New Tools May Have Allowed Hominins to Leave Africa Far Earlier Than Previously Known

(p. D1) The oldest stone tools outside Africa have been discovered in western China, scientists reported on Wednesday [July 11, 2018]. Made by ancient members of the human lineage, called hominins, the chipped rocks are estimated to be as much as 2.1 million years old.
The find may add a new chapter to the story of hominin evolution, suggesting that some of these species left Africa far earlier than once believed and managed to travel over 8,000 miles east of their evolutionary birthplace.
. . .
(p. D3) The trigger for that migration? Maybe it was figuring out how to make sharp stone tools.
“Suddenly you had a primate that could obtain meat from a carcass, and it opened up a new world for them,” Dr. Dennell said. “That simple technology was enough to get them out of Africa and right across Asia.”

For the full story, see:

Zimmer, Carl. “Ancient Tools Provide New Insight.” The New York Times (Tuesday, July 17, 2018): D1 & D3.

(Note: ellipsis, and bracketed date, added.)
(Note: the online version of the story has the date July 11, 2018, and has the title “Archaeologists in China Discover the Oldest Stone Tools Outside Africa.”)

Government Uses Cruel Painful Snare Traps to Kill Gorgeous Respectful Foxes

(p. A18) BRIGANTINE, N.J. — Red foxes can be found all over New Jersey, wandering out of the woods and poking through garbage at dusk in search of a meal. In many places, they might be overlooked, if not seen as a disease-carrying nuisance. But not in Brigantine, an island community where the fox has become an unofficial ambassador.
Many residents warmly share stories of their encounters, like the fox that would routinely come up to a back door or the time a children’s soccer game had to pause so one could cross the field. A fox makes an appearance on the cover of the city’s tourism guide, as much of an attraction as its golf course and pristine beaches. A real estate company regularly sends its mascot, Briggy the Fox, to community events.
Yet the island is also the seasonal home to piping plovers, a small bird that returns every year to dig its nests on the beach. The bird is an endangered species in New Jersey that state wildlife officials closely watch and fiercely protect, including from foxes, creating a bitter conflict that has caused an uproar as residents protest the trapping and killing of the animals.
Some are challenging the use of snare traps, a contraption that they describe as cruel and painful. The contretemps has also stirred a wider debate: Is it fair to kill one animal for the sake of protecting another?
“It disgusts me,” said Donna Vanzant, who owns a marina. “Why go after these gorgeous animals? Just let nature take its course.”
State lawmakers recently wrote a letter to wildlife officials expressing their “deep concern,” and the City Council passed a resolution condemning the “inhumane and indiscriminate killing of red foxes.” Briggy the Fox attended the meeting and held a sign: “Please stop killing my friends.”
“Everyone on the island cherishes the foxes and does not want them killed,” said Donna Grazioli DeAngelis, a retired teacher who started a petition online, which about 90,000 people have signed. “They have been so respectful, so perfect in every way,” she said of the foxes. “People paint them, photograph them. They haven’t been a nuisance in any way.”
. . .
“It’s an overreach and overreaction,” Philip J. Guenther, Brigantine’s longtime mayor, said of the fox trapping. “It just doesn’t seem to make any sense from a protection standpoint.”

For the full story, see:
Rick Rojas. “To Save One Precious Animal, a Town Must Sacrifice Another.” The New York Times (Monday, May 7, 2018: A18.
(Note: ellipsis added.)
(Note: the online version of the story has the date May 6, 2018, and has the title “Trapping Foxes to Save Plovers Sets Off Showdown at Jersey Shore.” The online version says the print version appeared on May 6 on p. A17 of the New York Edition. My print version, as usual, was the National Edition.)

