Sentience Institute, which was replicated by Oklahoma State University, found that nearly 50 percent of Americans desire a ban on slaughterhouses. A recent poll commissioned by NhRP found that almost half of all participants "agreed with a statement saying that animals deserve the same rights as humans," and "about half said they would support legislation to recognize legal rights for some animals."

The legalese of personhood is hard for many people to grasp, though, and the studies indicate that the public is divided nearly 50-50 in their views of animal rights.

Richard Cupp, a professor at Pepperdine School of Law, told Seeker that he supports legal efforts to improve the welfare of animals, but said the term “animal rights” is vague.

“My experience is that many people who initially say they support 'animal rights' actually support imposing appropriate legal responsibilities on humans to prohibit mistreatment of animals, rather than supporting legal personhood and accompanying legal rights for animals," he said.

The arguments against granting animals personhood rights, he said, range from chimps lacking "a sufficient level of moral agency to be justly held legally accountable" to "the potential societal chaos" that would ensue should legal personhood be extended to nonhuman animals.

"Rejecting nonhuman animal, legal personhood does not imply being satisfied with the status quo regarding how we treat animals," Cupp said. "Society has made important advances in animal welfare in recent years, and we are probably closer to the beginning of this significant period of animal welfare, legal evolution than we are to its future high point. As a society we need to continue our evolution toward increased protection of animals, but they should not be made legal persons."

He acknowledges that lawmakers and others need to do a better job of being explicit in statutes, ordinances, and court decisions that sentient animals are different from inanimate property. "Sentience" itself is a loaded topic, but Cupp uses the word to describe animals capable of suffering.

His views of the issue will soon be published in the University of Cincinnati Law Review. A draft of the article is available online. As Cupp admits in the article, however, not granting chimpanzees and other animals personhood does mean that they are "still property" in the eyes of the law.

If the New York court eventually does issue an "order to show cause" pursuant to the writ of habeas corpus, a hearing would take place, as it did in Hercules and Leo's case, which would shift the burden of proof from the NhRP to those currently holding the chimps captive. Then, if the owners cannot justify the legality of their detainment of the chimps, the court could rule that Kiko and Tommy are legal persons with the right to bodily liberty and offer "relief," which might mean transferring the chimps to a sanctuary.

If the owners cannot prove the legality of their detainment of the chimps, the court could then offer "relief," which might mean transferring the chimps to a sanctuary. Such a ruling would likely serve as precedent for other parties to seek habeas corpus relief for other chimpanzees in New York and could lead to similar rulings in other states.

A potential complication in the New York case has to do with the current location and status of Tommy. In 2016, various media outlets including The Dodo reported that Tommy was donated to the DeYoung Family Zoo in Wallace, Michigan, in September 2015.

Brittany Peet, director of captive animal law enforcement for PETA Foundation, told Seeker that New York State Department of Agriculture and Markets records provide evidence that the donation occurred. Representatives for the zoo, which is seasonal and reopens this year on May 1, have claimed to be unfamiliar with any chimpanzee named Tommy and have not confirmed his existence.

PETA filed a complaint against the zoo in 2016, which suggests that, even though the plaintiffs deny having a chimp named Tommy, they do "have a chimpanzee" that is then referred to as "Chimpanzee number 2" as well as a chimp called "Louie." PETA even issued a petition, urging that the zoo retire their chimpanzees to a reputable sanctuary.

The number-2 terminology is a stark reminder of what can happen when animals become nameless property. Death records often follow suit, which could mean that if Tommy did die, his name — and therefore the loss of him as a unique individual — might never be known.

Wise, however, said, "We have a strong basis for believing Tommy is alive and still in New York."
If that is the case, his condition remains unknown.

As for Kiko, NhRP believes that he is now in a cage in a cement storefront attached to a home in a residential area of Niagra Falls, New York. Whatever one thinks of this unusual arrangement, no welfare law appears to have been violated with the confinement of Kiko and Tommy.

"But this does not mean that their conditions of life are morally acceptable as they currently stand," Peña-Guzmán said.

Read more at Seeker

Dogs could be more similar to humans than we thought

The canine microbiome is quite similar to that of humans.

Dog and human gut microbiomes have more similar genes and responses to diet than we previously thought, according to a study published in the open access journal, Microbiome.

Dr Luis Pedro Coelho and colleagues from the European Molecular Biology Laboratory, in collaboration with Nestlé Research, evaluated the gut microbiome of two dog breeds and found that the gene content of the dogs microbiome showed many similarities to the human gut microbiome, and was more similar to humans than the microbiome of pigs or mice.

Dr Luis Pedro Coelho, corresponding author of the study, commented: "We found many similarities between the gene content of the human and dog gut microbiomes. The results of this comparison suggest that we are more similar to man's best friend than we originally thought."

The researchers found that changes in the amount of protein and carbohydrates in the diet had a similar effect on the microbiota of dogs and humans, independent of the dog's breed or sex. The microbiomes of overweight or obese dogs were found to be more responsive to a high protein diet compared to microbiomes of lean dogs; this is consistent with the idea that healthy microbiomes are more resilient.

Dr Luis Pedro Coelho, commented: "These findings suggest that dogs could be a better model for nutrition studies than pigs or mice and we could potentially use data from dogs to study the impact of diet on gut microbiota in humans, and humans could be a good model to study the nutrition of dogs.

"Many people who have pets consider them as part of the family and like humans, dogs have a growing obesity problem. Therefore, it is important to study the implications of different diets."

The researchers investigated how diet interacted with the dog gut microbiome with a randomized controlled trial using a sample of 64 dogs, half of which were beagles and half were retrievers, with equal numbers of lean and overweight dogs. The dogs were all fed the same base diet of commercially available dog food for four weeks then they were randomized into two groups; one group consumed a high protein, low carb diet and the other group consumed a high carb, low protein diet for four weeks. A total of 129 dog stool samples were collected at four and eight weeks. The researchers then extracted DNA from these samples to create the dog gut microbiome gene catalogue containing 1,247,405 genes. The dog gut gene catalogue was compared to existing gut microbiome gene catalogues from humans, mice and pigs to assess the similarities in gene content and how the gut microbiome responds to changes in diet.

Read more at Science Daily

3-D human 'mini-brains' shed new light on genetic underpinnings of major mental illness

Neurons

Major mental illnesses such as schizophrenia, severe depression and bipolar disorder share a common genetic link. Studies of specific families with a history of these types of illnesses have revealed that affected family members share a mutation in the gene DISC1. While researchers have been able to study how DISC1 mutations alter the brain during development in animal models, it has been difficult to find the right tools to study changes in humans. However, advancements in engineering human stem cells are now allowing researchers to grow mini-organs in labs, and gene-editing tools can be used to insert specific mutations into these cells.

