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Denisovans may have met us in the Pacific

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Enlarge / The highlands of Papua New Guinea.

David Kirkland | Getty Images

The inhabitants of the Pacific came in waves. Aboriginal Australians were the first to cross the area, and they were followed by separate populations that inhabited New Guinea and nearby island chains. Later still, the Polynesians, descendants of early East Asians, spread through the distant islands of the Pacific.

While modern genetics has made these rough outlines clear, it has also made it clear that these different populations sometimes interacted, sharing DNA along with technology and trade goods. Paleontology finds have made it clear that at least three distinct hominin species had occupied some of these islands before modern humans arrived, including the enigmatic Hobbits of Indonesia and a similarly diminutive species in the Philippines.

A recent study of the genomes of Pacific island populations provides a map of some of the major interactions that took place in the Pacific. And it suggests at least one of these involved the introduction of additional Denisovan DNA.

New genomes

The work started with the sequencing of over 300 genomes volunteered by individuals from 20 different populations throughout the Pacific. The research team grouped these populations according to whether they came from Near Oceania (Indonesia, New Guinea, and the Philippines) or more distant islands of the Pacific (collectively Far Oceania). The latter is largely populated by the Polynesians, who arrived relatively late and had a distinct genetic history. But there were clearly interactions between the two groups, and the border between the areas each occupies is fuzzy in locations.

By comparing the genome sequences with each other and ancestral populations, it’s possible to make estimates of which groups are related to which others, as well as the time at which the different populations branched off. In addition, it’s possible to detect interbreeding among the populations, based on the appearance of stretches of DNA that are found in one population but are more similar to those from another.

The people who live in the highlands of Papua New Guinea have the earliest split, separating from the populations of other islands about 40,000 years ago. The branches of that lineage who inhabit the Bismarck and Solomon Islands separated from each other about 20,000 years ago.

But things get much less neat in Vanuatu, a group of islands out past the eastern end of the Solomons. About a third of their genome comes from Bismarck islanders, and that was a recent arrival, the result of interactions that took place only about 3,000 years ago. The rest comes from a group that started out in Papua but interbred with the Solomon Islands population en route. All of that means that Vanuatu is like a melting pot of near oceanic populations.

Then there are the Polynesians. They seem to have interbred with both the Bismarck and Solomon islanders. The best fit to the data involves one interaction right as the Polynesians arrived in the area about 3,500 years ago and a second interaction that occurred a thousand years later.

Premodern humans

All of the populations sampled seem to have roughly similar amounts of Neanderthal DNA, present in similar locations in the genome, suggesting there was nothing unusual about their genetic history compared to other groups in the region. But that was not the case with the Denisovans. The amount of Denisovan DNA varied considerably among the populations, with the highest percentage found in those from the New Guinea highlanders.

Analysis of the Denisovan DNA segments was used to determine two things. The length of the DNA provided a measure of how long ago the interbreeding took place, as the Denisovan DNA segments would get shorter over time thanks to recombination. The sequence itself could be compared to the genome of a Denisovan bone in Siberia, which tells us a bit about how diverse the Denisovan population was.

East Asian populations and the Polynesians appear to have had two different periods of interbreeding with Denisovans, both of which were reasonably closely related to the Siberian population.

The people of Papua New Guinea also showed signs of two periods of interbreeding. But, rather critically, they weren’t the same ones seen in East Asians. The first involved interbreeding around 45,000 years ago with a population that had separated from the Siberian Denisovans by roughly 200,000 years—a genetic contribution shared with the East Asians and Polynesians. But the second interbreeding event took place about 25,000 years ago—after the point where the population was out in the Pacific.

And that’s a bit strange. In terms of fossil evidence, we know that Homo erectus was in the area before modern humans arrived, but its DNA would be substantially different from that of Denisovans. There are two other species—the Hobbits of Flores and an equally odd hominin from the island of Luzon. While these look very different from modern humans (having some traits shared with the earlier Australopiths), we can’t rule out that they are closely related to the Denisovans, which would explain the origin of this DNA.

The researchers checked, and the only signs of distantly related DNA can be accounted for by Neanderthals and Denisovans. So if these island species aren’t Denisovans, then it appears we didn’t interbreed with them in a way that left its mark on modern genomes.

What this tells us

Modern humans reached places that required travel across the open ocean very early during their expansion out of Africa. That would seem to suggest that ocean-going voyages were well within our abilities. But these data indicate that most populations remained relatively isolated from each other once they were established. That suggests that, even though the technology was available to manage this travel, it wasn’t widely used—certainly, there’s no indication of longstanding trade until the Polynesians arrive.

Once the Polynesians did arrive, however, there are indications that they interacted at least twice with the inhabitants of the islands near New Guinea. And Vanuatu, at the border between Near Oceania and Polynesia, seems to have an exceedingly complicated history.

