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paleoanthropology, genetics and evolution

Photo Credit: Rainy day at Amud Cave, Israel. John Hawks CC-BY-NC-ND

Hybrid origins of the straight-tusked elephants

Elephants are one of the most important comparisons for human origins. Like humans, they’re long-lived animals that have complex social behavior, they require extensive home ranges and sometimes migrate over long distances.

What genetics has discovered about their evolution and diversification over the last few years provides some fascinating parallels to human evolution in the Pleistocene. Mammoths are their own fascinating story—I wrote about them several years ago, and again in 2016, and the story continues to develop.

But in the last year, the other ancient elephants have been at the forefront of new discoveries. In particular, the “straight-tusked elephant”, Palaeoloxodon antiquus, has yielded two ancient genomes that have disrupted what paleontologists thought they knew about Pleistocene evolution.

Straight-tusked elephant skull and reconstruction from Torralba, Spain
Straight-tusked elephant skull and reconstruction from Torralba, Spain. Photo: José-Manuel Benito via Wikipedia

Last summer I wrote about sequencing work on the ancient straight-tusked elephant: “Genomes of straight-tusked elephants”.

At that time, Matthias Meyer and colleagues had demonstrated that the genomes of two individuals of Palaeoloxodon antiquus from Germany were closer to African forest elephants (Loxodonta cyclotis) than savanna elephants (Loxodonta africana).

That was newsworthy. Paleontologists had mostly thought that Palaeoloxodon was related to the Asian elephant and mammoth clade. It turns out that it’s one of the African elephants. The result also emphasized the deep phylogenetic separation of the savanna and forest elephants in Africa. Those two living African elephant populations, once assumed to be part of a single species, are substantially different genetically from each other, perhaps as much as mammoths and Asian elephants were.

It also raised new questions about the relationships of the extinct African lineage, Palaeoloxodon recki. Once widely known as Elephas recki, this was the major component of the elephant fauna in the Pleistocene African fossil record. Today’s savanna elephants, L. africana, are virtually unknown through much of the African Pleistocene. Nobody really knows where the living lineage may have been hiding, nor does anybody know why P. recki might have become extinct.

Palaeoloxodon antiquus tooth, by Khruner (Wikimedia)
P. antiquus tooth. Photo credit: Khruner, CC-BY.

In my post last June, I hinted that there might be more to the story. Ewen Callaway had reported on a conference presentation by Eleftheria Palkopoulou that discussed evidence for hybridization among these ancient elephants: “Elephant history rewritten by ancient genomes”.

Now, Palkopoulou’s analysis has been published in PNAS: “A comprehensive genomic history of extinct and living elephants”. The title is a bit overblown in my opinion, because I have many questions that the new paper doesn’t answer. But the paper does add two important details to Meyer’s results from last year.

First, Palkopoulou and colleagues show that the straight-tusked elephant genome from Neumark-Nord, some 120,000 years old, is not a simple branch of the elephant phylogeny. This individual’s ancestry derives mostly from a branch that stemmed from the common ancestors of savanna and forest elephants. But it also has substantial ancestry from woolly mammoths. And up to a third of its genome came from a population genetically similar to today’s forest elephants from Sierra Leone, in West Africa.

A third of the genome is pretty high to be interpreted as a “ghost population”. The straight-tusked elephant population of Europe in the early Late Pleistocene was apparently a mixture of two source populations, one with a long independent evolutionary history, and one with continuing strong genetic connections to African forest elephants.

This strong African forest connection was not with every population of forest elephants. The Sierra Leone L. cyclotis individual in the study bears strong similarity to the ancient straight-tusked elephant, but the Central African Republic-sampled L. cyclotis genome does not.

Second, Palkoupoulou and coworkers used a combination of analyses to jointly examine the effective population sizes of elephant species and genetic divergence times between them. There are lots of details in this analysis, with so many lineages sampled, and I wouldn’t trust many of these details too far until more individuals are added to the African elephant and Palaeoloxodon samples.