Researchers from Brigham and Women's Hospital are leveraging these new technologies to study the effects of DISC1 mutations in cerebral organoids -- "mini brains" -- cultured from human stem cells. Their results are published in Translational Psychiatry.

"Mini-brains can help us model brain development," said senior author Tracy Young-Pearse, PhD, head of the Young-Pearse Lab in the Ann Romney Center for Neurologic Diseases at BWH. "Compared to traditional methods that have allowed us to investigate human cells in culture in two-dimensions, these cultures let us investigate the three-dimensional structure and function of the cells as they are developing, giving us more information than we would get with a traditional cell culture."

The researchers cultured human induced pluripotent stem cells (iPSCs) to create three-dimensional mini-brains for study. Using the gene editing tool CRISPR-Cas9, they disrupted DISC1, modeling the mutation seen in studies of families suffering from these diseases. The team compared mini-brains grown from stem cells with and without this specific mutation.

DISC1-mutant mini-brains showed significant structural disruptions compared to organoids in which DISC1 was intact. Specifically, the fluid-filled spaces, known as ventricles, in the DISC1-mutant mini-brains were more numerous and smaller than in controls, meaning that while the expected cells are present in the DISC1-mutant, they are not in their expected locations. The DISC1-mutant mini-brains also show increased signaling in the WNT pathway, a pathway known to be important for patterning organs and one that is disrupted in bipolar disorder. By adding an inhibitor of the WNT pathway to the growing DISC1-mutant mini-brains, the researchers were able to "rescue" them -- instead of having structural differences, they looked similar to the mini-brains developed from normal stem cells. This suggests that the WNT pathway may be responsible for the observed structural disruption in the DISC1-mutants, and could be a potential target pathway for future therapies.

"By producing cerebral organoids from iPSCs we are able to carefully control these experiments. We know that any differences we are seeing are because of the DISC1-mutation that we introduced," said Young-Pearse. "By looking at how DISC1-mutations disrupt the morphology and gene expression of cerebral organoids, we are strengthening the link between DISC1-mutation and major mental illness, and providing new avenues for investigation of this relationship."

Read more at Science Daily

Clear as mud: Desiccation cracks help reveal the shape of water on Mars

Curiosity Mastcam image of the Old Soaker rock slab taken on Sol 1555. The red-toned bed is covered by ridges that are the remnants of sediment that filled cracks that formed in drying lake in Gale Crater some ~3.5 billion years ago. The slab is about 80 cm across.

As Curiosity rover marches across Mars, the red planet's watery past comes into clearer focus.

In early 2017 scientists announced the discovery of possible desiccation cracks in Gale Crater, which was filled by lakes 3.5 billion years ago. Now, a new study has confirmed that these features are indeed desiccation cracks, and reveals fresh details about Mars' ancient climate.

"We are now confident that these are mudcracks," explains lead author Nathaniel Stein, a geologist at the California Institute of Technology in Pasadena. Since desiccation mudcracks form only where wet sediment is exposed to air, their position closer to the center of the ancient lake bed rather than the edge also suggests that lake levels rose and fell dramatically over time.

"The mudcracks show that the lakes in Gale Crater had gone through the same type of cycles that we see on Earth," says Stein. The study was published in Geology online ahead of print on 16 April 2018.

The researchers focused on a coffee table-sized slab of rock nicknamed "Old Soaker." Old Soaker is crisscrossed with polygons identical in appearance to desiccation features on Earth. The team took a close physical and chemical look at those polygons using Curiosity's Mastcam, Mars Hand Lens Imager, ChemCam Laser Induced Breakdown Spectrometer (LIBS), and Alpha-Particle X-Ray Spectrometer (APXS).

That close look proved that the polygons -- confined to a single layer of rock and with sediment filling the cracks between them -- formed from exposure to air, rather than other mechanisms such as thermal or hydraulic fracturing. And although scientists have known almost since the moment Curiosity landed in 2012 that Gale Crater once contained lakes, explains Stein, "the mudcracks are exciting because they add context to our understanding of this ancient lacustrine system."

"We are capturing a moment in time," he adds. "This research is just a chapter in a story that Curiosity has been building since the beginning of its mission."

From Science Daily

Stone Age Cow Underwent Cranial Surgery 5,000 Years Ago

3D reconstruction of the cow skull showing internally and externally the hole produced by trepanation. Bar corresponds to 10 cm

The history of early surgical techniques, from limb amputations to draining infected wounds, likely goes deep into antiquity and therefore is largely unknown. The oldest surgical procedure for which there is archaeological evidence is thought to be cranial trepanation that involved drilling a hole in the head to expose the brain in hopes of treating seizures, migraines, and mental disorders.

While doing archaeological research online, biological anthropologist Alain Froment happened upon a photo of a cow skull in a 1999 paper in a French scientific journal. The 5,000-year-old skull appeared to have a trepanation hole, yet the study concluded that goring from the horn of another animal produced the gash that is about 2.5 inches long and 2 inches wide.

"I was not convinced by the explanation of cow goring," Froment, a researcher at the Museum of Man, located in Paris, told Seeker.

He and Fernando Ramirez Rozzi of the French National Center for Scientific Research analyzed the cow cranium and now believe that the Stone Age animal underwent trepanation. The findings, reported in the journal Scientific Reports, might be the earliest evidence of a veterinary surgery.

Alternatively, the researchers propose that Neolithic people could have practiced human surgical procedures on already dead animals. If so, the almost complete cow skull could provide the earliest known evidence for such an activity.

The fossil originally was found during archaeological excavations carried out from 1975 to 1985 at the Neolithic site of Champ-Durand at Vendée, France. By at least 5,000 years ago, this location near the Atlantic coast served as an important trade center for locals who specialized in salt production and raising livestock.

In addition to cow remains, fossils for pigs, sheep and goats were also unearthed at the site. Many of the bones had either cut marks or were burned — some were cut and burned.

To analyze the cow cranium in detail, Ramirez Rozzi and Froment created 3D reconstructions and studied them with a scanning electron microscope. They determined that the exterior of the hole becomes smaller internally, with borders of the inner and outer regions being irregular and not smooth.

"The traces of scraping are from a stone tool and not a metal one," Froment said.

Cut-marks in the cow skull (a, b, c) and in human skull (d, e) from the Neolithic Era suggest that the technique used for the trepanation in humans is the same as that employed in the cow skull. Bar corresponds to 1 cm.

He and his colleague argue that goring by another animal would have produced fracturing in and around the wound — characteristics absent from the cranium. They also negate the possibilities that the hole was produced by humans seeking bone for tools or by natural causes, such as a tumor or even intrusion by insects.

