Monday, March 14, 2016

How Gut Bacteria Are Shaking Up Cancer Research



 http://www.bloomberg.com/


  • Roche says it plans to study role of microbiome in cancer
  • Vedanta expects more drug companies to enter the field
Top scientists at Roche Holding AG and AstraZeneca Plc are sizing up potential allies in the fight against cancer: the trillions of bacteria that live in the human body.
"Five years ago, if you had asked me about bacteria in your gut playing an important role in your systemic immune response, I probably would have laughed it off," Daniel Chen, head of cancer immunotherapy research at Roche’s Genentech division, said in a phone interview. "Most of us immunologists now believe that there really is an important interaction there."
Two recent studies published in the journal Science have intrigued Chen and others who are developing medicines called immunotherapies that stimulate the body’s ability to fight tumors.
In November, University of Chicago researchers wrote that giving mice Bifidobacterium, which normally resides in the gastrointestinal tract, was as effective as an immunotherapy in controlling the growth of skin cancer. Combining the two practically eliminated tumor growth. In the second study, scientists in France found that some bacterial species activated a response to immunotherapy, which didn’t occur without the microbes.

Human Microbiome

That’s increased drugmakers’ interest in the human microbiome -- the universe of roughly 100 trillion good and bad bacteria, fungi and viruses that live on and inside the body. Roche is already undertaking basic research in the field and plans to investigate the microbiome’s potential for cancer treatment, Chen said.
"Certainly, we are already scanning the space for interesting opportunities as the science continues to emerge," he said. "We are very interested in testing these in a controlled setting."
Some experienced investors are skeptical and see the possibility of an approved product for cancer to be at least five years away.
"To therapeutically influence the microbiome long-term in humans is a big hurdle," said Sander van Deventer, managing partner at venture-capital firm Forbion Capital Partners. "The microbiome is very stubborn. Everything we’ve done so far has only had a temporary effect."

Nestle’s Investment

Earlier in his career, van Deventer chaired the department of gastroenterology and hepatology at the Academic Medical Center in Amsterdam, the first clinic in the world to perform fecal transplants to fight hospital infection Clostridium difficile with good bacteria. Forbion hasn’t yet invested in any microbiome biotechs, "but we’re looking at all of them all the time," he said.
Efforts are under way to turn bacteria into regulated pharmaceutical products to treat illnesses of the gut, where the microbes reside.
Nestle SA last January invested $65 million in ambridge, Massachusetts-based Seres Therapeutics Inc., which is developing a treatment for Clostridium difficile, which affects the digestive system. That follows early efforts to harness the microbiome’s benefits, which spawned probiotic foods and supplements as well as transplants of healthy bacteria.
The promise in cancer will draw more large drugmakers into exploring the human microbiome, said Bernat Olle, chief executive officer of Vedanta Biosciences, a Boston-based startup.

Treatment Potential

"That’s the sense we get based on how we’re being approached by new pharma groups and how serious they seem to be about wanting to enter the field,” Olle said in a phone interview. Vedanta last year announced a license agreement with Johnson & Johnson on its experimental microbiome drug for inflammatory bowel disease.
Another startup, 4D Pharma Plc, in November said it had discovered a bacterium that produces a response comparable to that of an immunotherapy in animal tests for breast and lung cancers. The London-listed company plans to start trials in patients by the end of this year. To support research in autoimmune and neurological diseases, in addition to cancer, the company has raised over 100 million pounds ($140 million) from investors over the last two years, CEO Duncan Peyton said in a phone interview.
French biotech Enterome is taking a different approach: developing treatments based on bacterial secretions. Enterome plans to close a private financing round of about 15 million euros this month, according to CEO Pierre Belichard. More news may be on the way.

‘Active Discussions’

"We are in active discussions with the usual suspects in the immunotherapy space," Belichard said in an interview in London.
Those active in the field include a wide range of pharma companies including AstraZeneca, Roche, Bristol-Myers Squibb Co., and Merck & Co.
"Personally, I think it’s a fascinating area," Susan Galbraith, head of oncology research at AstraZeneca, said in an interview in London.
Studies have shown that immunotherapies have varying degrees of success even in genetically identical mice, and the Science study from Chicago suggests that the diversity of the microbiome may help explain that variability, Galbraith said. AstraZeneca isn’t conducting its own research in the area and would prefer to wait to see evidence in human trials before getting involved, she said.
The sheer number of bacteria, some of which could actually switch off an immune response, and the question of how much bacteria is needed, make it a complex area of research, Roche’s Chen said. It’s possible that the same bacteria could induce both harmful and helpful responses, depending on the patient, he said.
Still, "it’s one of the most interesting developments we’ve seen in science over the last several years," he said.

