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paleoanthropology, genetics and evolution

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It’s a worthwhile perspective and many scientists will recognize their own experiences.

After much consideration, I believe that current peer-review processes often do the opposite of what they are supposed to achieve. That is, the double-blind system provides no assurance to me – and, by extension, the readers – that reviewers are qualified professionals. The blind review process can reduce accountability, leading to poor-quality service work, which reviewers can no doubt still count on in their annual evaluations without having properly served their journal, their discipline or their colleagues. The blinded format can encourage boorish and unethical behaviour. To top it off, troll reviews waste an incredible amount of professional time and energy of authors, editors and colleagues who reviewed earlier drafts.

“The prestige of your doctorate does matter insofar as it helps you get a more prestigious job,” Larremore explained. “But what we’ve found is, once you’re in the door to a faculty job, the training then doesn’t matter.” In other words, once in the same department, the productivity of faculty members who trained at more prestigious universities was indistinguishable from that of their colleagues who trained at less prestigious universities.

Relevant to me:

David said he suspects that building connections that had not previously existed might be key to success. “There’s an intellectual space that hasn’t really been occupied before,” he said. “And if you can draw on two different areas of expertise and take something that’s kind of unique to each of them and bring them together into a problem of your own, then you can stake out some territory that hasn’t been explored before.”

The sample consists of 489 scans taken from 431 specimens, representing 59 species of most Primate families. These data have transformative reuse potential as such datasets are necessary for conducting high power research into primate evolution, but require significant time and funding to collect. Similar datasets were previously only available to select research groups across the world.

Despite this rush to digitize, comparative morphology is experiencing a crisis as a mode of addressing large-scale evolutionary questions due to the difficulty involved in accruing datasets large enough to have high explanatory power, and the small community of researchers that can participate effectively. This presents a paradox: If so many researchers are putting large efforts into scanning, where are the massive samples? Though a few research groups have managed to generate large samples of scans comprehensively representing diversity in one clade or another, this work has been time consuming, and expensive: as a result these scans are not made widely accessible to non-collaborating researchers. This inequality in access to what is now essential, basic data clearly falls short of scientific ideals for meritocracy. Furthermore, a significant component of the unmanageable demand for 3D scan data experienced by museums may represent wasteful recollection of data already held by other research groups.

It was found that the closer humans lived to a nature preserve, the more likely dogs had penetrated it.
But perhaps most striking? The dogs were neither feral nor domestic — but somewhere in between.
“All the dogs we detected had an ‘owner’ or a person that the animal has a bond with,” Paschoal said. “The species population increases following human populations, exacerbating their potential impact on wildlife.”

With the aid of a specialized loom, they have also created woven installations nearly the size of a van that visualize the interconnectivity of the cosmic web. “We believe that art, as much as science, seeks to say something true about the nature of existence,” they wrote in a 2017 paper on their collaboration, “and that end is best served by artistic representation that grapples with real data and not only with allegorical concepts.”

The bottom line of the article is encompassed in the last paragraph:

“Applying the techniques from art definitely influences the way astronomers see and interact with their data,” English said. “I don’t think [techniques from art] in astronomy visualization can be relegated to a sidebar any longer. It really does enhance discovery science.”

“We had 3,000 individuals, all indigenous, in the ’80s,” Pickering marveled. “Rooms full of bones.” Locating the Aboriginal communities to return them to involved serious detective work. Many of the skeletons were mixed up, their labels faded or eaten by silverfish, and their origins were only traced through century-old correspondence and fading ledgers.
The unit’s centerpiece is a table where skeletons are laid out for tribal elders, who wrap the remains in kangaroo skin or wafer-thin paperbark to take back to Country. But not all of them want to handle the remains, Pickering said, often asking staff to do it instead. “It can be a harrowing experience for the elders,” says heritage officer Robert Kelly, who has worked in repatriation since 2003. “To see the skulls of their ancestors with serial numbers written on them, holes drilled for DNA tests, wires that were used for display mounts. They break down. They start crying when they see these things.”