Still, these analyses reinforce what the evidence for introgression shows. The two sampled forest elephants demonstrate a long divergence, with an estimated divergence time between 463,000 and 609,000 years ago for the populations that these two sampled individuals represent.

These two populations of forest elephants from different parts of Africa are around as different from each other as Neandertals and Denisovans were.

Clearly, we are not going to understand the evolution of the forest elephants, or their connection with straight-tusked elephants, until geneticists sample a lot more of them. Two genomes from each are not enough.

Another detail of the new analysis bears upon the long-time absence of the savanna elephant from the Pleistocene African fossil record:

The two savanna elephants had lower Ne relative to forest elephants for hundreds of thousands of years (Fig. 4D), potentially reflecting ecological competition from the African elephant Palaeoloxodon recki (including Palaeoloxodon iolensis) that dominated the African savannas until the Late Pleistocene (2, 19), or the high levels of male–male competition documented in this species.

That’s a possibility. I find it fascinating that the savanna elephant lineage is very ancient indeed, separated from forest elephants for the last 2 million years. The identity of the P. recki population remains obscure, and the great difference between today’s forest elephant samples suggests that a better sample of elephant DNA from across Africa may yield additional genetically differentiated lineages. It’s even conceivable that some lineage of forest elephant might turn out to be a close relative of P. recki or P. iolensis.

Or then again, maybe P. recki will turn out to be a true ghost, not closely related to P. antiquus at all. As I wrote last year:

Of course, without ancient DNA evidence, it’s not certain that these other extinct Palaeoloxodon species are closely related to the forest elephants and P. antiquus.

I just want to reiterate this sentiment. Discovering that P. antiquus isn’t what paleontologists once thought does not give me confidence that paleontologists really know where P. recki or P. namascus belong. For that matter, I have no confidence that P. recki within Africa is really a single lineage. Until recently, most biologists considered L. africana and L. cyclotis to be a single lineage.

I can’t wait to see results from a bigger sample of ancient elephants. The story of the straight-tusked elephants is likely much broader than two German skeletal samples. There are many challenges to ancient DNA study in temperate and low-latitude situations, but if there’s any species with plenty of tissue to sample, it should be elephants.

An ethnographic look at peer review recommends some big changes in training

Gemma Derrick in Nature: “Take peer pressure out of peer review”.

Derrick has done research in the U.K. including direct observation of peer review panels in action. Her Nature essay focuses upon a recent effort to include non-academic voices in grant panels to broaden the representation of the public in funding decisions. In her telling, academics are not shy to hijack the proceedings.

My own and others’ observations show that a peer-review panel is not like some collaborative mural, where everyone contributes a piece to the picture. It is more like a tug of war — with a rope that has many ends. Evaluators form alliances and join various ends of the rope. This sets the panel’s dominant mode for dictating how all proposals are assessed. Those outside this framework are quickly silenced, even if they were recruited for their perspective.

She encourages pre-evaluation training for all participants in peer review. I think this is a helpful suggestion. Discussing implicit bias, having referees discuss the role of public investment in diversifying and strengthening scientific inquiry, and giving explicit credit to effective collaborations.

What I strongly favor is the involvement of the public. I believe that public participation in grant review can help to build stronger support for scientific work. I think this process should be more open and responsive to public input, and that the voices of non-specialists should be taken seriously.

Anthropology would be in a much stronger position in the U.S. if we collaborated to develop a Board of Visitors or equivalent group for each of our departments and organizations, and organized our events to broaden the engagement of the public in anthropological research.

Link: Ancient genome brings light to Taíno ancestry

Lizzie Wade has a news story in Science that provides a review of a new paper by Hannes Schroeder and colleagues, who have sequenced the genome of 1000-year-old skeletal remains from Preacher’s Cave, in the Bahamas. This precontact individual is consistent with linguistic and archaeological evidence showing that the Caribbean islands were colonized from South America. The genome also shows that many living people in the Caribbean region have descended in part from this precontact population.