Oldest ever human genome sequence may rewrite human history



14 March 2016

https://www.newscientist.com/


Cavers

What secrets lurk in the pit of bones?

Javier Trueba, Madrid Scientific Films
The oldest ever human nuclear DNA to be reconstructed and sequenced reveals Neanderthals in the making – and the need for a possible rewrite of our own origins.
The 430,000-year-old DNA comes from mysterious early human fossils found in Spain’s Sima de los Huesos, or “pit of bones”.
The fossils look like they come from ancestors of the Neanderthals, which evolved some 100,000 years later. But a 2013 study found that their mitochondrial DNA is more similar to that of Denisovans (see video, below), who also lived later and thousands of kilometres away, in southern Siberia.
So who were the Sima people – and how are they related to us?
To find out, a team led by Matthias Meyer at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, pieced together parts of the hominin’s nuclear DNA from samples taken from a tooth and a thigh bone.

4_Homo-heidelbergensis_-Sima-de-los-Huesos_Credit-Javier-Trueba-Madrid-Scientific-Films

One of the Sima de los Huesos skeletons

Javier Trueba, Madrid Scientific Films
The results suggest they are more closely related to ancestors of Neanderthals than those of Denisovans – meaning the two groups must have diverged by 430,000 years ago. This is much earlier than the geneticists had expected.
It also alters our own timeline. We know that Denisovans and Neanderthals shared a common ancestor that had split from our modern human lineage. In light of the new nuclear DNA evidence, Meyer’s team suggests this split might have happened as early as 765,000 years ago.
Previous DNA studies had dated this split to just 315,000 to 540,000 years ago, says Katerina Harvati-Papatheodorou at the University of Tubingen in Germany.
But a date of 765,000 years ago actually brings the DNA evidence more in line with some recent fossil interpretations that also suggest an older divergence between modern humans and the ancestor of the Neanderthals and Denisovans.
“I am very happy to see that ideas about the divergence based on ancient DNA and on anatomical studies of the fossil record seem to be converging,” says Aida Gómez-Robles at George Washington University in Washington DC, who was involved in the fossil research.

Tree redrawn?

But if such an ancient split is correct, we might have to redraw parts of our evolutionary tree.
Conventional thinking is that modern humans, Neanderthals and Denisovans all evolved from an ancient hominin called Homo heidelbergensis.
However, H. heidelbergensis didn’t evolve until 700,000 years ago – potentially 65,000 years after the split between modern humans and the Neanderthals and Denisovans.
Instead, another, obscure species called Homo antecessor might now be in the frame as our common ancestor.
This species first appeared more than a million years ago – and its face is very similar to that of modern humans, says Chris Stringer at the Natural History Museum in London.

Further puzzles

“Research must now refocus on fossils from 400,000 to 800,000 years ago to determine which ones might actually lie on the respective ancestral lineages of Neanderthals, Denisovans and modern humans,” he says.
Another puzzle remains. The study confirmed a previous finding that the mitochondrial DNA of the Sima hominin is more similar to Denisovans than to Neanderthals – but no one knows why.
Perhaps there was another unidentified lineage of hominins in Eurasia that interbred with the ancestors of both – but not with the particular group of hominins that evolved into the Neanderthals.
Or, Meyer says, perhaps such mitochondrial DNA was typical of early Neanderthals and Denisovans, and it was only later that Neanderthals acquired different mitochondrial DNA from an African population of “proto-Homo sapiens“.
Journal reference: Nature, DOI: 10.1038/nature17405
Find out more about the oldest human genome dug up in Spain’s pit of bones:

 

Neanderthal diet: Only 20 percent vegetarian

Researchers have long debated the precise diet of early humans, but the latest study is the first to nail down precise percentages.
By Brooks Hays   |   March 14, 2016 at 12:33 PM
Fossil analysis suggests Neanderthals ate a diet of
80 percent meat. Photo by OrdinaryJoe/Shutterstock