Just as revolutionary was what Mungo Man meant for the understanding of Aboriginal culture. “Up until Mungo, Aboriginals had been frequently denigrated,” Bowler said bluntly. “They were ignorant savages, treacherous. Suddenly here was a new indication of extraordinary sophistication.” The reverent treatment of the body—the oldest ritual burial site ever found—revealed a concern for the afterlife eons before the Egyptian pyramids. Two of Mungo Man’s canine teeth, in the lower jaw, were also missing, possibly the result of an adolescent initiation ceremony, and there were the remains of a circular fireplace found nearby. “It took me a long time to digest the implications,” Bowler said. Today, Aboriginal people still use smoke to cleanse the dead. “It’s the same ritual, and there it was 40,000 years ago.” All the evidence pointed to a spectacular conclusion: Aboriginal people belong to the oldest continuous culture on the planet.
News of Mungo Man’s discovery, presented as a triumph by scientists, provoked outrage in the Aboriginal communities; they were furious that they had not been consulted about their ancestor’s removal from his homeland. “I read about it in the newspaper like everybody else,” recalls Mary Pappin, a Mutthi Mutthi elder. “We were really upset.” The first quiet protests over archaeological work had begun years earlier over Mungo Lady, led by her mother, Alice Kelly, who would turn up with other women at new digs and demand an explanation, carrying a dictionary so she could understand the jargon. “My mum wrote letters,” recalls her daughter. “So many letters!” Removing Mungo Man seemed the height of scientific arrogance. Tensions reached such a point by the end of the 1970s that the 3TTs placed an embargo on excavation at Lake Mungo.

The data set, which lists around 100,000 researchers, shows that at least 250 scientists have amassed more than 50% of their citations from themselves or their co-authors, while the median self-citation rate is 12.7%.
The data are by far the largest collection of self-citation metrics ever published. And they arrive at a time when funding agencies, journals and others are focusing more on the potential problems caused by excessive self-citation. In July, the Committee on Publication Ethics (COPE), a publisher-advisory body in London, highlighted extreme self-citation as one of the main forms of citation manipulation. This issue fits into broader concerns about an over-reliance on citation metrics for making decisions about hiring, promotions and research funding.
“When we link professional advancement and pay attention too strongly to citation-based metrics, we incentivize self-citation,” says psychologist Sanjay Srivastava at the University of Oregon in Eugene.

Second, as an application to osteology we examined intra-observer scanning protocol variability, using the coefficient of variation (CV) to quantify surface area and volume variance between repeated scans of eight porcine capital femoral epiphyses with undulating mammillary processes on one surface with amplitudes covering the range of the test block bas-relief offset values. The CoR showed each test-retest measurement from each instrument differed by no more than their CoR: 0.010 mm, 0.137 mm, 0.068 mm, 0.193 mm for the VHX, NE, HP and CMM, respectively. There was agreement between the instruments, but each instrument (NE, HP and CMM) overestimated bas-relief features as reported by the VHX, on average (bias) by 0.046 ± 0.038 mm, 0.025 ± 0.033 mm, 0.026 ± 0.033 mm for the NE, HP and CMM, respectively. Both scanners captured surface features as small as 0.1 m

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Since 1946 events have moved so rapidly that everyone is readjusting and what one said even a few years ago may be quite different from present belief. But it is necessary to look at the past a little more to understand subsequent events. I have mentioned Weidenreich and Hooton, not in the spirit of praise or blame, but as representatives of different traditions. In general, the Germans never accepted early Homo sapiens or Piltdown. The English accepted early sapiens, and the Americans have followed the English tradition. One might put the matter this way: apparently it was as hard for a German to believe in early Homo sapiens as it was for an Englishman to be a skeptic. Hrdlička followed the German tradition. I am no intellectual historian and make no pretense of having read the vast literature on fossil man, but the influence of the intellectual tradition on the interpretation of human fossils is so great that the record makes little sense without considering it. As a part of these traditions, we all have built-in preconceived notions. Was it dogmatic for Weidenreich to accept the result of Friederich’s study, showing that the Piltdown jaw was that of an ape? Or was it dogmatic for Hooton to reject this conclusion? Each acted in accord with previous belief and in accord with the tradition to which he belonged. Both were right. The jaw was that of an ape, but it was impossible that such a jaw should be associated with a sapiens skull by chance. Both were wrong in that neither saw the possibility of a fake as the explanation.
It is easy to refer to the other person’s guesses as preconceived and dogmatic, but from the point of view of the developing science of human evolution the essential point is that progress comes when the area open for personal debate is narrowed. The development of chemical dating methods makes it possible to settle some of the problems which up to now have been matters of personal opinion. Frequently human bones have been found under circumstances in which there is real doubt about their associations and the more such problems can be settled by methods which are independent of intellectual traditions the more rapidly our understanding of human evolution will progress.