The researchers instead argue that the almost square shape of the hole, the lack of any marks indicating pressure by an exterior force, and the presence of cut-marks around the hole all suggest that the injury resulted from a surgery. Since there is no evidence for healing, they believe that the procedure was performed on a dead cow, or that the cow did not survive.

The location of the hole interestingly matches where trepanation procedures typically occur on humans.

Froment explained, "This very place on the skull does not cause internal hemorrhage because there is no vein sinus under the bone in that place."

Ramirez Rozzi told Seeker that evidence for trepanation is found all over the world and across multiple time periods. Froment clarified that the most ancient trephined human skull was found in the Ukraine and is dated to about 7,300–6,200 BC. In France, the most ancient trephined human skull is about 7,000 years old, he added.

The researchers previously suspected that a Neolithic wild boar also underwent trepanation, but they could not directly study that particular skull.

Although their paper presents a few different scenarios explaining the bone surgery, both authors favor the idea that Neolithic people practiced surgical procedures on animals before applying them to humans.

Ramirez Rozzi said, "You see a great deal of expertise in human skull trepanation, and the question has always been, 'How could those who carried out these procedures have had the knowledge to do them so perfectly?' They certainly must have practiced before performing surgery on live humans."

Read more at Seeker

Mammal Mass Shrank as Hungry Humans Learned to Hunt

An illustration of a rabbit observing mastodons

In our defense, we were hungry.

Scientists examining the disappearance of large prehistoric mammals have found evidence that humans and their ancestors drove a sharp reduction in the size of land mammals as hunting skills and weaponry advanced. As a result, the average mammal mass has shrunk more than tenfold over the last 125,000 years, University of New Mexico paleoecologist Felisa Smith told Seeker.

That’s not because species are getting smaller — it’s because the biggest ones went extinct, most likely because they provided the most meat. And that trend has continued into the modern era: Earth’s largest land animal soon may be the domesticated cow, Smith said.

“We used to have animals on the Earth that weighed over 10 tons,” she said. “Now the biggest thing is an elephant that on average is only about three and a half-ish … and if they go extinct, then we’re talking about things no bigger than 900 kilos (2,000 pounds). And that’s maximum size. If you look at mean size, it’s much, much different.”

Smith has studied megafauna extinctions for about 15 years. She and a team from the University of California San Diego, the University of Nebraska, and Stanford University looked back at global fossil records dating back to the start of the Cenozoic Era, after the dinosaurs became extinct. Their findings, published Thursday in the research journal Science lay out a connection between the rise of humans and the shrinking of other mammals over the past 65 million years.

Megafauna like the mastodon, wooly rhinoceros, or the saber-toothed tiger lived on every continent until the Pleistocene epoch, about 125,000 years back, when the human branch of the evolutionary tree spread from Africa to other continents.

North America was rich in large animals, including giant sloths, a bear species that stood as tall as 12 feet, or the glyptodon, an armadillo-like creature “about the size of a Volkswagen Bug,” Smith said.

One finding Smith called surprising was that those trends didn’t appear to be affected by shifts in climate during that period. Animal species tended to adapt by changing their body size, or moving.  Meanwhile, it seems people were killers even before we were technically human.

“The only time we see a spike in extinction rates and this huge size bias, where large-bodied things are disproportionately at risk, was where hominids are involved,” she said. “From that, we conclude that it’s probably related to human exploitation of large-bodied animals.”

Evidence of large mammal extinctions appeared as early as the beginning of the Pleistocene in Africa, where human ancestors were evolving alongside them, Smith said. By 40,000 years ago, when today’s Homo sapiens edged out Neanderthals in Eurasia, mammalian body mass dropped about 50 percent. By the end of the Pleistocene, when the last great ice age ebbed, other human ancestors were gone, humans had settled the Americas and long-range weapons like spears and arrows were common — and the average mass of mammals had fallen from nearly 100 kg (220 pounds) to less than eight.

While Smith said climate did not appear to play a role in that process in the past, today may be a different story. With biodiversity facing threats from human encroachment and fossil fuel-driven climate change, the evolutionary escape routes that saved earlier mammal species have been largely closed off, she said.

“Now we’re in a situation where a lot of us are a lot more prosperous than we ever were before, and we have the luxury to say, ‘Oh, we don’t have to use everything to live, now we need to transition to being stewards of the land,’ ” she said.

Read more at Seeker

Overcoming bias about music takes work

Expectations and biases play a large role in our experiences. This has been demonstrated in studies involving art, wine and even soda. In 2007, Joshua Bell, an internationally acclaimed musician, illustrated the role context plays in our enjoyment of music when he played his Stradivarius violin in a Washington, D.C., subway, and commuters passed by without a second glance.

Researchers at University of Arkansas, Arizona State University and the University of Connecticut studied this phenomenon and recently published their results in Scientific Reports. They found that simply being told that a performer is a professional or a student changes the way the brain responds to music. They also found that overcoming this bias took a deliberate effort.

The study involved 20 participants without formal training in music. Inside a functional magnetic imaging, or fMRI, machine in the newly founded Brain Imaging Research Center at the University of Connecticut, the participants listened to eight pairs of 70-second musical excerpts, presented in a random order. Each pair consisted of two different performances of the same excerpt. The participants were told that one of the pairs was played by a "conservatory student of piano" and the other was a "world-renowned professional pianist." Although participants were actually listening to a student and professional performance, they heard each pair twice during the experiment with the labels reversed, ensuring that the researchers could investigate the effect of the label independent of the qualities of the performance itself.

Participants rated their enjoyment of each excerpt on a scale of one to 10, and they indicated which of the two excerpts in each pair they preferred. The researchers used the fMRI scans to examine regions of the brain that are associated with auditory processing, pleasure and reward, and cognitive control.

In order to study the brain activity associated with bias, the researchers compared brain images of the participants who preferred the "professional" excerpts with images of participants who preferred the "student" excerpts. They found that when a participant preferred the piece attributed to a professional player, there was significantly more activity in the primary auditory cortex, as well as a region of the brain associated with pleasure and reward.

This activity started when the participant was informed that the player was a professional -- before the music even began -- and remained consistent during the excerpt, suggesting that the belief that a musician is a professional caused these participants to pay more attention to the music and biased their listening experience not just at the start, but throughout the excerpt.

The researchers also examined the brain activity of participants who preferred the "student" recordings over the "professional" recordings. While these participants were listening to the recordings attributed to the professional, researchers saw higher activity in a region of the brain related to cognitive control and deliberative thinking throughout the course of the excerpt. They also found that these participants had more connectivity between the parts of their brain related to cognitive control and reward.

"It was different when people listened carefully enough to realize we were fooling them -- that is, when they realized they liked the performance labeled 'student' better," said Edward Large, a theoretical neuroscientist at UConn who made the fMRI available for the study.