TUBINGEN, Germany, March 14 (UPI) -- Neanderthals were apparently too busy hunting and scavenging to pay much attention to Michael Pollan's dietary advice: eat mostly plants.
New isotopic analysis suggests prehistoric humans ate mostly meat. As detailed in a new study published in the journal Quaternary International, the Neanderthal diet consisted of 80 percent meat, 20 percent vegetables.
Researchers in Germany measured isotope concentrations of collagen in Neanderthal fossils and compared them to the isotopic signatures of animal bones found nearby. In doing so, scientists were able to compare and contrast the diets of early humans and their mammalian neighbors, including mammoths, horses, reindeer, bison, hyenas, bears, lions and others.
"Previously, it was assumed that the Neanderthals utilized the same food sources as their animal neighbors," lead researcher Herve Bocherens, a professor at the University of Tubingen's Senckenberg Center for Human Evolution and Palaeoenvironment, said in a news release.
"However, our results show that all predators occupy a very specific niche, preferring smaller prey as a rule, such as reindeer, wild horses or steppe bison, while the Neanderthals primarily specialized on the large plant-eaters such as mammoths and woolly rhinoceroses," Bocherens explained.
All of the Neanderthal and animal bones, dated between 45,000 and 40,000 years old, were collected from two excavation sites in Belgium.
Researchers have long debated the precise diet of early humans, but the latest study is the first to nail down precise percentages.
Bocherens and his colleagues are hopeful their research will shed light on the Neanderthals' extinction some 40,000 years ago.
"We are accumulating more and more evidence that diet was not a decisive factor in why the Neanderthals had to make room for modern humans," he said.

Humans Interbred With Hominins on Multiple Occasions, Study Finds

Photo
Skulls of the Neanderthal man. Credit European Pressphoto Agency
The ancestors of modern humans interbred with Neanderthals and another extinct line of humans known as the Denisovans at least four times in the course of prehistory, according to an analysis of global genomes published on Thursday in the journal Science.
The interbreeding may have given modern humans genes that bolstered immunity to pathogens, the authors concluded.
“This is yet another genetic nail in the coffin of our over-simplistic models of human evolution,” said Carles Lalueza-Fox, a research scientist at the Institute of Evolutionary Biology in Barcelona who was not involved in the study.
The new study expands on a series of findings in recent years showing that the ancestors of modern humans once shared the planet with a surprising number of near relatives — lineages like the Neanderthals and Denisovans that became extinct tens of thousands of years ago.
Before disappearing, however, they interbred with our forebears on at least several occasions, and today we carry DNA from these encounters.
The first clues to ancient interbreeding surfaced in 2010, when scientists discovered that some modern humans — mostly Europeans — carry DNA that matches material recovered from Neanderthal fossils.
Later studies showed that the forebears of modern humans first encountered Neanderthals after expanding out of Africa more than 50,000 years ago.
But the Neanderthals were not the only extinct humans that our own ancestors found. A finger bone discovered in a Siberian cave, called Denisova, yielded DNA from yet another group of humans.
Research later indicated that all three groups — modern humans, Neanderthals and Denisovans — shared a common ancestor who lived roughly 600,000 years ago. And, perhaps no surprise, some ancestors of modern humans also interbred with Denisovans.
Some of their DNA has survived in people in Melanesia, a region of the Pacific that includes New Guinea and the islands around it.
Those initial discoveries left major questions unanswered, such as how often our ancestors interbred with Neanderthals and Denisovans. Scientists have developed new ways to study the DNA of living people to tackle these mysteries.
Joshua M. Akey, a geneticist at the University of Washington, and his colleagues analyzed a database of 1,488 genomes from people around the world. The scientists added 35 genomes from people in New Britain and other Melanesian islands in an effort to learn more about Denisovans in particular.
The researchers found that all the non-Africans in their study had Neanderthal DNA, while the Africans had very little or none. That finding supported previous studies.
But when Dr. Akey and his colleagues compared DNA from modern Europeans, East Asians and Melanesians, they found that each population carried its own distinctive mix of Neanderthal genes.
The best explanation for these patterns, the scientists concluded, was that the ancestors of modern humans acquired Neanderthal DNA on three occasions.
The first encounter happened when the common ancestor of all non-Africans interbred with Neanderthals.
The second occurred among the ancestors of East Asians and Europeans, after the ancestors of Melanesians split off. Later, the ancestors of East Asians — but not Europeans — interbred a third time with Neanderthals.
Earlier studies had hinted at the possibility that the forebears of modern humans had multiple encounters with Neanderthals, but until now hard data was lacking.
“A lot of people have been arguing for that, but now they’re really providing the evidence for it,” said Rasmus Nielsen, a geneticist at the University of California, Berkeley, who was not involved in the new study.