Today’s populations of the Caribbean islands, including Puerto Rico where genetics have been studied in substantial detail, have a blend of African, European, and Native American ancestry. The research paper is in PNAS: “Origins and genetic legacies of the Caribbean Taino”.

I don’t approve of the headline that Science gave Wade’s article: “Genes of ‘extinct’ Caribbean islanders found in living people”. Nature published an article with a similar headline about the Taíno in 2011 and had to issue a correction. I reflected on that instance at the time: “Watch who you call extinct!”

Despite its headline, Wade’s article puts the story into context well and quotes a variety of experts. I liked this section:

“These indigenous communities were written out of history,” says Jada Benn Torres, a genetic anthropologist at Vanderbilt University in Nashville who studies the Caribbean’s population history and has worked with native groups on several islands. “They are adamant about their continuous existence, that they’ve always been [on these islands],” she says. “So to see it reflected in the ancient DNA, it’s great.”

This is a complex ethnological issue, with living people constructing their ideas of identity in part based on traditions, and in part based on recent genetic work.

Human brain evolution looks gradual. If you ignore enough data...

Bernard Wood’s research group has a new paper on brain size evolution in hominins, led by Andrew Du in Proceedings of the Royal Society, Series B: “Pattern and process in hominin brain size evolution are scale-dependent”.

In this paper, I notice that the researchers have done a really weird thing: Their analyses include only hominin fossils before 500,000 years ago.

Here’s their main figure:

Figure 2 from Du and colleagues showing endocranial volumes of hominin fossils over time
Figure 2 from Du and colleagues (2018).

Each of the symbols in this figure represents a single fossil hominin specimen that has an estimate of endocranial volume. The specimens reflect every hominin species from Australopithecus afarensis up to “Homo heidelbergensis”. Modern humans and Neanderthals have been left out of the dataset—they don’t fall within the pre-500,000-year time range.

On the basis of this dataset, the authors conclude that the entire hominin lineage is compatible with a single pattern of gradual evolutionary increase over time:

Figure 3b from Du and colleagues showing the data fitting a gradual model of brain size increase over time
Figure 3b from Du and colleagues (2018). Each point here is the data average in each 200,000-year-long interval, connected by a line. The shaded area indicates a range consistent with gradual linear increase over time.

The mean for each time interval of 200,000 years is plotted here, and none of the means fall outside the predicted error range for a gradual linear increase.

So what’s weird about this?

Let’s look at what the data show if we don’t impose an artificial limit of 500,000 years ago:

Same figure as above with hominin endocranial volume data, but this time with Homo naledi and Homo floresiensis added
Same figure as above, but this time with Homo naledi and Homo floresiensis added.

Hey, look at that! There are two species entirely missing from the data examined by Du and colleagues. The fossil records of endocranial volume in Homo naledi and Homo floresiensis both date to the last 300,000 years. When you include them, they both reject the notion of gradual monotonic increase in brain size.

It is likely that Homo naledi branched from the lineage of Neanderthals and modern humans more than a million years ago, maybe much longer. In other words, H. naledi ancestors must have existed throughout much of the last phase of our evolutionary history, and we haven’t found them yet. The same is true of H. floresiensis—and I don’t assume that Flores is the only place where such a population may have existed. The real message of these species is that the Lower and Middle Pleistocene records must undersample hominin diversity.

In neither case is it clear whether the small brains of these hominins resulted from a reversal from a larger-brained ancestor, or whether their small brain size was retained from the common ancestor of Homo.

The paper doesn’t justify its exclusion of this key evidence, so I don’t really know why the authors chose to ignore the data. There are other strange decisions underlying the analyses here—including the strange assumption that a gradual monotonic increase is an appropriate model across many species that are not a single ancestor-descendant lineage. I think that what looks like a “fit” is actually just an illustration of how weak the data are.