"The participants who could resist the bias (who decided they liked the performance primed as student or disliked the one primed as professional) had to recruit regions devoted to executive control -- it looked like work for them to suppress the bias," said Elizabeth Margulis, distinguished professor of music theory and music cognition at the University of Arkansas. "These data demonstrate how critical factors outside the notes themselves, like the information you have about a performer (explicitly in the form of a prime or implicitly in the form of positioning on stage at Carnegie Hall or on a subway platform) can transform what you are able to hear and how you evaluate a musical performance."

Read more at Science Daily

Study reveals new Antarctic process contributing to sea level rise and climate change

This is the Mertz Glacier in January 2017.

A new IMAS-led study has revealed a previously undocumented process where melting glacial ice sheets change the ocean in a way that further accelerates the rate of ice melt and sea level rise.

Led by IMAS PhD student Alessandro Silvano and published in the journal Science Advances, the research found that glacial meltwater makes the ocean's surface layer less salty and more buoyant, preventing deep mixing in winter and allowing warm water at depth to retain its heat and further melt glaciers from below.

"This process is similar to what happens when you put oil and water in a container, with the oil floating on top because it's lighter and less dense," Mr Silvano said.

"The same happens near Antarctica with fresh glacial meltwater, which stays above the warmer and saltier ocean water, insulating the warm water from the cold Antarctic atmosphere and allowing it to cause further glacial melting.

"We found that in this way increased glacial meltwater can cause a positive feedback, driving further melt of ice shelves and hence an increase in sea level rise."

The study found that fresh meltwater also reduces the formation and sinking of dense water in some regions around Antarctica, slowing ocean circulation which takes up and stores heat and carbon dioxide.

"The cold glacial meltwaters flowing from the Antarctic cause a slowing of the currents which enable the ocean to draw down carbon dioxide and heat from the atmosphere.

"In combination, the two processes we identified feed off each other to further accelerate climate change."

Mr Silvano said a similar mechanism has been proposed to explain rapid sea level rise of up to five metres per century at the end of the last glacial period around 15,000 years ago.

"Our study shows that this feedback process is not only possible but is in fact already underway, and may drive further acceleration of the rate of sea level rise in the future.

"Currently the ice shelves resist the flow of ice to the ocean, acting like a buttress to hold the ice sheet on the Antarctic continent.

"Where warm ocean waters flow under the ice shelves they can drive rapid melting from below, causing ice shelves to thin or break up and reducing the buttressing effect.

"This process leads to rising sea levels as more ice flows to the ocean.

"Our results suggest that a further increase in the supply of glacial meltwater to the waters around the Antarctic shelf may trigger a transition from a cold regime to a warm regime, characterised by high rates of melting from the base of ice shelves and reduced formation of cold bottom waters that support ocean uptake of atmospheric heat and carbon dioxide," Mr Silvano said.

From Science Daily

New ancestor of modern sea turtles found in Alabama

This is a reconstruction of the new species (Peritresius martini).

A sea turtle discovered in Alabama is a new species from the Late Cretaceous epoch, according to a study published April 18, 2018 in the open-access journal PLOS ONE by Drew Gentry from the University of Alabama at Birmingham, Alabama, USA, and colleagues.

Modern day sea turtles were previously thought to have had a single ancestor of the of the Peritresius clade during the Late Cretaceous epoch, from about 100 to 66 million years ago. This ancestral species, Peritresius ornatus, lived exclusively in North America, but few Peritresius fossils from this epoch had been found in what is now the southeastern U.S., an area known for producing large numbers of Late Cretaceous marine turtle fossils. In this study, the research team analyzed sea turtle fossils collected from marine sediments in Alabama and Mississippi, dating from about 83 to 66 million years ago.

The researchers identified some of the Alabama fossils as representing a new Peritresius species, which they named Peritresius martini after Mr. George Martin who discovered the fossils. Their identification was based on anatomical features including the shape of the turtle's shell. Comparing P. martini and P. ornatus, the researchers noted that the shell of P. ornatus is unusual amongst Cretaceous sea turtles in having sculptured skin elements which are well-supplied with blood vessels. This unique feature may suggest that P. ornatus was capable of thermoregulation, which could have enabled Peritresius to keep warm and survive during the cooling period of the Cretaceous, unlike many other marine turtles that went extinct.

These findings extend the known evolutionary history for thePeritresius clade to include two anatomically distinct species from the Late Cretaceous epoch, and also reveal that Peritresius was distributed across a wider region than previously thought.

Drew Gentry says: "This discovery not only answers several important questions about the distribution and diversity of sea turtles during this period but also provides further evidence that Alabama is one of the best places in the world to study some of the earliest ancestors of modern sea turtles."

From Science Daily

Martian moons model indicates formation following large impact

This composite image compares how big the moons of Mars appear, as seen from the surface of the Red Planet, in relation to the size that our Moon appears from Earth’s surface. While Earth’s Moon is 100 times bigger than the larger Martian moon Phobos, the Martian moons orbit much closer to their planet, making them appear relatively larger in the sky. Deimos, at far left, and Phobos, beside it, are shown together as photographed by NASA’s Mars rover Curiosity on Aug. 1, 2013.

Southwest Research Institute scientists posit a violent birth of the tiny Martian moons Phobos and Deimos, but on a much smaller scale than the giant impact thought to have resulted in the Earth-Moon system. Their work shows that an impact between proto-Mars and a dwarf-planet-sized object likely produced the two moons, as detailed in a paper published today in Science Advances.

The origin of the Red Planet's small moons has been debated for decades. The question is whether the bodies were asteroids captured intact by Mars gravity or whether the tiny satellites formed from an equatorial disk of debris, as is most consistent with their nearly circular and co-planar orbits. The production of a disk by an impact with Mars seemed promising, but prior models of this process were limited by low numerical resolution and overly simplified modeling techniques.

"Ours is the first self-consistent model to identify the type of impact needed to lead to the formation of Mars' two small moons," said lead author Dr. Robin Canup, an associate vice president in the SwRI Space Science and Engineering Division. Canup is one of the leading scientists using large-scale hydrodynamical simulations to model planet-scale collisions, including the prevailing Earth-Moon formation model.

"A key result of the new work is the size of the impactor; we find that a large impactor -- similar in size to the largest asteroids Vesta and Ceres -- is needed, rather than a giant impactor," Canup said. "The model also predicts that the two moons are derived primarily from material originating in Mars, so their bulk compositions should be similar to that of Mars for most elements. However, heating of the ejecta and the low escape velocity from Mars suggests that water vapor would have been lost, implying that the moons will be dry if they formed by impact."

