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john hawks weblog

paleoanthropology, genetics and evolution

Photo Credit: Dental chipping in Homo naledi. Ian Towle and colleagues

Link: Why are captive gorillas getting heart disease?

The Atlantic has a wonderful long-read story by Krista Langlois looking into the heart health of captive male gorillas in the U.S.: “Something Mysterious Is Killing Captive Gorillas”.

Like many captive male gorillas, Mokolo suffers from heart disease—specifically, fibrosing cardiomyopathy, a condition that turns red, healthy heart muscle into bands of white scar tissue too rigid to pump blood. Although heart disease is nearly absent in wild populations, it’s the leading killer of captive male gorillas around the world. Roughly 70 percent of adult male gorillas in North America have heart disease, and often die prematurely as a result. Other great apes, such as orangutans and chimpanzees, suffer at similar rates.
For more than a decade, zookeepers, veterinarians, epidemiologists and others have struggled to figure out why heart disease is so prevalent among captive apes, and how to prevent the animals from developing it. Now they may be closing in on answer—one that lies not in the 20-ounce time bombs housed in gorillas’ chests, but in the microscopic bacteria that flourish in their guts.

The article covers the history of health and diet in zoo gorillas, talks about the ways that zoos have changed over the years, and focuses in on some of the science of diet in primates.

It’s such a good account of these issues that I’ve assigned the article to my 300 students.

Link: Finding identity in an historical photograph

Following on my last post about massive genealogy research, the Globe and Mail has an interesting story about how genealogical and census information allowed researchers to uncover the probable identity of a young girl pictured in a famous 1913 Toronto photograph: “A little girl in Toronto lost to history – and now found”.

The life of Dorothy Cooperman suddenly comes into focus on the genealogy site Ancestry. A user related to the Coopermans through an in-law has sketched the key moments in Dorothy's life, from her birth in Kiev (then part of the Russian Empire) to her marriage, the births of her children and her death in 1979 in Oak Park, Mich., a suburb of Detroit.

The faces that look out of old photos and paintings are people of the past. All of them are connected to the living, although those connections have often been lost. A large fraction of people in past generations have no living descendants. Others have them, but no full accounting of them exists.

It is part of my profession to recover what science can of the histories of unknown ancient peoples. The individual histories of recent people are no less interesting, and in many cases are unknown.

Link: Interview with Yaniv Erlich and massive human genealogy

The Atlantic has a nice interview with Yaniv Erlich, the geneticist who this week revealed the largest scientific analysis of a single human genealogical tree, including some 13 million people: “The ‘Genome Hacker’ Who Mapped a 13-Million-Person Family Tree”.

The interview is by reporter Sarah Zhang, and she focuses on the effective collaboration of private and university interests in this kind of research.

Zhang: Your study is published now, but it seems like this is a beginning rather than an end. I’d imagine what you’re really interested in is overlaying genetic data on top of the family tree.
Erlich: Exactly. At MyHeritage, we started to offer DNA tests to users in November 2016. Since then we’ve collected 1.2 million DNA profiles of users.
Zhang: And why make the jump to MyHeritage? Are there things you can do at a company you couldn’t do in academia?
Erlich: I think this is a model for the future. There are certain things that you can only do in academia. There are certain things you can only do in companies. If you want to move in scientific endeavors, collaborating with companies is a very fruitful direction.

The research involving the genealogical data has documented the genealogical effects of some interesting social changes over the last two hundred years. But once genetics starts to be added into the tree, people are going to find a lot of discordance, a lot of natural selection, and possibly a good amount of segregation distortion.

It will be interesting to shine a light into odd corners of inheritance. I’m not sure people are anticipating what discoveries will be made using their own genealogical research.

Ancient footprints emerge from the coast of South Africa

According to the Canadian Broadcasting Corporation, the hominin footprints discovered in South Africa and published last week were discovered by some dedicated avocational paleontologists: “Ancient human footprints discovered by B.C. family on vacation in South Africa”.