What’s obvious that the conclusions would be different if all the evidence were included.

Link: An Ethiopian government transition

Ethiopia is undergoing an unexpected government transition, and Yohannes Gedamu in The Conversation gives some context: “Premier quitting and state of emergency signal urgent need for reform in Ethiopia”.

All eyes are now on the ruling coalition as it deals with the prime minister’s resignation and scrambles to fill his position.
Things are changing quickly in Ethiopia and it is difficult to predict what the ruling coalition will do next. One thing is clear: rather than declaring a state of emergency the ruling regime should come to terms with the popular demand for democracy, the rule of law and political and economic fairness.

Link: Sicilian wine from the Copper Age retrieved from deep in geothermal caves

The Conversation has a nice article by Davide Tanasi reviewing recent work uncovering historic secrets locked away by sulfuric cave fumes in Sicily: “Prehistoric wine discovered in inaccessible caves forces a rethink of ancient Sicilian culture”.

It’s pretty neat. Deep in an unexpected area they found jars and jars of ancient offerings, including wine.

Initially I did not fully grasp the import of such a discovery. It was only when I vetted the scientific literature on alcoholic beverages in prehistory that I realized the Monte Kronio samples represented the oldest wine known so far for Europe and the Mediterranean region. An incredible surprise, considering that the Southern Anatolia and Transcaucasian region were traditionally believed to be the cradle of grape domestication and early viticulture. At the end of 2017, research similar to ours using Neolithic ceramic samples from Georgia pushed back the discovery of trace of pure grape wine even further, to 6,000-5,800 B.C.

This sounds like a magical archaeological context.

What keeps astronomers from publishing their results?

An article in Science by Daniel Clery investigates the mystery of why half the astronomers who are granted telescope time never seem to publish their results: “‘Still working’: Astronomers explain why they don’t publish”.

I’ve often compared anthropology to astronomy in terms of data sharing and data generation. Astronomy is moving toward massive open datasets from enormous sky survey telescopes. But some of the most expensive and largest telescopes apportion time to researchers based upon a proposal system, allocating hours of observation time on instruments that cost hundreds of millions of dollars to build and maintain.

Ferdinando Patat surveyed scientists who were granted observation time between 2006 and 2013 but still haven’t produced any peer-reviewed outputs:

They got a surprisingly high number of responses—80%—and the most common one was, perhaps unsurprisingly, “I am still working on the data.” [Ferdinando] Patat says, “That’s the easiest answer you can give, like when you ask a student why they haven’t submitted their essay on time.” But perhaps they’re not trying to pull a fast one. Patat says other studies have shown an asymptotic curve of publication delay, which takes about 3.5 years to reach 50% of the total number of publications and 10 years to reach 95%.

I’ve heard many people suggest that there is a tradeoff between doing work in a reasonable time and doing work of high quality.

However, there are many reasons why taking a long time tends to degrade the quality of work. How many times have you looked at a draft of a paper from five years ago, and now you can’t remember the details that go into its analyses?

When you remove a publication to a time long after data collection, details on how the data were collected may be lost. Indeed, generating new datasets to compare to the original ones may be impossible.

Most science today is done by teams, and team members move, change jobs, or go on to new projects, all of which can negatively impact the quality of a team product. Especially when team members know that a piece of research is on the slow track, many will not give it the priority in their workflow that would result in the highest quality output.

What is a problem in the astronomy case is that telescope time is viewed as a valuable research goal in itself, setting aside that it is necessary for original analyses:

Patat says you can never get to 100% because it is part of the scientific process that some risky proposals may never produce results. Part of the shortfall he ascribes to the trend throughout science to avoid publishing negative results. “This reflects what may be a growing cultural problem in the community as scientists tend to concentrate on appealing results, especially if they have limited resources, and the need to focus predominantly on projects that promise to increase their visibility,” Patat says. But he also suspects there are some proposals that are not well thought through or are thrown in to show a team is busy. “It’s a perverse system where winning time on its own is seen as important,” he says.