Ancient Skeletons Harbor a Common Cause of Liver Cancer

(p. A9) Scientists reported on Wednesday [May 9, 2018] that they have recovered DNA from the oldest viruses known to have infected humans — and have succeeded in resurrecting some of them in the laboratory.
The viruses were all strains of hepatitis B. Two teams of researchers independently discovered its DNA in 15 ancient skeletons, the oldest a farmer who lived 7,000 years ago in what is now Germany.
Until now, the oldest viral DNA ever recovered from human remains was just 450 years old.
The research may provide clues to the continuing evolution of hepatitis B, a plague that infects an estimated 257 million people worldwide and contributes to an epidemic of liver cancer.
. . .
Chronic infections can lead to liver cancer. Each year, the World Health Organization estimates, hepatitis B kills 887,000 people. Researchers have long wondered how it became a worldwide menace.
. . .
. . . the skeletons in which the Cambridge geneticists found hepatitis range from 820 to 4,500 years old. The research, published in the journal Nature, demonstrates that hepatitis B existed across Europe and Asia as early as the Bronze Age.
. . .
Johannes Krause and his colleagues examined DNA extracted from the teeth of 53 ancient people in what is now Germany. Three of them were infected with hepatitis B, it turned out: one who lived about 1,000 years ago, a second person who lived 5,300 years ago and a third who lived 7,000 years ago.
. . .
Dr. Krause and his colleagues found that their Stone Age viruses were most closely related to strains of hepatitis B found today only in chimpanzees and gorillas.
He speculated that the virus jumped from apes to humans early in the history of our species in Africa. “It’s more likely this is really an old pathogen in humans for the last hundred thousand years or more,” he said.

For the full story, see:
Zimmer, Carl. “In Ancient Skeletons, Scientists Discover a Modern Foe: Hepatitis B.” The New York Times (Thursday, May 10, 2018): A9.
(Note: ellipses, and bracketed date, added.)
(Note: the online version of the story has the date MAY 9, 2018. The print version cited above is the National Edition.)

The paper by the Cambridge geneticists, mentioned above, is:
Mühlemann, Barbara, Terry C. Jones, Peter de Barros Damgaard, Morten E. Allentoft, Irina Shevnina, Andrey Logvin, Emma Usmanova, Irina P. Panyushkina, Bazartseren Boldgiv, Tsevel Bazartseren, Kadicha Tashbaeva, Victor Merz, Nina Lau, Václav Smrčka, Dmitry Voyakin, Egor Kitov, Andrey Epimakhov, Dalia Pokutta, Magdolna Vicze, T. Douglas Price, Vyacheslav Moiseyev, Anders J. Hansen, Ludovic Orlando, Simon Rasmussen, Martin Sikora, Lasse Vinner, Albert D. M. E. Osterhaus, Derek J. Smith, Dieter Glebe, Ron A. M. Fouchier, Christian Drosten, Karl-Göran Sjögren, Kristian Kristiansen, and Eske Willerslev. “Ancient Hepatitis B Viruses from the Bronze Age to the Medieval Period.” Nature 557, no. 7705 (May 9, 2018): 418-23.

The paper co-authored by Krause, and mentioned above, is:
Krause-Kyora, Ben, Julian Susat, Felix M. Key, Denise Kühnert, Esther Bosse, Alexander Immel, Christoph Rinne, Sabin-Christin Kornell, Diego Yepes, Sören Franzenburg, Henrike O. Heyne, Thomas Meier, Sandra Lösch, Harald Meller, Susanne Friederich, Nicole Nicklisch, Kurt W. Alt, Stefan Schreiber, Andreas Tholey, Alexander Herbig, Almut Nebel, and Johannes Krause. “Neolithic and Medieval Virus Genomes Reveal Complex Evolution of Hepatitis B.” eLife 7 (2018): e36666.