A B.C. family's hobby of hunting for fossils has led to the discovery of a rare set of ancient human footprints on the south coast of South Africa.
The existence of the tracks, estimated to be approximately 90,000 years old, was revealed in an article published in the open-access journal Scientific Reports, maintained by the editors of the UK publication Nature.
The lead author of the report is Charles Helm, a former family physician in Tumbler Ridge, B.C., who is originally from South Africa.

This is such a great story, a case study in how discoveries are made. Some new scientific discoveries come from exploring where nobody else has been before. But most discoveries emerge from someone looking in a well-trodden area with new eyes. They may see something that no one else has noticed before.

These footprints are actually embedded within the walls and ceiling of a cave. What is today a cave actually formed within a dune sand breccia. The erosion naturally happened along ancient natural surfaces, leaving the impressions preserved within layers that had originally filled in the footprints, stratigraphically above them.

Imagine, studying footprints on the ceiling of a cave!

Footprints in figure 4a of Helm et al 2018
Footprints illustrated in figure 4a of Helm et al. (2018)

The research paper is in Scientific Reports, which is open access: “A New Pleistocene Hominin Tracksite from the Cape South Coast, South Africa”. The paper makes it clear that this was no chance discovery. These hominin footprints were just the most interesting results of a systematic survey of coastal sites for trackway evidence.

The hominin tracks reported here were discovered as part of a ground survey by the senior author along a 275 km stretch of coastline from Witsand in the west to Robberg in the east, undertaken between 2007 and 2016 (Fig. 1). Over 100 Late Pleistocene vertebrate tracksites were identified in coastal aeolianites, and in 2016 natural cast tracks on the ceiling of a ten-metre long cave (Fig. 2) were identified as human in origin. In 2017 further hominin tracks were identified in this cave on a lower layer. The focus of this paper is to describe these tracks and to briefly place them in their sedimentary and palaeoecological context.

The larger footprints are 23 cm long, and there are shorter ones that are around 17 cm long. The paper suggests that all these footprints likely belong to modern humans. That is by no means impossible, but I note that all these footprints are within the size range that I would expect for Homo naledi as well.

It may take some time for archaeologists to change their outdated assumption that the entire African Pleistocene record documents a linear succession of modern human ancestors. With every discovery, we need to be critical about documenting context and associations.

New excavations starting at Rising Star, an article pointing to some ways to follow the expedition

Newsweek is running a great story by Meghan Bartels about our renewed excavations in the Rising Star cave over the next month, and the strategies the team is following for sharing its underground progress: “Explore the cave where mysterious human ancestor Homo naledi was discovered in live broadcasts from South Africa”. She corresponded with Lee Berger and he shared some of the motivations for integrating live outreach directly into the excavation protocols:

For Berger, that broadcast is not just about sharing cool findings, it's about making science as a whole more accessible to non-scientists. "I believe we must pull all aspects of science from the “black box” where it typically resides," Berger wrote in an email to Newsweek. He is particularly dismayed by the secrecy often surrounding subject areas like human origins, with only a limited few gaining access to information around discoveries. As he sees it, "these fossils and this science is about our shared human heritage."

The team had some tremendous successes engaging schools and the public from our expedition in September of last year, and I’m really excited about some of the ways we’ll be building on those activities over the next month.

He plans to livestream regularly to the public and to classrooms, including both conversations and footage of the actual excavation work. Other outreach projects associated with the dig include an account tweeting and streaming video updates in Sesotho and Setswana, two local African languages. The team is also using 3D cameras to film the site and wants to explore virtual reality technology as well.

That account is from team member Mathebela Tsikoane, and I encourage anyone to follow him on Twitter, where he tweets in English as well as other languages.

Building participation and engagement in African languages is so important to the project, as is engaging with technologies that work with phones, which are the primary internet tool across Africa.

I’m following along with the expedition right now, until I join the team in South Africa in a couple of weeks. They’ve already found some new fossil material of Homo naledi in an unexpected part of the cave chamber.