To an extent, it seems that, outside of Vanuatu, these people groups interacted with each other about as often as their ancestors interacted with the Denisovans. The genomic data provides evidence of several distinct periods of interbreeding, including one that for now appears specific to a group that is native to the Philippines. This indicates that some of the interbreeding likely went on after modern humans had migrated out into the Pacific islands.

Since we don’t know of any Denisovan remains in the region, it suggests two possibilities. One is that the Denisovans were in the area undetected—not a huge surprise, given how long their presence in Asia went undetected. But the more intriguing prospect is that one of the species we’re aware of from skeletal remains—Homo luzonensis or Homo floresiensis—represents a branch of the Denisovan lineage. So far, all attempts to extract DNA from these skeletons have failed, so it’s not clear if or how we’d be able to figure this out.

Nature, 2021. DOI: 10.1038/s41586-021-03236-5  (About DOIs).

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Researchers peek at proprietary data of US particle physics lab Fermilab

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Multiple unsecured entry points allowed researchers to access data belonging to Fermilab, a national particle physics and accelerator lab supported by the Department of Energy.

This week, security researchers Robert Willis, John Jackson, and Jackson Henry of the Sakura Samurai ethical hacking group have shared details on how they were able to get their hands on sensitive systems and data hosted at Fermilab.

After enumerating and peeking inside the fnal.gov subdomains using commonly available tools like amass, dirsearch, and nmap, the researchers discovered open directories, open ports, and unsecured services that attackers could have used to extract proprietary data.

A naked FTP server

Among the exposed assets was Fermilab’s FTP server, ftp.fnal.gov, containing heaps of data that allowed “anonymous” login without a password.
Enlarge / Among the exposed assets was Fermilab’s FTP server, ftp.fnal.gov, containing heaps of data that allowed “anonymous” login without a password.

Sakura Samurai

The server exposed configuration data for one of the Fermilab’s experiments called “NoVa,” which concerns studying the purpose of neutrinos in the evolution of cosmos.

The researchers discovered that one of the tar.gz archives hosted on the FTP server contained Apache Tomcat server credentials in plaintext:

Sakura Samurai

The researchers verified that the credentials were valid at the time of their discovery but ceased experimenting further so as to keep their research efforts ethical.

Thousands of documents and project tickets exposed

Likewise, in another set of unrestricted subdomains, the researchers found over 4,500 tickets used for tracking Fermilab’s internal projects. Many of these contained sensitive attachments and private communications.

Sakura Samurai

And yet another server ran a web application that listed the full names of users registered under different workgroups, along with their email addresses, user IDs, and other department-specific information.

A fourth server identified by the researchers exposed 5,795 documents and 53,685 file entries without requiring any authentication.

“I was surprised that a government entity, which has over a half a billion-dollar budget, could have so many security holes,” Willis, the Sakura Samurai researcher, told Ars in an interview. “I don’t believe they have even basic computer security after this engagement, which is enough to keep you up at night. I wouldn’t want a malicious actor to steal important data, which has cost the US hundreds of millions to produce, while also leaving the potential to manipulate equipment that could have a severe impact.”

Serious flaws resolved swiftly

The research activities performed by Willis, Jackson, and Henry were consistent with Ferminab’s vulnerability disclosure policy. Fermilab was quick to respond to the researchers’ initial report and squashed the bugs swiftly.

“Fermilab managed the interactions regarding the findings in a quick and positive way. They didn’t question the authenticity of our vulnerabilities and immediately dug in and patched—acknowledging the sense of urgency,” Jackson said. “The first thought that we had was about the possibility of a nation-state threat actor acquiring this data, especially because it’s no surprise that Fermilab works on groundbreaking scientific research.”

“We knew we had to act quickly and inform Fermilab. Nonetheless, still crazy to see the ease in which we acquired sensitive data, which included credentials to scientific equipment and servers,” he added.

This discovery of a US government-funded national lab having serious security flaws that are trivial to exploit comes as multiple US federal agencies continue to be targets of cyberattacks.

Just last week, Ars reported that threat actors had potentially hacked at least five US government agencies via Pulse Connect Secure VPN vulnerabilities. Separately, the FBI is investigating an extortion attempt by ransomware operators against the Metropolitan Police Department in Washington, DC.

Fermilab declined to comment.

The researchers’ detailed findings related to the research are provided in their blog post.

Ax Sharma is a security researcher, engineer, and reporter who publishes in leading publications. His expertise lies in malware research, reverse engineering, and application security. He’s an active community member of the OWASP Foundation and the British Association of Journalists.