Horse-sized dinosaur shows how T. rex became king

AFP
Paleontologist, Hans Sues, of the Smithsonian Museum of Natural History, compares a T-Rex tooth (L) to the tooth of a newly discovered dinosaur during a news conference at the museum, March 14, 2016 in Washington, DC
Paleontologist, Hans Sues, of the Smithsonian Museum of Natural History, compares a T-Rex tooth (L) to the tooth of a newly discovered dinosaur during a news conference at the museum, March 14, 2016 in Washington, DC (AFP Photo/Mark Wilson)
Washington (AFP) - A newly discovered cousin of the T. rex may explain how the legendary dinosaur leapt in size to become undisputed king of the food chain, scientists said Monday.
Until now, researchers have had little evidence of how the iconic predator became one of the largest carnivores to ever roam the Earth before the dinosaurs went extinct 65 million years ago.
The answers could lie in the brain of Timurlengia euotica, a previously unknown relative of the T. rex.
Timurlengia euotica was far smaller than the elephant-sized T. rex, but had already developed the large brain it needed to track and devour prey.
While researchers cautioned that the discovery represents just one animal in a long lineage, its features help illustrate how small tyrannosaurids evolved to grow smarter and larger over time, thanks to keen senses that could help keep their bellies filled.
"The ancestors of T. rex would have looked a whole lot like Timurlengia, a horse-sized hunter with a big brain and keen hearing that would put us to shame," said Steve Brusatte of the University of Edinburgh's School of GeoSciences.
"Only after these ancestral tyrannosaurs evolved their clever brains and sharp senses did they grow into the colossal sizes of T. rex.
"Tyrannosaurs had to get smart before they got big."
The first tyrannosaurs appeared about 170 million years ago and were about the size of a human.
The bones of Timurlengia euotica were uncovered in Uzbekistan, where it lived about 90 million years ago.
By the Late Cretaceous Period, between 66 and 80 million years ago, the T. rex was the don of the big lizards, often weighing more than seven tons.
Not much is known about how the T. rex got so big, "largely because of a frustrating 20-plus-million-year gap in the mid-Cretaceous fossil record, when tyrannosauruses transitioned from small-bodied hunters to gigantic apex predators but from which no diagnostic specimens are known," said the study published in the Proceedings of the National Academy of Sciences.
The new discovery is "the first distinct tyrannosauroid species from this gap."
The specimen was discovered between 1997 and 2006 by a team of palaeontologists, led by researchers at the University of Edinburgh, working in the Kyzylkum Desert in northern Uzbekistan.
"The early evolution of many groups like tyrannosaurs took place in the coastal plains of central Asia in the mid-Cretaceous," said professor Alexander Averianov of Saint Petersburg State University.
Timurlengia's skull was much smaller than that of the T. rex, suggesting it did not grow as big, but its skull shape reveals "that its brain and senses were already highly developed," the report said.
"Timurlengia was a nimble pursuit hunter with slender, blade-like teeth suitable for slicing through meat," said professor Hans Sues, of the National Museum of Natural History in Washington.
"It probably preyed on the various large plant-eaters, especially early duck-billed dinosaurs, which shared its world."