The new Mars model invokes a much smaller impactor than considered previously. Our Moon may have formed when a Mars-sized object crashed into the nascent Earth 4.5 billion years ago, and the resulting debris coalesced into the Earth-Moon system. The Earth's diameter is about 8,000 miles, while Mars' diameter is just over 4,200 miles. The Moon is just over 2,100 miles in diameter, about one-fourth the size of Earth.

While they formed in the same timeframe, Deimos and Phobos are very small, with diameters of only 7.5 miles and 14 miles respectively, and orbit very close to Mars. The proposed Phobos-Deimos forming impactor would be between the size of the asteroid Vesta, which has a diameter of 326 miles, and the dwarf planet Ceres, which is 587 miles wide.

"We used state-of-the-art models to show that a Vesta-to-Ceres-sized impactor can produce a disk consistent with the formation of Mars' small moons," said the paper's second author, Dr. Julien Salmon, an SwRI research scientist. "The outer portions of the disk accumulate into Phobos and Deimos, while the inner portions of the disk accumulate into larger moons that eventually spiral inward and are assimilated into Mars. Larger impacts advocated in prior works produce massive disks and more massive inner moons that prevent the survival of tiny moons like Phobos and Deimos."

These findings are important for the Japan Aerospace Exploration Agency (JAXA) Mars Moons eXploration (MMX) mission, which is planned to launch in 2024 and will include a NASA-provided instrument. The MMX spacecraft will visit the two Martian moons, land on the surface of Phobos and collect a surface sample to be returned to Earth in 2029.

Read more at Science Daily

Natural selection gave a freediving people in Southeast Asia bigger spleens

This image shows a Bajau diver hunting fish underwater using a traditional spear.

The Bajau people of Southeast Asia, known as Sea Nomads, spend their whole lives at sea, working eight-hour diving shifts with traditional equipment and short breaks to catch fish and shellfish for their families. In a study published April 19 in the journal Cell, researchers report that the extraordinary diving abilities of the Bajau may be thanks in part to their unusually large spleens. The adaptation, the researchers say, is a rare example of natural selection in modern humans -- and one that could provide medically relevant insight into how humans manage acute hypoxia.

"Humans are pretty plastic beings. We can adapt to a number of different extreme environments just through our lifestyle changes or our behavioral changes, so it wasn't necessarily likely that we would find an actual genetic adaptation to diving," says first author Melissa Ilardo, a doctoral student at the University of Copenhagen working with co-senior researchers Rasmus Nielsen (@ras_nielsen) of the University of California, Berkeley, and Eske Willerslev of the University of Copenhagen and the University of Cambridge. "The first sign that we were maybe onto something was when we saw that both the Bajau divers and non-divers had larger spleens than the Saluan, a nearby, non-diving population."

Spleen size is significant because of the organ's role in the human dive response, which occurs when our faces are submerged in water and we hold our breath. As our heart rate slows and blood vessels in our extremities constrict, the spleen contracts, releasing oxygenated red blood cells and making more oxygen available in the bloodstream. A larger spleen means that more oxygen gets released. Perhaps for this reason, large spleens have also been documented in diving seals.

The Bajau having larger spleens than their non-diving neighbors suggested that their diving culture had shaped their physiology. But the fact that non-divers and divers both had larger spleens suggested that it wasn't just a plastic response to spending so much time under water. There was likely something different about the Sea Nomads' DNA.

When the researchers scanned the genomes of the Bajau, they identified 25 sites that differed significantly from two comparison populations, the Saluan and the Han Chinese. Of these, one site on a gene known as PDE10A was found to be correlated with the Bajau's larger spleen size, even after accounting for confounding factors like age, sex, and height. In mice, PDE10A is known for regulating a thyroid hormone that controls spleen size, lending support for the idea that the Bajau might have evolved the spleen size necessary to sustain their long and frequent dives.

"The chance of finding evidence of population-specific natural selection, even in a population as extreme as the Bajau, was pretty slim. It was very exciting to find, and it just opens up so many possibilities," says Ilardo.

Understanding how the human body responds to a lack of oxygen, for instance, is important in a lot of medical contexts, from chronic obstructive pulmonary disease to surgery. Hypoxia has been well studied in populations living at high altitudes, where the lack of oxygen is much more chronic. But not as much research has been done on diving populations. "Here it's more of an acute hypoxia, almost similar to what's experienced with sleep apnea," she says. By making their data freely available to other researchers, she and her co-authors hope that some of what they've learned from the Bajau can be applied in medical contexts.

For the Bajau, Ilardo believes that the decision to participate in this research is about better understanding themselves. "I basically just showed up at the house of the chief of the village, this bizarre, foreign girl with an ultrasound machine asking about spleens," she says. "They're the most welcoming people I've ever met, but I wanted to make sure that they understood the science behind what I was doing, so that it wasn't just me taking measurements from them without giving back. And we do have a trip planned to return to the community to explain the results to them."

"They're explorers, so I think they're inherently curious and want to know more about the world, including about their own biology," she says.

Read more at Science Daily

Marine fish won an evolutionary lottery 66 million years ago

An evolutionary history of major groups of acanthomorphs, an extremely diverse group of fish.

Why do our oceans contain such a staggering diversity of fish of so many different sizes, shapes and colors? A UCLA-led team of biologists reports that the answer dates back 66 million years, when a six-mile-wide asteroid crashed to Earth, wiping out the dinosaurs and approximately 75 percent of the world's animal and plant species.

Slightly more than half of today's fish are "marine fish," meaning they live in oceans. And most marine fish, including tuna, halibut, grouper, sea horses and mahi-mahi, belong to an extraordinarily diverse group called acanthomorphs. (The study did not analyze the large numbers of other fish that live in lakes, rivers, streams, ponds and tropical rainforests.)

The aftermath of the asteroid crash created an enormous evolutionary void, providing an opportunity for the marine fish that survived it to greatly diversify.

"Today's rich biodiversity among marine fish shows the fingerprints of the mass extinction at the end of the Cretaceous period," said Michael Alfaro, a professor of ecology and evolutionary biology in the UCLA College and lead author of the study.

To analyze those fingerprints, the "evolutionary detectives" employed a new genomics research technique developed by one of the authors. Their work is published in the journal Nature Ecology and Evolution.

When they studied the timing of the acanthomorphs' diversification, Alfaro and his colleagues discovered an intriguing pattern: Although there were many other surviving lineages of acanthomorphs, the six most species-rich groups of acanthomorphs today all showed evidence of substantial evolutionary change and proliferation around the time of the mass extinction. Those six groups have gone on to produce almost all of the marine fish diversity that we see today, Alfaro said.

He added that it's unclear why the other acanthomorph lineages failed to diversify as much after the mass extinction.

"The mass extinction, we argue, provided an evolutionary opportunity for a select few of the surviving acanthomorphs to greatly diversify, and it left a large imprint on the biodiversity of marine fishes today," Alfaro said. "It's like there was a lottery 66 million years ago, and these six major acanthomorph groups were the winners."