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Earliest known burial in Africa is that of a small, fragile child

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Mohammad Javad Shoaee

78,000 years ago, a child died two to three years into their life in the coastal highlands of what is now Kenya. Archaeological evidence suggests that survivors wrapped the small body tightly before laying it, curled on one side with the tiny head resting on a pillow, in a carefully dug pit in Panga ya Saidi cave. The child’s grave is now the oldest known example of people in Middle Stone Age Africa burying their dead.

A child called Mtoto

A thesaurus is a handy thing, but sometimes seemingly tiny differences in meaning can actually have a huge impact. Consider the implications of “disposing of bodies” versus “laying the dead to rest.” One of the things archaeologists are most interested in about the lives of the earliest members of our species—and our close relatives, now extinct—is when and how we first began to make that distinction.

When did early humans stop viewing a dead human body as something smelly to be removed from the living area before it attracted scavengers and sickness? When did they decide it needed to be treated carefully to ensure safe passage to an afterlife—or perhaps give peace for the living?

Short of time travel, the best way archaeologists can figure out when people started believing in concepts like a spirit or an afterlife is to figure out when people started burying their dead with, as paleoanthropologist Louise Humphrey of the National History Museum of London puts it, “an investment of time and resources beyond what is strictly required to dispose or make use of the corpse.” That could mean placing the body carefully in a particular position, wrapping it in a shroud or supporting it with pillows, or even burying objects in the grave.

Mtoto is what archaeologists named the 78,000-year-old toddler’s skeleton recently unearthed at Panga ya Saidi Cave in Kenya (Mtoto is a Swahili word for child). And Mtoto clearly received that kind of tender attention from their community.

The remains were located by paleoanthropologist Maria Martinon-Torres, of Spain’s National Research Center on Human Evolution, and her colleagues. They found the small grave pit dug into several older layers of sediment in the cave, with the pit filled in with a mix of sediment scooped up from the cave floor. Inside, a few “fragile and degraded” pieces of bone were all that remained: the base of the skull and part of the lower jaw, part of the spine and ribs, and some fragments of arm and leg bones. The remains were so fragile that archaeologists had to wrap the whole burial pit in plaster and bring the plaster-wrapped chunk of sediment back to a lab at the Museum of Kenya to excavate under better conditions.

Mtoto lay on the right side, with the legs curled up to the chest. The child’s right collarbone and upper ribs had been turned and pressed inward, exactly the way archaeologists would expect if someone had wrapped the child’s upper body tightly, perhaps with a cloth or hide, before burial. Sometime after burial, the head and neck had collapsed downward, as if a support—maybe a cushion or a wooden block—had decayed away underneath it. And a few large shells mixed in with the grave soil may (or may not) have been funeral offerings.

When Martinon-Torres and her colleagues examined a few of Mtoto’s teeth—a mixture of deciduous, or baby, teeth and adult molars that hadn’t emerged from the jaw yet—they saw that the child was clearly a member of our species, Homo sapiens. And optically stimulated luminescence, a dating technique that measures when rock or sediment last saw sunlight, placed the grave soil at around 78,000 years old. That makes Mtoto the oldest human with a formal, deliberate grave in Africa.

Life and death in the Middle Stone Age

What does that actually tell us about the lives and beliefs of ancient people or the gradual emergence of the first human cultures? The Middle Stone Age was a period when what archaeologists think of as “modern human behavior” started taking the world by storm. It had been going on for about 200,000 years when Mtoto died, and it lasted for at least another 50,000 years. Modern human behavior, in this case, includes things like using symbols, creating art, and making jewelry, and people at several places in Africa were definitely doing those things long before Mtoto’s people grieved their loss.

In Europe and the Levant, archaeologists have found evidence that people—both Homo sapiens and Neanderthals—buried their dead in or near their living spaces as early as 120,000 years ago. That’s also what seems to have happened with Mtoto at Panga ya Saidi.

“Burial in residential localities, such as at Panga ya Saidi, has been suggested to reflect mourning behavior and the intention to keep the dead nearby,” wrote Martinon-Torres and her colleagues. Of course, that’s an informed guess; archaeologists can’t really know what ancient people were thinking. But it fits what we know about similar choices in several modern cultures.

But all of that—burials dating to 120,000 years ago in the Levant, combined with evidence of symbolic thinking and art much earlier than that in Africa—makes it seem a little surprising that the earliest actual burial in Africa is just 78,000 years old. After all, burial seems like such a key piece of evidence about ancient spiritual beliefs, and people clearly had laid the cultural groundwork for those beliefs long before Mtoto’s time.

The key may be that “laying the dead to rest” doesn’t always mean “digging a hole and filling it up with dirt afterward.” A quick look at modern cultures around the world reveals lots of different ideas about the proper way to lay the dead to rest, and each culture has its own reasons for what it does. Many of those funeral practices wouldn’t be likely to leave archaeological traces tens of thousands of years in the future.