Saturday, March 12, 2016

Scientists create chickens with dinosaur legs, because why not

Scientists create chickens with dinosaur legs, because why not
Oh how the mighty dinosaurs have fallen. It’s a bit sad that the descendants of the magnificent creatures who once ruled the Earth have stubby wings and are the most commonly consumed meat in America (yes, I’m talking about the chicken). Such is the circle of life. And now, in an attempt to restore a bit of the glory of dinosaurs (or just create a truly bizarre looking animal), scientists have genetically modified chickens to give them dinosaur legs. Because science.
Interestingly enough, because of the close genetic relationship the modern day chicken shares with the prehistoric giant, the researchers involved with the wacky task simply had to silence a gene that chickens typically express. No gene insertion or further manipulation — just a (highly complex) flip of a switch.
The precise gene suppressed by the Chilean scientists, headed by Joâo Botelho
At Universidad de Chile is one called the Indian Hedgehog. This gene is crucial to the development of chicken’s bones, and when turned off, apparently allows the birds to develop a bone structure that looks just like the lower leg of a raptor. Chicken on top, dinosaur on the bottom.
RelatedJust For the Tech of It: Martian crops and dinosaur chickens
This is by no means the first time that Botelho or other scientists have engineered a bird to go back to its more magnificent origins. Botelho also managed to undo the backward-facing perching toe common in birds to produce a front-facing toe — much like what dinosaurs had. And at Yale, a chicken was given a dinosaur-esque snout when its gene expression was altered at the embryo stage.
This sort of work is taking place across the country, and indeed, across the world, says Jack Horner, a famous paleontologist whose expertise was consulted in each and every one of the Jurassic Park films. At his lab at Montana State University, scientists are working to “ genetically alter a chicken egg to produce a more prehistoric version of the animal, complete with velociraptor-shaped head, arms, clawed hands and long tail,” the Post Register reports. But don’t worry, researchers say that we won’t be plunged into a real life version of the movies anytime soon.
“The experiments are focused on single traits, to test specific hypotheses,” says Alexander Vargas, who heds the lab in which Botelho works. “Not only do we know a great deal about bird development, but also about the dinosaur-bird transition, which is well-documented by the fossil record. This leads naturally to hypotheses on the evolution of development, that can be explored in the lab.”
Just call it scientific curiosity, and enjoy the strange but wonderful results that have come out of it … thus far.
Also watch: Raimond de Hullu’s vision for Oas1s green buildings
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Oh how the mighty dinosaurs have fallen. It’s a bit sad that the descendants of the magnificent creatures who once ruled the Earth have stubby wings and are the most commonly consumed meat in America (yes, I’m talking about the chicken). Such is the circle of life. And now, in an attempt to restore a bit of the glory of dinosaurs (or just create a truly bizarre looking animal), scientists have genetically modified chickens to give them dinosaur legs. Because science.
Interestingly enough, because of the close genetic relationship the modern day chicken shares with the prehistoric giant, the researchers involved with the wacky task simply had to silence a gene that chickens typically express. No gene insertion or further manipulation — just a (highly complex) flip of a switch.
The precise gene suppressed by the Chilean scientists, headed by Joâo Botelho
At Universidad de Chile is one called the Indian Hedgehog. This gene is crucial to the development of chicken’s bones, and when turned off, apparently allows the birds to develop a bone structure that looks just like the lower leg of a raptor. Chicken on top, dinosaur on the bottom.
RelatedJust For the Tech of It: Martian crops and dinosaur chickens
This is by no means the first time that Botelho or other scientists have engineered a bird to go back to its more magnificent origins. Botelho also managed to undo the backward-facing perching toe common in birds to produce a front-facing toe — much like what dinosaurs had. And at Yale, a chicken was given a dinosaur-esque snout when its gene expression was altered at the embryo stage.
This sort of work is taking place across the country, and indeed, across the world, says Jack Horner, a famous paleontologist whose expertise was consulted in each and every one of the Jurassic Park films. At his lab at Montana State University, scientists are working to “ genetically alter a chicken egg to produce a more prehistoric version of the animal, complete with velociraptor-shaped head, arms, clawed hands and long tail,” the Post Register reports. But don’t worry, researchers say that we won’t be plunged into a real life version of the movies anytime soon.
“The experiments are focused on single traits, to test specific hypotheses,” says Alexander Vargas, who heds the lab in which Botelho works. “Not only do we know a great deal about bird development, but also about the dinosaur-bird transition, which is well-documented by the fossil record. This leads naturally to hypotheses on the evolution of development, that can be explored in the lab.”
Just call it scientific curiosity, and enjoy the strange but wonderful results that have come out of it … thus far.

Monday, March 7, 2016

Rare Bacterial Infection Claims 18 Lives in Wisconsin, Leading CDC to Launch Investigation

People
Rare Bacterial Infection Claims 18 Lives in Wisconsin, Leading CDC to Launch Investigation
Rare Bacterial Infection Claims 18 Lives in Wisconsin, Leading CDC to Launch Investigation
Following a slew of deaths and reported illnesses in Wisconsin, the Centers for Disease Control and Prevention has announced they are investigating how individuals are contracting Elizabethkingia, a bacterial infection that was previously found in London.

The infection results from a naturally occurring bacteria, which is found in soil, fresh water and reservoirs, health officials said.

While the agency is unsure as to how infected individuals came in contact with the bacteria – seeing as it's rare – they do know that it is resistant to antibiotics and are prone to target people who are 65 years old with underlying health issues.

"At this time, the source of these infections is unknown and the department is working diligently to contain this outbreak," state officials said in a press release, adding that since surveillance was established, "there has been a rapid identification of cases and healthcare providers have been able to treat and improve outcomes for patients."

So far, there have been 18 deaths and 44 cases infection in Wisconsin since first being reported between Dec. 29 and Jan. 4. Symptoms in patients include fever, shortness of breath, chills or cellulitis.

"Determining the source of the bacteria affecting patients in Wisconsin is a complex process," Wisconsin State Health Officer Karen McKeown said in a press release. "While we recognize there will be many questions we cannot yet answer, we feel it is important to share the limited information we have about the presence of the bacteria, as we continue our work to determine the source."