The findings also closely match fossil evidence of acanthomorphs' evolution, which also shows a sharp rise in their anatomical diversity after the extinction.

The genomic technique used in the study, called sequence capture of DNA ultra-conserved elements, was developed at UCLA by Brant Faircloth, who is now an assistant professor of biological sciences at Louisiana State University. Where previous methods used just 10 to 20 genes to create an evolutionary history, Faircloth's approach creates a more complete and accurate picture by using more than 1,000 genetic markers. (The markers include genes and other DNA components, such as parts of the DNA that turn proteins on or off, and cellular components that play a role in regulating genes.)

The researchers also extracted DNA from 118 species of marine fish and conducted a computational analysis to determine the relationships among them. Among their findings: It's not possible to tell which species are genetically related simply by looking at them. Seahorses, for example, look nothing like goatfish, but the two species are evolutionary cousins -- a finding that surprised the scientists.

Read more at Science Daily

340,000 stars' DNA interrogated in search for sun's lost siblings

A schematic of the HERMES instrument showing the light path of how star light from the telescope AAT is split into four different channels.

An Australian-led group of astronomers working with European collaborators has revealed the "DNA" of more than 340,000 stars in the Milky Way, which should help them find the siblings of the Sun, now scattered across the sky.

This is a major announcement from an ambitious Galactic Archaeology survey, called GALAH, launched in late 2013 as part of a quest to uncover the formulation and evolution of galaxies. When complete, GALAH will investigate more than a million stars.

The GALAH survey used the HERMES spectrograph at the Australian Astronomical Observatory's (AAO) 3.9-metre Anglo-Australian Telescope near Coonabarabran, NSW, to collect spectra for the 340,000 stars.

The GALAH Survey today makes its first major public data release.

The 'DNA' collected traces the ancestry of stars, showing astronomers how the Universe went from having only hydrogen and helium -- just after the Big Bang -- to being filled today with all the elements we have here on Earth that are necessary for life.

"No other survey has been able to measure as many elements for as many stars as GALAH," said Dr Gayandhi De Silva, of the University of Sydney and AAO, the HERMES instrument scientist who oversaw the groups working on today's major data release.

"This data will enable such discoveries as the original star clusters of the Galaxy, including the Sun's birth cluster and solar siblings -- there is no other dataset like this ever collected anywhere else in the world," Dr De Silva said.

Dr. Sarah Martell from the UNSW Sydney, who leads GALAH survey observations, explained that the Sun, like all stars, was born in a group or cluster of thousands of stars.

"Every star in that cluster will have the same chemical composition, or DNA -- these clusters are quickly pulled apart by our Milky Way Galaxy and are now scattered across the sky," Dr Martell said.

"The GALAH team's aim is to make DNA matches between stars to find their long-lost sisters and brothers."

For each star, this DNA is the amount they contain of each of nearly two dozen chemical elements such as oxygen, aluminium, and iron.

Unfortunately, astronomers cannot collect the DNA of a star with a mouth swab but instead use the starlight, with a technique called spectroscopy.

The light from the star is collected by the telescope and then passed through an instrument called a spectrograph, which splits the light into detailed rainbows, or spectra.

Associate Professor Daniel Zucker, from Macquarie University and the AAO, said astronomers measured the locations and sizes of dark lines in the spectra to work out the amount of each element in a star.

"Each chemical element leaves a unique pattern of dark bands at specific wavelengths in these spectra, like fingerprints," he said.

Dr Jeffrey Simpson of the AAO said it takes about an hour to collect enough photons of light for each star, but "Thankfully, we can observe 360 stars at the same time using fibre optics," he added.

The GALAH team has spent more than 280 nights at the telescope since 2014 to collect all the data.

The GALAH survey is the brainchild of Professor Joss Bland-Hawthorn from the University of Sydney and the ARC Centre of Excellence for All Sky Astrophysics in 3 Dimensions (ASTRO 3D) and Professor Ken Freeman of the Australian National University (ANU). It was conceived more than a decade ago as a way to unravel the history of our Milky Way galaxy; the HERMES instrument was designed and built by the AAO specifically for the GALAH survey.

Measuring the abundance of each chemical in so many stars is an enormous challenge. To do this, GALAH has developed sophisticated analysis techniques.

PhD student Sven Buder of the Max Planck Institute for Astronomy, Germany, who is lead author of the scientific article describing the GALAH data release, is part of the analysis effort of the project, working with PhD student Ly Duong and Professor Martin Asplund of ANU and ASTRO 3D.

Mr. Buder said: "We train [our computer code] The Cannon to recognize patterns in the spectra of a subset of stars that we have analysed very carefully, and then use The Cannon's machine learning algorithms to determine the amount of each element for all of the 340,000 stars." Ms. Duong noted that "The Cannon is named for Annie Jump Cannon, a pioneering American astronomer who classified the spectra of around 340,000 stars by eye over several decades a century ago -- our code analyses that many stars in far greater detail in less than a day."

The GALAH survey's data release is timed to coincide with the huge release of data on 25 April from the European Gaia satellite, which has mapped more than 1.6 billion stars in the Milky Way -- making it by far the biggest and most accurate atlas of the night sky to date.

In combination with velocities from GALAH, Gaia data will give not just the positions and distances of the stars, but also their motions within the Galaxy.

Professor Tomaz Zwitter (University of Ljubljana, Slovenia) said today's results from the GALAH survey would be crucial to interpreting the results from Gaia: "The accuracy of the velocities that we are achieving with GALAH is unprecedented for such a large survey."

Dr Sanjib Sharma from the University of Sydney concluded: "For the first time we'll be able to get a detailed understanding of the history of the Galaxy."

Read more at Science Daily

Black hole and stellar winds form giant butterfly, shut down star formation in galaxy

Researchers at the University of Colorado Boulder have completed an unprecedented "dissection" of twin galaxies in the final stages of merging.

The new study, led by CU Boulder research associate Francisco Müller-Sánchez, explores a galaxy called NGC 6240. While most galaxies in the universe hold only one supermassive black hole at their center, NGC 6240 contains two -- and they're circling each other in the last steps before crashing together.

The research reveals how gases ejected by those spiraling black holes, in combination with gases ejected by stars in the galaxy, may have begun to power down NGC 6240's production of new stars. Müller-Sánchez's team also shows how these "winds" have helped to create the galaxy's most tell-tale feature: a massive cloud of gas in the shape of a butterfly.

"We dissected the butterfly," said Müller-Sánchez of CU Boulder's Department of Astrophysical and Planetary Sciences (APS). "This is the first galaxy in which we can see both the wind from the two supermassive black holes and the outflow of low ionization gas from star formation at the same time."