Human Ancestors May Have Had Capacity for Symbolic Thought 600,000 Years Ago

(p. D1) On Thursday [February 22, 2018], a team of researchers offered compelling evidence that Neanderthals bore one of the chief hallmarks of mental sophistication: they could paint cave art. That talent suggests that Neanderthals could think in symbols and may have achieved other milestones not preserved in the fossil record.
“When you have symbols, then you have language,” said João Zilhão, an archaeologist at the University of Barcelona and co-author of the new study.
. . .
(p. D6) But a second study, which Dr. Zilhão and his colleagues published Thursday [February 22, 2018], in the journal Science Advances, hints that Neanderthals might well have been painting long before 64,000 years ago.
The scientists traveled to a cave on the coast of Spain where Dr. Zilhão had earlier discovered shells that had been drilled with holes and painted with ocher.
. . .
He and his colleagues discovered a layer of flowstone sitting atop the rock where they had found the shell jewelry. That flowstone turned out to be about 115,000 years old.
. . .
The colored, pierced shells themselves are probably not much older than that. Up until about 118,000 years ago, the cave was flooded, thanks to higher sea levels.
That finding provides strong evidence that the shells were made by Neanderthals. They were definitely living in Spain 115,000 years ago, while modern humans would not arrive in Europe for another 70,000 years.
The two new studies don’t just indicate that Neanderthals could make cave art and jewelry. They also establish that Neanderthals were making these things long before modern humans — a blow to the idea that they simply copied their cousins.
The earliest known cave paintings made by modern humans are only about 40,000 years old, while Neanderthal cave art is at least 24,000 years older. The oldest known shell jewelry made by modern humans is about 70,000 years old, but Neanderthals were making it 45,000 years before then.
“These results imply that Neanderthals were not apart from these developments,” said Dr. Zilhão. “For all practical purposes, they were modern humans, too.”
The new studies raise another intriguing possibility, said Clive Finlayson, director of the Gibraltar Museum: that the capacity for symbolic thought was already present 600,000 years ago in the ancestors of both Neanderthals and modern humans.
He agreed with Dr. Zilhão that the new study supports the idea that Neanderthals used language. In addition to the evidence of symbolic thought, researchers have also found that the inner ears of Neanderthals were tuned to the frequencies of speech, much like our own.
“We don’t know how they spoke or what they said,” said Dr. Finlayson. “But they had the ability of speech.”
The cave paintings that Dr. Pike and his colleagues have dated are generally abstract. There’s no evidence so far that Neanderthals painted images of lions and other animals, as modern humans did thousands of years later.
But Dr. Pike doesn’t think a lack of animal imagery marks a mental deficiency in Neanderthals. It could simply reflect a cultural preference.’

For the full story, see:
Zimmer, Carl. “MATTER; The Neanderthal, the Artist.” The New York Times (Tuesday, February 27, 2018): D1 & D6.
(Note: ellipses, and bracketed date, added.)
(Note: the online version of the story has the date FEB. 22, 2018, and has the title “MATTER; Neanderthals, the World’s First Misunderstood Artists.”)

The first article mentioned above and co-authored by Zilhão, is:

Hoffmann, D. L., C. D. Standish, M. García-Diez, P. B. Pettitt, J. A. Milton, J. Zilhão, J. J. Alcolea-González, P. Cantalejo-Duarte, H. Collado, R. de Balbín, M. Lorblanchet, J. Ramos-Muñoz, G. Ch Weniger, and A. W. G. Pike. “U-Th Dating of Carbonate Crusts Reveals Neandertal Origin of Iberian Cave Art.” Science 359, no. 6378 (Feb. 23, 2018): 912-915.

The second article mentioned above and co-authored by Zilhão, is:
Hoffmann, Dirk L., Diego E. Angelucci, Valentín Villaverde, Josefina Zapata, and João Zilhão. “Symbolic Use of Marine Shells and Mineral Pigments by Iberian Neandertals 115,000 Years Ago.” Science Advances 4, no. 2 (Feb. 22, 2018): 1-6.

Proof of Concept for Regenerating Limbs and Internal Organs

(p. D3) Scientists have decoded the genome of the axolotl, the Mexican amphibian with a Mona Lisa smile. It has 32 billion base pairs, which makes it ten times the size of the human genome, and the largest genome ever sequenced.
The axolotl, endangered in the wild, has been bred in laboratories and studied for more than 150 years. It has the remarkable capacity to regrow amputated limbs complete with bones, muscles and nerves; to heal wounds without producing scar tissue; and even to regenerate damaged internal organs.
This salamander can heal a crushed spinal cord and have it function just like it did before it was damaged. This ability, which exists to such an extent in no other animal, makes its genes of considerable interest.
. . .
The researchers have identified some of the genes involved in regeneration, and some genes that exist only in the axolotl, but there is much work still to be done.