Dinosaur-era geckos and chameleons perfectly preserved in amber

https://www.newscientist.com/

Lizards in amber
Gloriously well preserved
Florida Museum of Natural History/Kristen Grace
They probably hid from feathered dinosaurs, only to end up stuck in redwood sap.
A new collection of 12 lizards preserved in amber dates back to middle of the Cretaceous period – when dinosaurs such as the massive Argentinosaurus were still around – and may include the ancestors of geckos and chameleons.
The specimens come from Myanmar’s Kachin state and are thought to have lived in tropical forest. Each is embedded in Burmese amber, which previous studies dated to about 100 million years old. Previously, we knew of only a few fragments of amber lizards from the time of the dinosaurs – when modern lizard groups first evolved, according to genetic analyses.
The lizards, discovered in private amber collections on loan to the American Museum of Natural History and Harvard University, are immaculate and unusually diverse. As such they suggest that major lizard groups were already established at that time. The specimens will now go on display at the Houston Museum of Natural Science.
“One of them is perhaps the best fossil gecko that is known in the world,” says Juan Daza of Sam Houston State University in Texas, whose team revealed the finds, and then used CT scans to study them (click on image below). It was so detailed the team initially thought it looked like a modern animal.
Lizard scans
Florida Museum of Natural History/Kristen Grace
But it wasn’t recent. “We started looking at the characteristics we describe in modern species, and none of those match,” Daza says. The adhesive toe pads are already present in these ancient specimens, suggesting the gecko’s climbing lifestyle evolved much earlier than thought.
Another specimen has its tongue stuck out. With a narrow, extended tip, it matches no snake or lizard tongue ever found.
One small lizard is trapped next to a scorpion-like animal and a millipede. That proximity, plus the fact that modern lizards in tropical forests hunt arthropods, suggest these animals preyed on them, Daza says.
That particular lizard is doubly interesting. Its bone structure resembles that of a newborn chameleon, although it is about four times the age of the oldest chameleon-like fossils previously known.
It even has a weak jaw, which wouldn’t be good for biting prey – possible evidence that the modern chameleon’s method of grabbing prey with a projectile tongue is really an old adaptation, Daza says. The find may also challenge current view that chameleons originated in Africa.
The new specimens are beautiful and very exciting, says Michael Caldwell of the University of Alberta in Edmonton, Canada. “We really have had little to no previous fossil record detailing that part of the family tree of lizards,” he says.
But closer anatomical studies are now needed to determine where each lizard is best classified – especially the putative chameleon, he adds.

Read more: Stunning fossils: The seven most amazing ever found

Tuesday, March 1, 2016

Invasive Species Aren’t Always Unwanted

The New York Times

In Spain, nonnative crayfish serve as prey for migratory 
wetland birds. Credit Rafa Huertas/Reuters
Invasive species are bad news, or so goes the conventional wisdom, encouraged by persistent warnings from biologists about the dangers of foreign animals and plants moving into new territories.
Conservation organizations bill alien species as the foremost threat to native wildlife. Cities rip out exotic trees and shrubs in favor of indigenous varieties. And governments spend millions on efforts to head off or eradicate biological invaders.
“I think the dominant paradigm in the field is still a ‘when in doubt, kill them’ sort of attitude,” said Dov Sax, an associate professor of ecology and evolutionary biology at Brown University.
But a growing number of scientists are challenging this view, arguing that not all invasive species are destructive; some, they contend, are even beneficial. The assumption that what hails from elsewhere is inherently bad, these researchers say, rests more on xenophobia than on science.
“It’s almost a religious kind of belief, that things were put where they are by God and that that’s where they damn well ought to stay,” said Ken Thompson, an ecologist and retired senior lecturer at the University of Sheffield in England, who wrote the 2014 book “Where Do Camels Belong: Why Invasive Species Aren’t All Bad.”
“We’re actually moving plants and animals around the world all the time,” he said. “We have been for centuries.”
Dr. Thompson and other scientists have called for a more nuanced approach to evaluating whether the presence of a species is harmful or beneficial. Eradicating most invasive species is virtually impossible in an era of globalization, they note. And as climate change pushes more species out of their home ranges and into new areas, the number of so-called invaders is likely to multiply exponentially.
Yet the notion that a species should not be judged on its origins is highly controversial, as Mark Davis, a biology professor at Macalester College in Minnesota, discovered when he and 18 other researchers submitted an article in 2011 saying just that in the journal Nature.
The response was immediate — and signed by 141 scientists, many of them specialists in the field known as invasion biology. Their approach, they said, was already sufficiently “nuanced,” thank you very much.
Asian carp are taking over many rivers in the Midwest.  
Credit Travis Heying/Wichita Eagle, via Getty Images
“Most conservation biologists and ecologists do not oppose nonnative species per se,” wrote Daniel Simberloff, a professor of environmental science at the University of Tennessee, who led the group that wrote the rebuttal. He added that Dr. Davis and his colleagues had vastly played down the severe harm that alien species caused.
But in the five years since that contentious exchange, the idea that invasive species should be assumed guilty until proven innocent has begun to wane, the shift prompted in part, Dr. Davis speculated, by concerns over the use of chemical pesticides and the disruption of landscapes caused by many eradication efforts.
Some alien species are undeniably harmful, a fact that neither Dr. Davis nor others who share his view dispute. The fungus that causes chestnut blight, for example, decimated thousands of trees and changed the American landscape in the early 1900s. The Zika virus is invading new regions, carried by infected mosquitoes that some say are being driven northward by warmer temperatures. The vampirelike lamprey, sneaking into the Great Lakes in the 19th century, gradually champed its way through the fish population.
Islands and mountaintops are especially vulnerable to damage from invaders because their native species often evolved in isolation and lack natural defenses against predators or immunity to exotic diseases. The brown tree snake, accidentally transported to Guam, has virtually eliminated the bird population there.
But, Dr. Davis noted, “all species have negative impacts on something,” and the danger, he said, is often exaggerated.
A study published Feb. 17 in the journal Biology Letters, for example, concluded that alien species “are the second most common threat associated with species that have gone completely extinct” since 1500 A.D.
But the study, Dr. Davis and other experts said, relies on subjective judgments about extinction and does not distinguish between island species — which are far more vulnerable — and land or ocean species.
In some instances, nonnatives offer clear benefits. In California, for example, monarch butterflies prefer to spend their winters in the branches of the eucalyptus, an exotic tree transplanted to the state more than 150 years ago and viewed by some as an invasive fire hazard. In Spain, non-native crayfish serve as prey for migratory wetland birds, including some endangered species.