The team zeroed in on NGC 6240, in part, because galaxies with two supermassive black holes at their centers are relatively rare. Some experts also suspect that those twin hearts have given rise to the galaxy's unusual appearance. Unlike the Milky Way, which forms a relatively tidy disk, bubbles and jets of gas shoot off from NGC 6240, extending more than 30,000 light years into space and resembling a butterfly in flight.

"Galaxies with a single supermassive black hole never show such a phenomenal structure," Müller-Sánchez said.

In research that will be published April 18 in Nature, the team discovered that two different forces have given rise to the nebula. The butterfly's northwest corner, for example, is the product of stellar winds, or gases that stars emit through various processes. The northeast corner, on the other hand, is dominated by a single cone of gas that was ejected by the pair of black holes -- the result of those black holes gobbling up large amounts of galactic dust and gas during their merger.

Those two winds combined evict about 100 times the mass of Earth's sun in gases from the galaxy every year. That's a "very large number, comparable to the rate at which the galaxy is creating stars in the nuclear region," Müller-Sánchez said.

Such an outflow can have big implications for the galaxy itself. He explained that when two galaxies merge, they begin a feverish burst of new star formation. Black hole and stellar winds, however, can slow down that process by clearing away the gases that make up fresh stars -- much like how a gust of wind can blow away the pile of leaves you just raked.

Read more at Science Daily

New new genus and species of extinct baleen whale identified

Burial in the ancient sea of Zealandia: a Toipahautea whale skeleton is slowly covered by sand 27-28 million years ago, on its path to become a fossil.

University of Otago palaeontologists are rewriting the history of New Zealand's ancient whales by describing a previously unknown genus of baleen whale, alive more than 27.5 million years ago and found in the Hakataramea Valley.

The new genus and species of extinct baleen whale is based on a skull and associated bones unearthed from the Kokoamu Greensand, a noted fossil-bearing rock unit in the South Canterbury and Waitaki district from the Oligocene period, which extends from about 33.9 million to 23 million years ago. At this time, New Zealand was an archipelago surrounded by shallow, richly productive seas.

Former PhD student in the University of Otago's Department of Geology, Cheng-Hsiu Tsai and his supervisor, Professor Ewan Fordyce, have named the new genus Toipahautea waitaki, which translates in Māori as a baleen-origin whale from the Waitaki region.

Professor Fordyce says the discovery is significant in New Zealand's fossil history.

"This is a pretty old whale that goes almost half-way back to the age of the dinosaurs. We are tracking whale history back through time," Professor Fordyce explains.

"This newly-named whale lived about 27.5 million years ago. It's about as old a common ancestor as we have for the living baleen whales like the minke whales and the right whales."

Baleen whales are a group of Mysticeti, large whales usually from colder waters that lack teeth but have baleen plates in the upper jaw which are used to filter food such as krill out of large quantities of seawater.

The fossil was actually recovered from the Hakataramea Valley in South Canterbury 30 years ago in January 1988. However, it was only worked up in recent years with Dr Tsai -- who is now currently working at the National Taiwan University -- beginning his thesis only a few years ago. The thesis provided the analytical framework to identify and name the new whale.

The research paper announcing the new archaic baleen whale was published today in the scientific journal Royal Society Open Science.

While the skeleton of the whale was disarticulated when it was excavated, the bones were closely associated, which gave the palaeontologists plenty of material to work with. In particular, the highly diagnostic earbones were preserved, helping with identification.

The skull was about one metre long and the body about five metres, which means it was a reasonably small species, Professor Fordyce says. "That's about half the size of an adult minke whale."

It was previously known that the baleen whales can take on board thousands of litres of water in the lower jaws which they scoop open to get great mouthfuls of water and food. Toipahautea waitaki's jaws were toothless, long and narrow, Professor Fordyce says, suggesting that it fed in a similar way to the modern-day minke whales.

The researchers were not able to determine how this whale died. Professor Fordyce says it could have been attacked by a shark, stranded on a beach or died of disease. When it died, it sank to the bottom of the sea floor with its skeleton falling apart and becoming a hub for coral and other organisms to grow on.

Professor Fordyce expects the ancient whales' history books may keep being rewritten in years to come.

"We are pretty sure there are some species [of baleen whale] that will be older than these. But right now it anchors the modern baleen whale lineage to at least 27.5 million years."

Read more at Science Daily

Some human cancers are 'evolutionary accidents'

New research, published in Biological Reviews and conducted by researchers from the University of Liverpool and Escola Superior de Ciências da Saúde (Brasília, Brazil) has found some type of cancers unique to humans may be a result of evolutionary accidents.

Cancer is a major cause of death worldwide. But humans are not the only species affected by cancer; in fact, only a few primitive animals are thought to escape the disease. Furthermore, incidence rates and cancer types differ widely among species. However, how cancer patterns in humans compare to those of other species remains largely unknown.

Researchers, led by Dr Joao Pedro De Magalhaes from the University of Liverpool's Institute of Ageing and Chronic Disease, aimed to identify further clues about cancer and its evolutionary underpinnings in humans and across a wide range of animals by conducting the largest survey of animal cancer data to date.

The researchers began examining data relating to primates then continued onto other mammals before examining cancer in birds, amphibians, reptiles, fish and finally invertebrates and plants. They then reviewed the cancer incidence and types for humans and animal types.

They found that some types of cancer are widespread across nearly all species, like blood cancers (lymphomas and leukemia), and there are some types of cancer that seem to be unique of humans, like lung cancer, prostate and testicular cancers. These could be evolutionary accidents, a product of random events in the evolution of our species.

Dr De Magalhaes, said: "Perhaps unique mutations during the evolution of the human lineage contribute to the disproportionately high incidence of some cancers in our species when compared to all other studied species."

Another hypothesis is that the increasing life expectancy of humans is allowing the appearance of cancers that would not have affected our ancestors.

First author Thales Albuquerque, said: "Cancer rates among humans are high, and they are bound to keep increasing. We still do not know all mechanisms that lead to such a high incidence of cancer in our species, but one hypothesis is that cultural changes and technological advances have produced the greatest of evolutionary mismatches -- a situation where the environment changes into something different from that which a species is adapted to, and that provokes stress and may increase susceptibility to cancer.

Dr De Magalhaes: "Our work highlights the different evolutionary pressures acting on cancer early in life (with a high prevalence of blood cancers presumably driven by the need to fight pathogens) and cancer late in life that escapes natural selection, including human-specific cancers that may be evolutionary accidents or related to a mismatch with the modern environment and lifestyle."

From Science Daily

Scientists decipher the magma bodies under Yellowstone

Graphic by University of Oregon scientists provides new structural information, based on supercomputer modeling, about the location of a mid-crustal sill that separates magma under Yellowstone.