Roopkund Lake is a small body of water (~40 m in diameter) that is colloquially referred to as Skeleton Lake due to the remains of several hundred ancient humans scattered around its shores (Fig. 1). Little is known about the origin of these skeletons, as they have never been subjected to systematic anthropological or archaeological scrutiny, in part due to the disturbed nature of the site, which is frequently affected by rockslides, and which is often visited by local pilgrims and hikers who have manipulated the skeletons and removed many of the artifacts.

Since a forest ranger stumbled across the ghostly scene during World War II, explanations for why hundreds of people died there have abounded. These unfortunates were invading Japanese soldiers; they were an Indian army returning from war; they were a king and his party of dancers, struck down by a righteous deity. A few years ago, a group of archaeologists suggested, after inspecting the bones and dating the carbon within, that the dead were travelers caught in a lethal hailstorm around the ninth century.

The following section is an edited version of an unpublished report generated before genetic data were available by co-author Prof. Subhash Walimbe. The goal of our edits is to synthesize the anthropological discussions included in that report with the genetic findings. Newly added statements dealing directly with the genetic results are shown in italics. Some of the content of the original reports was used as part of the script of a National Geographic television documentary that was made describing the Roopkund Lake Site, so there are similarities between parts of the text that follows and that script.

Another explanation inevitably comes to mind as we survey this assemblage of beings who dwelt on the slopes of Mount Carmel---an explanation which, though intriguing in its own right, would illuminate but little the origins of that creature in which we are intensely interested, namely, ourselves. Can it be---so runs the little disturbing thought which will not be quieted---can it be that we are dealing with a group of mixed bloods, of hybrids between Neanderthal and a type already essentially modern?

The fault does not lie in this unique and invaluable discovery which, among other things, has demonstrated that an essentially modern brain and facial structure already existed in the Riss-Wurm Interglacial. It lies in our inadequate knowledge of human genetics and the processes which influence or determine the rapidity of human evolution. Only as our knowledge of the Ice Age population of Palestine increases and the science of genetics grows more sure will the vistas of human prehistory opened by the sleepers in the cave of Mugharet es Skhul be capable of interpretation by modern eyes.

Lawrence Krauss, a physicist who retired from Arizona State University, even continued defending Epstein after his 2008 conviction, telling the Daily Beast in 2011: “As a scientist I always judge things on empirical evidence and he always has women ages 19 to 23 around him, but I’ve never seen anything else, so as a scientist, my presumption is that whatever the problems were I would believe him over other people.” He added, “I don’t feel tarnished in any way by my relationship with Jeffrey; I feel raised by it.”
Other scientists seem to have been drawn to the attention and spotlight that Epstein gave them. Evolutionary biologist George Church, one of the few researchers who has apologized for having contact with Epstein, which he attributes to “nerd tunnel vision”, told STAT News that “he is used to financiers, technologists, and celebrities seeking him out, and has become a quasi-celebrity himself”.

But it’s not just broken hyperlinks that frustrate scientists. As papers get more data-intensive and complex, supplementary files often become many times longer than the manuscript itself—in some extreme cases, ballooning to more than 100 pages. Because these files are typically published as PDFs, they can be a pain to navigate, so even if they are available, the information within them can get overlooked. “Most supplementary materials are just one big block and not very useful,” Cooper says.
Another issue is that these files are home to most of a study’s published data, and “you can’t extract data from PDFs except using complex software—and it’s a slow process that has errors,” Murray-Rust tells The Scientist. “This data is often deposited as a token of depositing data, rather than people actually wanting to reuse it.”

Mark Hahnel, the CEO and founder of figshare, says that he started the company during his doctoral studies out of frustration with the limitations of supplemental files. “We expected to play this role for people who were producing outputs of research that didn’t fit into the model of publishing PDFs,” he tells The Scientist. But increasingly, academics also are using figshare for other reasons, he adds, such as being able to freely reuse material associated with a published paper without worrying about infringing upon copyrights. (While research outputs such as figures in a traditional journal may be subject to a publisher’s copyright policies, those deposited to repositories like figshare are usually published with a creative commons license that allows others to use the material without restrictions.)

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Spy 2B taken at many wavelengths, from Mathys et al. 2019