You may think it’s a stretch to compare this to anthropological fieldwork, but there are many, many researchers who view fieldwork as a goal in itself, rather than a means to publishing original research. Many have constructed fieldwork as an enterprise that occurs over two or three weeks a year, very much like telescope observation time is a limited number of nights.

Link: Finding the lost rice of the American South

The New York Times has a fascinating story about a lost strain of rice that once was widely grown by slaves and freedmen in the South: “Finding a Lost Strain of Rice, and Clues to Slave Cooking”.

Mr. Dennis had heard about hill rice — also known as upland red bearded rice or Moruga Hill rice — through the culinary organization Slow Food USA and the Carolina Gold Rice Foundation, the group that brought back Carolina Gold in the early 2000s. He’d also heard stories about it from elderly cooks in his community. Like everyone else, he thought the hill rice of the African diaspora was lost forever.
But then, on a rainy morning in the Trinidad hills in December 2016, he walked past coconut trees and towering okra plants to the edge of a field with ripe stalks of rice, each grain covered in a reddish husk and sprouting spiky tufts.
“Here I am looking at this rice and I said: ‘Wow. Wait a minute. This is that rice that’s missing,’” he said.

I love the human stories in food, and the way that our commensal organisms and crops can tell the stories of people who may have left little or no written legacy.

Ideological purity tests are not the way to build public engagement with science

Undark is running an op/ed by Aspen Reese, a former visiting scientist at the American Museum of Natural History, about the recent (and ongoing) flap concerning the politics of a museum trustee, Rebekah Mercer: “There’s an Anti-Science Conservative on Your Museum’s Board. So What?”

I find my opinion on this series of events closely aligned with Reese’s.

If the stated intent behind all the hullabaloo is to protect the reputation of the institution, garnering it a new one of being anti-conservative seems very dangerous indeed. We must not bar the doors of scientific institutions to anyone, whether it’s done explicitly, or by making them feel, as a class, unwelcome. Science cannot be known purely as a place for liberals. It has to be inclusive to be done right, for in trying to describe the world we must necessarily include all of it. Scientific institutions may feel more comfortable in the absence of dissenting voices, but by excluding people on the basis of their politics, those same institutions would sacrifice the opportunity to share science where it is most likely to win new converts to reason and empiricism.

As we repeatedly tell students, science is not a series of facts about the world. Science is a methodology, a way of finding better and better descriptions of natural phenomena by means of observation and deduction.

My science does not yield to any politics, and I find it neither necessary nor desirable for all scientists to agree with any set of political notions. If we base the public support of the scientific enterprise on ideological uniformity, science will indeed find itself in a precarious position.

A genomic look at hybridization in citrus fruits

I just love this article about hybridization and the origins of different varieties of citrus fruits: “Genomics of the origin and evolution of Citrus.

Here’s the key figure:

Hybridization and origins of different varieties of citrus fruits
Figure 2b from Wu et al. 2018. Original caption: "Genealogy of major citrus genotypes. The five progenitor species are shown at the top. Blue lines represent simple crosses between two parental genotypes, whereas red lines represent more complex processes involving multiple individuals, generations and/or backcrosses. Whereas type-1 mandarins are pure species, type-2 (early-admixture) mandarins contain a small amount of pummelo admixture that can be traced back to a common pummelo ancestor (with P1 or P2 haplotypes). Later, additional pummelo introgressions into type-2 mandarins gave rise to both type-3 (late-admixture) mandarins and sweet orange. Further breeding between sweet orange and mandarins or within late-admixture mandarins produced additional modern mandarins. Fruit images are not to scale and represent the most popular citrus types."