Using supercomputer modeling, University of Oregon scientists have unveiled a new explanation for the geology underlying recent seismic imaging of magma bodies below Yellowstone National Park.

Yellowstone, a supervolcano famous for explosive eruptions, large calderas and extensive lava flows, has for years attracted the attention of scientists trying to understand the location and size of magma chambers below it. The last caldera forming eruption occurred 630,000 years ago; the last large volume of lava surfaced 70,000 years ago.

Crust below the park is heated and softened by continuous infusions of magma that rise from an anomaly called a mantle plume, similar to the source of the magma at Hawaii's Kilauea volcano. Huge amounts of water that fuel the dramatic geysers and hot springs at Yellowstone cool the crust and prevent it from becoming too hot.

With computer modeling, a team led by UO doctoral student Dylan P. Colón has shed light on what's going on below. At depths of 5-10 kilometers (3-6 miles) opposing forces counter each other, forming a transition zone where cold and rigid rocks of the upper crust give way to hot, ductile and even partially molten rock below, the team reports in a paper in Geophysical Research Letters.

This transition traps rising magmas and causes them to accumulate and solidify in a large horizontal body called a sill, which can be up to 15 kilometers (9 miles) thick, according to the team's computer modeling.

"The results of the modeling matches observations done by sending seismic waves through the area," said co-author Ilya Bindeman, a professor in the UO's Department of Earth Sciences. "This work appears to validate initial assumptions and gives us more information about Yellowstone's magma locations."

This mid-crustal sill is comprised of mostly solidified gabbro, a rock formed from cooled magma. Above and below lay separate magma bodies. The upper one contains the sticky and gas-rich rhyolitic magma that occasionally erupts in explosions that dwarf the 1980 eruption of Mount St. Helens in Washington state.

Similar structures may exist under super volcanoes around the world, Colón said. The geometry of the sill also may explain differing chemical signatures in eruptive materials, he said.

Colón's project to model what's below the nation's first national park, which was sculpted 2 million years ago by volcanic activity, began soon after a 2014 paper in Geophysical Research Letters by a University of Utah-led team revealed evidence from seismic waves of a large magma body in the upper crust.

Scientists had suspected, however, that huge amounts of carbon dioxide and helium escaping from the ground indicated that more magma is located farther down. That mystery was solved in May 2015, when a second University of Utah-led study, published in the journal Science, identified by way of seismic waves a second, larger body of magma at depths of 20 to 45 kilometers (12-27 miles).

However, Colón said, the seismic-imaging studies could not identify the composition, state and amount of magma in these magma bodies, or how and why they formed there.

To understand the two structures, UO researchers wrote new codes for supercomputer modeling to understand where magma is likely to accumulate in the crust. The work was done in collaboration with researchers at the Swiss Federal Institute of Technology, also known as ETH Zurich.

The researchers repeatedly got results indicating a large layer of cooled magma with a high melting point forms at the mid-crustal sill, separating two magma bodies with magma at a lower melting point, much of which is derived from melting of the crust.

"We think that this structure is what causes the rhyolite-basalt volcanism throughout the Yellowstone hotspot, including supervolcanic eruptions," Bindeman said. "This is the nursery, a geological and petrological match with eruptive products. Our modeling helps to identify the geologic structure of where the rhyolitic material is located."

The new research, for now, does not help to predict the timing of future eruptions. Instead, it provides a never-before-seen look that helps explain the structure of the magmatic plumbing system that fuels these eruptions, Colón said. It shows where the eruptible magma originates and accumulates, which could help with prediction efforts further down the line.

"This research also helps to explain some of the chemical signatures that are seen in eruptive materials," Colón said. "We can also use it to explore how hot the mantle plume is by comparing models of different plumes to the actual situation at Yellowstone that we understand from the geologic record."

Colón is now exploring what influences the chemical composition of magmas that erupt at volcanoes like Yellowstone.

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Can we tell black holes apart?

Can we tell black holes apart? Astrophysicists at Goethe University Frankfurt answer this question by computing images of feeding non-Einsteinian black holes: at present it is hard to tell them apart from standard black holes.

One of the most fundamental predictions of Einstein's theory of relativity is the existence of black holes. In spite of the recent detection of gravitational waves from binary black holes by LIGO, direct evidence using electromagnetic waves remains elusive and astronomers are searching for it with radio telescopes. Astrophysicists at Goethe University Frankfurt, and collaborators in the ERC-funded project BlackHoleCam in Bonn and Nijmegen have created and compared self-consistent and realistic images of the shadow of an accreting supermassive black hole -- such as the black-hole candidate Sagittarius A* (Sgr A*) in the heart of our galaxy -- both in general relativity and in a different theory of gravity. The goal was to test if Einsteinian black holes can be distinguished from those in alternative theories of gravity.

Not all of the light rays (or photons) produced by matter falling into a black hole are trapped by the event horizon, a region of spacetime from which nothing can escape. Some of these photons will reach distant observers, so that when a black hole is observed directly a "shadow" is expected against the background sky. The size and shape of this shadow will depend on the black-hole's properties but also on the theory of gravity.

Because the largest deviations from Einstein's theory of relativity are expected very close to the event horizon and since alternative theories of gravity make different predictions on the properties of the shadow, direct observations of Sgr A* represent a very promising approach for testing gravity in the strongest regime. Making such images of the black-hole shadow is the primary goal of the international Event Horizon Telescope Collaboration (EHTC), which combines radio data from telescopes around the world.

Scientists from the BlackHoleCam team in Europe, who are part of the EHTC, have now gone a step further and investigated whether it is possible to distinguish between a "Kerr" black hole from Einstein's gravity and a "dilaton" black hole, which is a possible solution of an alternative theory of gravity.

The researchers studied the evolution of matter falling into the two very different types of black holes and calculated the radiation emitted to construct the images. Furthermore, real-life physical conditions in the telescopes and interstellar medium were used to create physically realistic images. "To capture the effects of different black holes we used realistic simulations of accretion disks with near-identical initial setups. These expensive numerical simulations used state-of-the-art codes and took several months on the Institute's supercomputer LOEWE," says Dr. Yosuke Mizuno, lead author of the study.

Moreover, expected radio images obviously have a limited resolution and image fidelity. When using realistic image resolutions, the scientists found, to their surprise, that even highly non-Einsteinian black holes could disguise themselves as normal black holes.

"Our results show that there are theories of gravity in which black holes can masquerade as Einsteinian, so new techniques of analyzing EHT data may be needed to tell them apart," remarks Luciano Rezzolla, professor at Goethe University and leader of the Frankfurt team. "While we believe general relativity is correct, as scientists we need to be open-minded. Luckily, future observations and more advanced techniques will eventually settle these doubts," concludes Rezzolla.

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