Burial just happens to be one of the practices that’s most likely to leave remains mostly intact for archaeologists to find, and it’s also relatively easy to recognize a deliberate burial. But in tropical settings like coastal Kenya, buried bones don’t always last millennia; even what was left of Mtoto’s skeleton was in a “fragile and degraded” state, after all. It’s reasonably likely that for every burial like Mtoto’s, there are others that have long since vanished without a trace—lives, deaths, and afterlives forever beyond knowing.

“The absence of a behavior does not necessarily imply that the capacity for such behavior was lacking,” wrote Martinon-Torres and her colleagues.

There’s more than one way to hide a body

People in Africa evidently laid their dead to rest very deliberately, although in other ways, perhaps for hundreds of thousands of years before Mtoto’s burial—and possibly before Homo sapiens had technically come into being. Paleoanthropologists Lee Berger and John Hawks contend that Homo naledi carried their dead through the narrow tunnels into the darkness of Rising Star Cave in South Africa around 300,000 years ago. Archaeologists are still debating that claim, but if Berger and Hawks are correct, Rising Star is an example of a funerary cache—a place where people put their dead without necessarily digging a hole to bury them in. Sima de los Huesos cave in Spain may have served a similar purpose for other hominins there around 400,000 years ago.

The other two earliest human “burials” in Africa are a 68,000-year-old grave in Taramsa, Egypt, and a 58-to 74,000-year-old one at Border Cave, South Africa. But they’re also technically funerary caches rather than burials, according to the researchers. Regardless of the technicalities, at both sites, people clearly took time and effort to lay the remains to rest with care; the infant at Border Cave was even interred with a perforated shell, painted with ocher.

And that’s the really unsettling thing all three of Africa’s oldest human graves have in common: they all belong to young children. It suggests, wrote Martinon-Torres and her colleagues, that “Homo sapiens populations were intentionally preserving the corpses of young members of their groups between about 78,000 and 69,000 years ago.” In fact, if we look at every known Homo sapiens or Neanderthal burial from 120,000 years ago to the end of the Pleistocene, slightly more than half belong to children.

Children’s bones are smaller, more fragile, and less likely to survive millennia in the ground or the recesses of a cave than those of adults. That may tell us something about ancient demographics; it could point to a higher percentage of children in the population, a higher child mortality rate, or likely a combination of both.

Nature, 2021 DOI: 10.1038/s41586-021-03457-8  (About DOIs).

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World waits to see where a Chinese booster will come down

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Enlarge / An artist’s depiction of the Tianhe station module. While that’s safely in orbit, the booster that got it there isn’t in a stable orbit.

In late April, China successfully launched a major component of its planned space station. Since then, the booster that put the component into orbit has been circulating in an unstable orbit, and various tracking organizations are indicating that it’s likely to come back in a completely uncontrolled manner. It’s a big-enough piece of hardware that some parts are likely to survive until they reach the ground. While odds are that will happen over the ocean, there’s no guarantee re-entry won’t happen over a populated area.

As Ars’ Eric Berger described last year, the Long March 5B has an unusual design. Meant for heavy lifts to orbit, the rocket doesn’t have an upper stage; instead, its main stage travels all the way to orbit with its payload. Once there, one option is to leave it in a stable orbit, where it would add to the increasing clutter in low Earth orbit. The alternative is to de-orbit the stage.

Most countries have settled on a controlled de-orbit, in which control is maintained over the booster and enough fuel is retained to allow decisions to be made about when the hardware re-enters the atmosphere. That allows any material that survives re-entry to land harmlessly in the ocean.

China has apparently not chosen this path. Following the launch of a Long March 5B last year, the rocket re-entered the atmosphere while on an orbit that took it directly over New York City. Material from that booster ended up causing damage on the far side of the Atlantic in the Ivory Coast, although fortunately nobody was injured. According to experts, the Long March booster was the largest object to make an uncontrolled re-entry in nearly 30 years. And that size makes a difference, since it means larger parts that are more likely to survive the violent trip to the Earth’s surface.

China, however, was not chastened by the threat posed by its hardware. In late April, it launched a key piece of its planned space station, Tianhe, a 22-ton module that will include the crew quarters, atop a Long March 5B. Since then, the main booster has been tumbling uncontrolled in an unstable orbit, and the EU’s space tracking program indicates simulations suggest it will re-enter on May 8 or 9. The booster’s orbit only takes roughly 90 minutes, so predicting where its debris might land is impossible given that uncertainty.

Predictions regarding its re-entry will undoubtedly improve given additional time to monitor its orbit. But, because of the tumbling, its interactions with the thin atmosphere are going to make any certainty difficult.

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