For the full story, see:
NICHOLAS BAKALAR. “TAKE A NUMBER; 32 Billion.” The New York Times (Tuesday, February 6, 2018): D3.
(Note: ellipsis added.)
(Note: the online version of the story has the date FEB. 1, 2018, and has the title “TAKE A NUMBER; The Smiling Axolotl Hides a Secret: A Giant Genome.”)

Environment Can Affect Which Genes Are Activated

(p. D5) In September 1944, trains in the Netherlands ground to a halt. Dutch railway workers were hoping that a strike could stop the transport of Nazi troops, helping the advancing Allied forces.
But the Allied campaign failed, and the Nazis punished the Netherlands by blocking food supplies, plunging much of the country into famine. By the time the Netherlands was liberated in May 1945, more than 20,000 people had died of starvation.
The Dutch Hunger Winter has proved unique in unexpected ways. Because it started and ended so abruptly, it has served as an unplanned experiment in human health. Pregnant women, it turns out, were uniquely vulnerable, and the children they gave birth to have been influenced by famine throughout their lives.
When they became adults, they ended up a few pounds heavier than average. In middle age, they had higher levels of triglycerides and LDL cholesterol. They also experienced higher rates of such conditions as obesity, diabetes and schizophrenia.
. . .
“How on earth can your body remember the environment it was exposed to in the womb — and remember that decades later?” wondered Bas Heijmans, a geneticist at Leiden University Medical Center in the Netherlands.
Dr. Heijmans, Dr. Lumey and their colleagues published a possible answer, or part of one, on Wednesday in the journal Science Advances. Their study suggests that the Dutch Hunger Winter silenced certain genes in unborn children — and that they’ve stayed quiet ever since.
While all cells in a person’s body share the same genes, different ones are active or silent in different cells. That program largely is locked in place before birth.
But scientists have learned that later experiences — say, exposure to a virus — can cause cells to quiet a gene or boost its activity, sometimes permanently.
The study of this long-term gene control is called epigenetics. Researchers have identified molecules that cells use to program DNA, but how those tools work isn’t entirely clear. One of the best studied is a molecular cap called a methyl group.
At millions of spots across our DNA, genes may carry a methyl group. They seem to silence genes — at least, researchers have found that silenced genes often have a collection of methyl groups lurking nearby.

For the full story, see:
Zimmer, Carl. “Dutch Genes Still Bear Scars of a Famine.” The New York Times (Tuesday, February 6, 2018): D5.
(Note: ellipsis added.)
(Note: the online version of the story has the date JAN. 31, 2018, and has the title “MATTER; The Famine Ended 70 Years Ago, but Dutch Genes Still Bear Scars.”)

Biodiversity May Increase If We “Let the Winners Go on Winning”

(p. C7) In 2004 Mr. Thomas, a biologist at the University of York, garnered headlines with a study predicting that at least a fifth of land animals and plants would be “committed to extinction” by 2050. In “Inheritors of the Earth,” Mr. Thomas does not disavow those findings. A mass extinction is in full swing, he concedes. But the “gloom-merchants” are ignoring the success stories, Mr. Thomas argues, of animals and plants that are thriving in the Anthropocene. Nature, in many respects, “is coping surprisingly well,” he writes, and we shouldn’t ignore “the gain side of the great biological equation of life.”
In some corners of the planet, warmer, wetter conditions have allowed a greater variety of species to survive than would have just decades ago, he points out, while modern transport keeps new immigrants rolling in. The result is a greater number of species in many regions–more local biodiversity–even if the global picture may be trending toward less.
Many species that contribute to diverse and functioning ecosystems aren’t native–they did not evolve where they now occur. And introduced species can jump-start evolutionary processes. They compete with established species, prey on them, or breed with them, and they can occupy ecological niches once occupied by organisms that have died out or are faring poorly.
Mr. Thomas describes a honeysuckle in Pennsylvania that’s a hybrid of species from several remote continents, and yet delicious to local flies, which began to interbreed out of a shared love of its berries; there’s a deer with Japanese genes that’s doing just fine in Scotland’s woods. We should be cheering on these victors, he says, but instead many have been subjected to dubious campaigns to eradicate them.
Conservation usually aims to help the most imperiled species, and favors those with a longer claim to the habitats they occupy. But rather than “always try to defend the losers,” Mr. Thomas proposes, what if we embraced the dynamism of evolution and let the winners go on winning?