It’s a great example of human-induced evolution for several reasons. I imagine that most people assume that the different varieties of citrus are something like “species” in the traditional sense. People may have a vague idea that these are propagated clonally today, but may not realize the incredible complexity involved in generating the different phenotypic configurations that have become common in today’s citrus agriculture.

The real history involves wild progenitor species that have become extinct in the face of human activity, and are only visible today through their genetic traces in living farmed citrus trees. The story includes contacts between far-off human populations, and trans-oceanic dispersal of citrus species prior to the origin of humans.

It’s truly epic, and all in the pursuit of flavor.

Time to publish peer referee comments?

A meeting at the Howard Hughes Medical Institute last week asked whether journals should start publishing the reviews they receive on papers. As reported by Jeffrey Brainard in Science, the consensus was yes: “Researchers debate whether journals should publish signed peer reviews”.

Publishing the reviews would advance training and understanding about how the peer-review system works, many speakers argued. Some noted that the evaluations sometimes contain insights that can prompt scientists to think about their field in new ways. And the reviews can serve as models for early career researchers, demonstrating how to write thorough evaluations.
“We saw huge benefits to [publishing reviews] that outweigh the risks,” said Sue Biggins, a genetics researcher at the Fred Hutchinson Cancer Research Center in Seattle, Washington, summarizing one discussion.

Personally, I have mixed feelings about this.

I favor transparency. I also would like to see some sunlight shed on the worst abuses of the peer referee system. I’ve been witness to terrible, abusive, reviews, and I believe that anonymity and the power of secrecy tend to make these worse. Making individuals sign their reviews and publish them would give them an incentive to be responsible and temperate in their comments.

However, referee comments apply to earlier revisions of articles, before the final published version. This inevitably leads to confusion if the peer commentaries are published, because the paper is likely to have changed in response to the comments. Some journals, like eLife do a pretty good job of presenting the peer commentary along with the author responses, in a way that a reader can follow the actual changes that were made in the review and editorial process. But that takes extra work and responsibility on the part of the editors.

But when PLoS ONE used to publish peer comments early in its history, I saw many readers cherry-picking review comments to criticize the article, even though the article had been altered to satisfy them. This is one of the fears cited in Brainard’s article, and it’s not just a theoretical fear. It really happened when reviewer comments were published along with the articles.

What I suspect is that when referee reports are published alongside papers routinely, we will witness that referees have many blind spots. Some papers get very superficial review, and others get highly critical review in parts that don’t deserve it. Meanwhile, we’ll see that a large fraction of referees suggest additional unnecessary analyses. At least, if the reviews are signed, we’ll know when a referee is delaying a paper intentionally to try to scoop its results!

The so-called Toba bottleneck didn't happen

Chad Yost and colleagues have a long and detailed article in the current Journal of Human Evolution about why the Toba volcanic eruption 74,000 years ago did not drive ancient humans near extinction.

I want to quote the last two paragraphs of this paper, which give a crystal clear discussion, with references, of why there is no evidence for a massive Toba effect on human populations.