The fungus that causes chestnut blight decimated trees and changed the American landscape in the early 1900s. Credit Scientifica, via Corbis
And some notorious invaders can have positive effects. Western states have spent a fortune trying to eradicate the tamarisk tree, which many experts believe hogs more than its share of water and damages the habitat of native species.
But Julian D. Olden, an associate professor in the School of Aquatic and Fishery Sciences at the University of Washington, said tamarisks had been found to provide shelter for birds like the southwestern willow flycatcher. Some studies have also concluded that the tree’s water use is not significantly different from that of other tree species.
The antipathy to foreign plants and wildlife is relatively recent. While the distinction between native and non-native species dates to the 18th century, the term “invasion” was first used in a 1958 book — “The Ecology of Invasions by Animals and Plants,” by Charles Elton — that drew on the militaristic vocabulary of the post-World War II era.
But the moniker did not achieve its full derogatory weight until the 1990s and early 2000s, when academic interest in the subject peaked and the number of papers on the subject generated by invasion biologists grew proportionately.
Tamarisk trees have been blamed for damaging the habitat 
of native species in the West, but they have also been found
 to provide shelter for birds.  
Credit Kevin Moloney for The New York Times
To biologists like Dr. Simberloff, taking action to head off alien species early on makes sense, allowing governments to address threats before invaders take firm hold. Non-native species are far more likely to do harm than native plants and animals, he argued, adding that the debate was “a phony controversy.”
Whether a species is viewed as native, however, often depends on when you arrived on the scene. Much of what Americans eat was originally imported: The horse, an icon of the American West, for example, was reintroduced by the Spanish thousands of years after the original North American horse became extinct. Several states list the honeybee as their state insect. But like many other state fish, insects and flowers, the bees are in fact immigrants.
In at least one case, a species that was long extinct in its native range was treated as an interloper when it finally returned home.
Beavers were common in Britain until they were hunted to extinction centuries ago. But when a group of the toothy dam builders took up residence along the River Tay in western Scotland several years ago, local farmers and fishermen greeted the animals with hostility, saying they posed a threat to farmland and salmon runs and were potential carriers of disease. 
Horses were reintroduced to America by Spaniards. 
Credit Caitlin O'Hara for The New York Times
Scottish Land and Estates, an organization representing landowners, insisted that the beavers’ centuries of absence from Britain nullified their resident status, the Independent reported in 2010.
“It’s just silly,” Dr. Thompson said, of the reaction to the Tay beavers. “I don’t think we would have ended up in this ridiculous situation if we hadn’t been so bombarded by propaganda about invasive species.”
Often, he and others say, “invasion” is just another word for “change.” And the only thing that is certain is that more change is to come. Already, the flora and fauna of countries around the world are more homogeneous than they once were, as globalization has, accidentally or intentionally, moved exotic species from one place to another.
“From birds to plants to fish to mammals, there’s strong evidence that things are becoming more similar,” Dr. Olden said, likening the phenomenon to “the popping up of big-box retailers and the loss of mom-and-pop shops.”
Honeybees, frequently honored as state insects, are actually
immigrants Credit Joe Raedle/Getty Images
As more species migrate, new quandaries are likely to arise. And as the human population increases, driving more animals and plants toward extinction, a species’ second home may be the only one it has.
In a paper published last month in the journal Conservation Biology, two scientists in California, Michael P. Marchetti and Tag Engstrom, describe the “paradox” of species that are under threat in their native range but are viewed as invasive in other places they have settled.
They include the Monterey pine, endangered in California and Mexico but treated as a pest in Australia and New Zealand, and the Barbary sheep, endangered in Morocco and other countries but running rampant in the Canary Islands and elsewhere.
“This is a challenge,” Dr. Olden said. “If we identify a plant or animal that might not be able to respond to climate change, do we roll the dice and intentionally move that species northward, or up in elevation?”
“We’re playing a little bit of ecological roulette here,” he added.