For the full review, see:
Jennie Erin Smith. “Picking Sides in the Fight for Survival.” The Wall Street Journal (Sat., Sept. 23, 2017): C7.
(Note: the online version of the review has the date Sept. 22, 2017.)

The book under review, is:
Thomas, Chris D. Inheritors of the Earth: How Nature Is Thriving in an Age of Extinction. New York: PublicAffairs, 2017.

“Insects Can Solve Problems, They Can Learn”

(p. D6) Never underestimate the power of the bee brain.
In the latest triumph for one of humanity’s favorite insects, bumblebees learned how to push a ball to the center of a platform for a sugary treat.
That may not make them a threat on the chess board, but soccer or even Skee-Ball might be within their intellectual grasp — if it were scaled down in size, of course.
The new research finding is one more reason that scientists who study insects, of all sorts, would like to point out that just because a brain is small, doesn’t mean it is simple.
Clint Perry, one of the bumblebee trainers at Queen Mary University of London, and a confirmed small brain partisan, said, “I’ve actually been asked if bees have brains.”
In fact, a number of recent experiments have shown that “insects can solve problems, they can learn,” he said. And scientists have yet to define the limits of insects’ mental abilities.
. . .
The task of pushing a little ball to the center of a platform was completely arbitrary. Bees don’t do anything like this in nature, where they seek out flowers for nectar and pollen. So it was a brand new behavior demanding some kind of general ability to learn.
The way the bees learned was important, too. They were pre-trained to expect a treat in the center of a platform. But having to push a ball to the center to get the treat was something they hadn’t seen.
Then the researchers tried several ways of teaching the bees what to do. The bees learned best by watching a fellow bee perform the feat. After that kind of observation, 10 of 10 bees solved the problem on the first try. On later tries, they continued to improve, taking less time.

For the full story, see:
Gorman, James. “SCIENCETAKE; The Power of the Bumblebee Brain.” The New York Times (Weds., FEB. 28, 2017): D6.
(Note: ellipsis added.)
(Note: the online version of the story has the date FEB. 23 [sic], 2017, and has the title “SCIENCETAKE; Bumblebees Demonstrate the Power of Insect Brains.”)

“Basic Fairness Is Probably Written into Our Genetic Code”

(p. C2) Basic fairness is probably written into our genetic code. Human societies depend on the expectation of reciprocity: We assume that a neighbor will collect our mail if we’ve mowed their lawn, or that drivers will take turns braking at stop signs.
Fundamental as this trait might seem, however, its evolutionary origins are hazy. Previous research has shown that chimpanzees–one of our closest relatives–are less motivated by fairness than by what they immediately stand to gain from a transaction.
A new study shows that chimps can go beyond such reflexive selfishness and cooperate, even if it costs them something. But they don’t just give up what’s theirs, even to their kin. They are particular about when they will share some of their food, according to research led by University of Vienna biologist Martin Schmelz and just published in Proceedings of the National Academy of Sciences.
Like many of us, the team found, chimps keep score: They’re most likely to allot treats to a partner if that chimp helped them first.

For the full commentary, see:
SUSAN PINKER. “MIND AND MATTER: What Chimps Understand About Reciprocity.” The Wall Street Journal (Sat., July 22, 2017): C2.
(Note: the online version of the commentary has the date July 21, 2017.)

The full academic article that is summarized above, is:
Schmelz, Martin, Sebastian Grueneisen, Alihan Kabalak, Jürgen Jost, and Michael Tomasello. “Chimpanzees Return Favors at a Personal Cost.” Proceedings of the National Academy of Sciences 114, no. 28 (July 11, 2017): 7462-67.