4.7. A falsified Toba catastrophe hypothesis
Since the publication of Ambrose (1998), the Toba supereruption and its proposed 6-year-long volcanic winter continues to be cited repeatedly, particularly in introductory paragraphs, as the natural catastrophe that brought humanity to the brink of extinction (human populations reduced to 10,000 individuals). Recent studies have clearly shown that volcanic winter conditions never occurred in East Africa after the eruption (Lane et al., 2013a ; Jackson et al., 2015), and we have shown that there was a very limited vegetation perturbation in the Southern Rift Valley of East Africa after the eruption. Further, we demonstrated the overestimation of SO2 injections in Toba supereruption climate model simulations by one or two orders of magnitude. This overestimation includes the early models of Rampino and Self (1992) that helped to build the volcanic winter model proposed in Ambrose (1998). The hypothesis that Toba triggered the 1000-year GS-20 cold period is also unlikely to be correct given that rapid cooling in the NH actually started a few hundred years before the Toba eruption, not to mention the fact that modeling by Robock et al. (2009) using a 900× Pinatubo SO2 injection failed to initiate NH glaciation.
Numerous genetic analyses have not detected a bottleneck that coincides with the Toba eruption. In fact, if the source population for the OOA expansion suffered a severe bottleneck, there should be a poorer linear fit to the decline of heterozygosity with distance from Africa (Henn et al., 2012). With the advancement of whole genome sequencing, the once elusive 100–50 ka Late Pleistocene human genetic bottleneck is now converging on ∼50 ka (Lippold et al., 2014; Karmin et al., 2015 ; Malaspinas et al., 2016) and is being attributed to an OOA founder effect bottleneck (Mallick et al., 2016) instead of a population reduction bottleneck. Studies focusing on reconstructing population histories are identifying a possible population reducing bottleneck between ∼150 and ∼130 ka (Li and Durbin, 2011 ; Kidd et al., 2012), which coincides with the penultimate ice ace during MIS 6. However, the peak in Ne at ∼150 ka could have also arisen from increased genetic diversity due to population structure involving separation and admixture (Li and Durbin, 2011), which is reasonable to expect during a cooler and drier MIS 6 climate in Africa. The hypothesis that human populations were reduced to 10,000 individuals after the Toba eruption is currently unsupported, as AMH populations were always relatively low, started to decline around 150 ka, and continued to decrease until ∼30 ka (see Discussion above). As paleoenvironmental, archaeological, and genetic research continues to accumulate, it is becoming increasingly hard to find evidence in favor of the Toba catastrophe hypothesis.

There is no question that the Toba eruption was a massive geological event. Investigating this event in earth systems research has always been a valuable idea.

But it has been a massive distraction for archaeologists.

The Toba bottleneck idea came from the initial observation that there might be a coincidence between population expansion times and the Toba eruption, made 20 years ago. But many geneticists (including me) quickly pointed out that the dates of population expansion have little connection to the dates of population contraction, and that effective population size might be orders of magnitude smaller than the actual human population. Even in 20-year-old mitochondrial DNA data, it was clear that a single short bottleneck post-Toba could not account for the pattern of variation found in African populations.

Meanwhile, human populations in the coldest climate zones, like the Neandertals of Europe, never seemed to show any obvious signs of population reduction at the time of the Toba event. Later, it became clear that the archaeological record much closer to Toba, in India and later Sumatra itself, showed no signs of a major interruption caused by the volcano. It also became clear that the aerosols that cool global climate, like sulfur dioxide, did not scale with the volume of rock ejected by the Toba eruption.

Yet this idea remains surprisingly entrenched in the minds of the public and of documentary filmmakers. I’m surprised there hasn’t been a Toba feature movie. Worse, it seems to dominate an unusual degree of attention in the minds of paleoclimatologists, and in their grant applications.

This is such an example of the failure to communicate effectively between geneticists, geologists, and paleoclimatologists about the limits of their data. The “coincidence” of these events from genetics and geology was only a small overlap between enormous confidence limits.

The idea was still worth investigating, sure, but on the other side of the balance were several negative indicators that were ignored or minimized at the time. If the Toba eruption had massively shocked global climate, that should have been evident in ice core data available in the 1990s, yet there was no such pattern. At the time, researchers dismissed this contradictory observation, suggesting that the Toba eruption might have initiated a longer-term cold cycle that was apparent in the ice cores (now known to have started before the eruption). And while the lack of any effect of the eruption on Neanderthals was fairly clear, the archaeological data were also dismissed as too sparse to disprove some population discontinuity. After all, proponents of the idea reasoned, even if Neanderthals seemed to be going strong for 30,000 years after the Toba eruption, a massive volcanic winter still might have softened them up a little.