Neanderthals may have used manganese dioxide for fire

 

Such expertise would prove a departure from current scientific understanding of the cave-dwellers' cognitive abilities. By Brooks Hays   |   March 1, 2016 at 1:06 PM

















Manganese dioxide blocs collected from Neanderthal
archaeological sites in France. Photo by Leiden University/NWO

LEIDEN, Netherlands, March 1 (UPI) -- Until now, researchers assumed high concentrations of the black ore known as manganese dioxide at Neanderthal sites was explained by its use as a coloring agent in cave and body painting.
But new research suggests Neanderthals may have deliberately sourced the organic chemical for making fire.
Lab experiments conducted by a team of researchers in the Netherlands proved that the presence of manganese dioxide reduces auto-ignition temperature of wood and boosts its rate of char combustion -- making it easier to start and maintain hot and efficient fires.
As the scientists argue in their new paper on the subject -- published in the journal Scientific Reports -- regular fires would have provided Neanderthals with plenty of ash and charcoal for coloring. Collecting manganese dioxide for cave and body painting would have been redundant and an unwise use of energy.
If Neanderthals did selectively source manganese dioxide for making fire, such expertise would prove a departure from current scientific understanding of the cave-dwellers' cognitive abilities.
"We don't know how Neanderthals made fire but given their skills with lithics, we might start with an assumption they used sparks and tinder," study author Peter Heyes, a researcher at Leiden University, said in a press release. "We don't bring it out particularly in the paper but manganese dioxide added to wood shavings or other tinder increases the efficiency with which the tinder captures a spark and lights."
Using manganese dioxide for fire suggests a distinct level of sophistication with regard to Neanderthals' use of fuel.
"Finding evidence to support a view on Neanderthal management of wood fuel resources is a very remote possibility," Heyes added. "It could nevertheless have been an important aspect of subsistence. If Neanderthals could devote time and resources to collecting manganese dioxide for fire making, it is perhaps not unreasonable to assume they could manage wood fuel resources effectively."

Study of Neanderthal Y chromosome hints at fertility problems

April 7, 2016
 
Washington (AFP) - The first examination of a long-extinct Neanderthal's Y chromosome suggests that fertility problems may have prevented Neanderthal men from successfully mating with modern human females, researchers said.
The study in the American Journal of Human Genetics is based on a male Neanderthal whose 49,000-year-old remains were found in El Sidron, Spain.
Until now, researchers have only sequenced the DNA of female Neanderthal fossils, and have found that one to four percent of European and Asian people's DNA can be traced to Neanderthals.
But researchers at Stanford University found that the Neanderthal's Y chromosome is completely lacking in males today.
The Y chromosome is one of two human sex chromosomes (X and Y) and is passed on exclusively from father to son.
The findings suggest that Neanderthal Y chromosomes may never have been passed along when Neanderthals and humans mingled and mated some 50,000 years ago.
That could be because women may have miscarried male fetuses sired by Neanderthals, or produced very few healthy male babies that could pass on this Y-chromosome lineage.
Researchers are probing the hypothesis that modern women's immune systems might have attacked male fetuses carrying certain Neanderthal mutations.
The scientists say they found mutations in certain immune system genes from the El Sidron Neanderthal that have been blamed for transplant rejection when modern males donate organs to women.
"The functional nature of the mutations we found suggests to us that Neanderthal Y chromosome sequences may have played a role in barriers to gene flow, but we need to do experiments to demonstrate this and are working to plan these now," said senior author Carlos Bustamante, professor of biomedical data science and genetics at the Stanford University School of Medicine.
"We've never observed the Neanderthal Y chromosome DNA in any human sample ever tested," Bustamante added.
"That doesn't prove it's totally extinct, but it likely is."
Previous studies have shown that modern human and Neanderthal lineages diverged between 400,000 and 800,000 years ago.
The Neanderthals died out some 30,000 years ago.