Link: Kate Clancy testimony from congressional hearing on sexual harassment

Yesterday, the U.S. Congress conducted a hearing on the topic of sexual harassment in science. Anthropologist Kate Clancy provided testimony at the hearing, and she has now shared her spoken remarks on her blog: “Transcript of my oral testimony from February 27th Congressional hearing on sexual misconduct in the sciences”.

Everyone should read her full remarks. I will quote a section that resonates with me:

We say that asking a nasty question at a colloquium is how we push people to be better scientists. We say when we see an all-male research team that it must just be that the best scientists for the job were all men....
Too often I’ve heard that harassment and bad behavior are the price we must pay for star scientists. But are they really doing star science? When I’m writing my papers or analyzing my data on sexual harassment in the sciences, I’m thinking of the victims and the science we’ve lost. We lost their ideas, we lost their perspectives. We scientists do this work because we want to give the best of ourselves to the advancement of science. Women keep trying to give us their best, and we blow ash in their faces and push them down mountains.

The last sentence is a reference to alleged behavior by Antarctic researcher David Marchant.

Wired magazine also has coverage of the congressional hearing: “Congress takes on sexual harassment in the sciences”.

STAT news has a very good interview with Clancy from the lead-up to the hearing: “Sexual harassment pervades science. This scientist is talking to Congress about how to change that”. One of the most powerful points she makes is that employers, including universities, select online training programs which they know are ineffective, because Title IX requires training but does not rely upon data about effectiveness.

Sexual harassment training itself is a great example. There are so many papers that show that the type of sexual harassment training that most universities offer, which is often online with really extreme examples, can backfire. That they reinforce gendered beliefs, that they develop resentment, that they increase the risk of retaliation. At best, what they do is increase the knowledge base of the people taking them so they know what the worst types of sexual harassment are. But it doesn’t ever seem to change the climate.

My perception is that the climate is changing. Many researchers have committed to be inclusive when they build scientific projects, and use their leadership to create healthy workplaces and field situations.

How can scientific conferences make more of a difference in the cities where they meet?

I’d like to draw attention to this effort from the American Association for the Advancement of Science to make an impact on local schools where they have their annual meeting: “AAAS Classroom Science Days”.

For over 25 years, AAAS has produced a day of science in conjunction with the AAAS Annual Meeting, working with the local community—--including informal educators, teachers and scientists—--to leave strengthened connections to communities that don’t get needed exposure to science or scientists. At the 2017 meeting in Boston, we talked with groups of scientists from different universities in the Boston area who want to initiate, expand, or improve programs that help scientists engage with K-12 students and teachers. They believe that AAAS can be a hub for these various groups to network, find resources, recruit scientists and connect with teachers. We organized 20 scientists (undergraduate, graduate students, postdocs, professors and researchers in industry) to visit 20 schools and give short talks about their educational and career paths. Scientists, teachers and students all agreed that the talks were a success! Some scientist teacher pairs made plans for future events including lab tours and more talks.

I think this is important.

Consider that every scientist who visits those meetings spends an average of $1500+ on airfare, hotel, meeting registration, meals. A scientific conference is a multimillion dollar investment in a city. It would be great to see that multimillion dollar presence pay off in real public and educational engagement, beyond what would happen otherwise.

What’s unfortunate is that AAAS has built its effort upon entirely local scientists, postdocs, and students. Last year, it had 20 volunteers, this year only 30. That’s a very tiny impact.

Still, AAAS is an exception. Other scientific societies I’m involved with do vastly less. Maybe they organize a teacher workshop, or give a single public lecture.

We should be aiming much higher. Why don’t we see real public forums involving our major scientists associated with conferences? Why don’t we see many more school visits and events, across a broader geographic area than the immediate city? Why don’t we see television programming associated with the conferences?

I hope that scientific societies will think about how they can better leverage the exceptional opportunities that these conferences create for engagement on a local and regional scale.

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.