Here’s the thing: It’s very hard to disprove the idea that the Toba eruption had some effect on ancient humans. As a massive event, it probably was not unnoticed by ancient humans who lived at the time of the eruption, 74,000 years ago. Many of those ancient people may have suffered from some adverse effects of the eruption, both locally and around the world. Many people around the world suffered adverse effects from the Mt. Pinatubo eruption in 1991, and we know from observations and climate modeling that those effects are not always noticeable even to the people who experience them!

But that doesn’t justify what has become a widespread public belief that Late Pleistocene humans were an endangered species, driven near extinction by a volcano. It is a myth that we now know is false.

We now have an opportunity to explain to people how many scientists got this wrong, how paleoclimate science and genetics have both progressed, and how massively the archaeological record has grown.

We also have the opportunity to exhibit some appropriate skepticism at other hypotheses about strong climate forcing in human prehistory. We need a better understanding of how ancient humans may actually have responded to local and regional changes in environments.

Link: Sci-Hub profiled

Verge has a long article on Sci-Hub, focusing on its founder, Alexandra Elbakyan: “Science’s Pirate Queen”.

If you have not heard of Sci-Hub, it is a major search engine and repository allowing people around the world to download scientific research articles for free, without paying publishers. Some describe it as piracy, others as a necessary workaround to provide access to people who cannot afford to spend $30 to read an article.

Sci-Hub provided press, academics, activists, and even publishers with an excuse to talk about who owns academic research online. But that conversation — at least in English — took place largely without Elbakyan, the person who started Sci-Hub in the first place. Headlines reduced her to a female Aaron Swartz, ignoring the significant differences between the two. Now, even though Elbakyan stands at the center of an argument about how copyright is enforced on the internet, most people have no idea who she is.

The story is fascinating, involving Russian politics that are obscure to the rest of the world, and emphasizing the recent legal efforts by the American Chemical Society to shut down the Sci-Hub repository.

Link: Robots in retail

MIT Technology Review has an interview with an exec from a company making robots for Walmart: “Walmart’s new robots are loved by staff—and ignored by customers”.

Erin: How have employees responded to the robots? Have you received any pushback because of the “robots are taking my job” idea?
Martin: When we first deployed a robot in a store, the associates were the people that understood it first. This boring, repetitive task of scanning the shelves—we have yet to meet someone who has liked to do that. Employees instantly become the advocates for the robot.
One way they do that is by giving it a name—the robots all have Walmart name badges on. The employees have competitions to see what the right name is for each robot. They also advocate for the robot to the general public. It’s the store staff saying, “It’s helping me.” We see them now defending the robot.

My department used to have a course on the books called “Robotics: Human Dimensions”, which was had been 1970s-era course that looked at the social changes from robotics in manufacturing. For some time, I thought it would be fun to revive the class to make it actually about robotics and the integration of robots into human societies.

Now I see that the two are blending together.

Link: China CRISPR-ing away

Gizmodo: “China Has Already Gene-Edited 86 People With CRISPR”.

In China’s 2015 CRISPR trial, the WSJ reports, 36 patients with cancers of the kidney, lung, liver and throat had cells removed from their bodies, altered with CRISPR, and then infused back into their bodies to fight the cancer. Other Chinese trials have sought to use CRISPR to treat HIV, esophaegeal cancer, and leukemia. A trial slated for this year in China will enroll 16 patients. Meanwhile, the first human CRISPR trial in the U.S., at University of Pennsylvania, will enroll just 18 people, and is designed primarily to test whether CRISPR is safe.

In an unrelated related story, Donald Trump’s State of the Union Address is notable for his mention of “Right to Try” legislation. From Ike Swetlitz at STAT: “In State of the Union, Trump endorses ‘right to try’ for terminally ill patients”

“We also believe that patients with terminal conditions should have access to experimental treatments that could potentially save their lives,” Trump said in his speech. “People who are terminally ill should not have to go from country to country to seek a cure — I want to give them a chance right here at home. It is time for the Congress to give these wonderful Americans the ‘right to try.’”

I expect that gene editing experiments are not far off in the U.S.