Human Species Is Highly Adaptable to Climate Variation

(p. A15) In “Evolution’s Bite,” paleoanthropologist Peter S. Ungar follows the stories encapsulated in our enamel-coated anatomy.
Mr. Ungar’s story isn’t so much about teeth themselves as about the sweeping tale of human evolution as seen through the mouth.
. . .
Unpredictability in climate and resources, Mr. Ungar emphasizes, has made us a species adapted to variation. Drawing from the work of researchers like Elisabeth Vrba and Rick Potts, he underscores how environmental shifts influence our evolution just as they have for other animals. The invention of culture did not somehow free us from nature. Our existence and continuing evolution are still influenced by shifts in climate and their effects. Humans didn’t become locked into just one narrow mode of life but rather became a flexible species as comfortable above the Arctic Circle as on the equator. “Climate change,” he writes, “drove human evolution, in large part by swapping out food options available on the biospheric buffet.”
This new story–that humans became adapted to the variability of the world rather than any one set of conditions–hasn’t had time to become pop-culture canon just yet. Images of Man the Hunter stepping out onto the savanna in search of big game still dominate. “The story used to be simpler,” Mr. Ungar writes, when it seemed that “the spreading savanna coaxed our ancestors down from the trees, and the challenges it brought made them human.” All the same, the mounting swell of research doesn’t show a slow and steady transition from a chilly Ice Age world to the warmer one we know today. Instead, Mr. Ungar points out, temperatures dipped and spiked in a haphazard pattern prior to our influence on the climate, having an overall trajectory that we can detect now but that probably would have seemed simply chaotic to the people and creatures living through it.

For the full review, see:
Brian Switek. “BOOKSHELF; Chewing Over History.” The Wall Street Journal (Weds., May 31, 2017): A15.
(Note: ellipsis added.)
(Note: the online version of the review has the date May 30, 2017, and the title “BOOKSHELF; Chewing Over Humanity’s History.”)

The book under review, is:
Ungar, Peter S. Evolution’s Bite: A Story of Teeth, Diet, and Human Origins. Princeton, NJ: Princeton University Press, 2017.

“Unfettered Science, If We Have the Courage to Let It Unfold”

(p. 26) “How to Tame a Fox” sets out to answer a simple-seeming question: What makes a dog a dog? Put another way, how did an animal that started out as a bloodthirsty predator become one that now wants nothing more than a nice belly rub and the chance to gaze adoringly at a member of another species? In the late 1950s, a Russian scientist named Dmitri Belyaev decided to address this puzzle by taking the unheard-of tack of replicating the domestication process in real time. He and his colleagues took silver foxes, widely bred in vast Siberian farms for their luxurious pelts, and made them into friendly house pets. It was a deceptively simple process: Take the puppies from only the friendliest foxes, breed them and repeat. Lyudmila Trut, the current lead researcher of the silver fox experiment, who began work as Belyaev’s intern, along with Lee Alan Dugatkin, an American scientist and writer at the University of Louisville, documents their monumental effort in this sparkling new book.
Belyaev died in 1985, but the experiment is still ongoing, with 56 generations of foxes bred to date — a far cry from the snarling creatures that used to snap at the hands of their caretakers when the research began. The new foxes run toward people, jump on the bed and nuzzle one another as well as their human caretakers. Such a behavioral transformation was to some degree expected, since they were bred from the tamest members of their groups. Perhaps more intriguing, they also look more doglike, with floppy ears, wagging tails and piebald fur.
. . .
The book, . . . , is not only about dogs, or foxes, or even science under siege from political interests. . . . It may serve — particularly now — as a parable of the lessons that can emerge from unfettered science, if we have the courage to let it unfold.

For the full review, see:
MARLENE ZUK. “Fox and Friends.” The New York Times Book Review (Sun., MAY 7, 2017): 26.
(Note: ellipses added.)
(Note: the online version of the review has the date MAY 5, 2017, and has the title “How Do You Make a Fox Your Friend? Fast-Forward Evolution.”)

The book under review, is:
Dugatkin, Lee Alan, and Lyudmila Trut. How to Tame a Fox (and Build a Dog): Visionary Scientists and a Siberian Tale of Jump-Started Evolution. Chicago: University of Chicago Press, 2017.