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Date: Monday, 22 Oct 2012 16:08

Download the Universe, the science ebook review I started up with some colleagues nine months ago, continues to grow. Here’s the latest batch of reviews:

The Most Ingenious Book: How to Rediscover Micrographia My survey of the digital experiences of Robert Hooke’s 1665 masterpiece.

NASA’s 30 years of Shuttle Missions Is Both Dull and Compelling John Timmer explores NASA’s online history

The Long Quest to Catch a Poisoner Deborah Blum finds the science in a true-crime thriller.

A Medieval Bestiary: When a Book Breaks Your Heart Maggie Koerth-Baker has great hopes for an ebook from the British Library. Hopes are dashed.

Did You Like My Ebook? Don’t Lie! Maia Szalavitz reviews Sam Harris’s ebook on lying.

The Beautiful Planet Meets The Immortal Cassini I take a look at an elegant collection of NASA’s images of Saturn.

Death and Other Options: How To Think (Hopefully!) About Global Health Tom Levenson reviews a TED book on the medical future of our species

Deep Water: A Pretty Good TED Ebook (Really!) About Climate Change John Dupuis considers the strengths and weaknesses of an ebook on climate change.

Interplanetary Cuisine What do people eat in space? Veronique Greenwood tucks in.

The Science of Sports: An eBook ...

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Date: Monday, 22 Oct 2012 05:29

I have mentioned the PLoS Genetics paper, The Date of Interbreeding between Neandertals and Modern Humans, before because a version of it was put up on arXiv. The final paper has a few additions. For example, it mentions the generally panned (at least in the circles I run in) PNAS paper which suggested that ancient population structure could produce the same patterns which were earlier used to infer admixture with Neandertals (the authors also point to Yang et al. as a support for the proposition of admixture rather than structure). The primary result, dating the admixture between Neandertals and anatomically modern humans ~40-80,000 years before the present, is reiterated.

An interesting aspect is that their method is to utilize linkage disequilibrium (LD) decay. It’s interesting because tens of thousands of years is a hell of a long time to be able to detect an admixture event via LD! In particular because there’s likely a palimpsest effect where there are intervening admixtures and other assorted demographic events (e.g., bottlenecks and selective sweeps can also generate LD). So how’d they do it? Basically the authors figured out a way to ...

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Date: Friday, 19 Oct 2012 13:00

Carbon-dating is a widely used technique that allows us to gauge the age of archaeological samples from up to 60,000 years ago. But it’s not a straightforward method.

It relies on a radioactive version of carbon called carbon-14, which is formed in the atmosphere and is taken up by plants (and whatever eats the plants). Once these die, the carbon-14 in their bodies decays away at a steady, predictable rate. By measuring it, we can calculate how old an ancient sample is.

But there’s a catch. The levels of carbon-14 in the atmosphere vary from year to year, so scientists need some way of assessing these fluctuations to correct their estimates. They need long-running timetables, where each year in the past several millennia can be “read”, but where true levels of atmospheric carbon-14 can be measured.

And now, in the bottom of a Japanese lake, scientists have found the best such timetable yet. As I write in The Scientist:

The sediment of a Japanese lake has preserved a time capsule of radioactive carbon, dating back to 52,800 years ago. By providing a more precise record of this element in the atmosphere, the new ...

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Date: Thursday, 18 Oct 2012 16:30

Since the invention of agriculture 11,000 years ago, human 
population has trended up—but the boom may be drawing to an end. Birthrates are falling around the world; by the end of the century the number of people on the planet may top out and, in an unprecedented reversal, start to decline. Good news, right? The answer is not so simple. Growing populations are associated with progress; shrinkage has often correlated with cultural decline. One stark example comes from Tasmania, an island off southeast Australia. Nearly the size of Ireland, it was colonized 34,000 years ago by people with sophisticated toolmaking skills who came across a land bridge from Australia. By the 18th century, Tasmanians used simple technology, hunting with rocks and crude clubs. In 2004 anthropologist Joseph Henrich used a mathematical model of cultural evolution to tackle this mystery [pdf]. He concluded that the island’s population, about 4,000 in the 18th century, at some point fell below the level necessary for complex skills to be passed from generation to generation. Scientists increasingly think population size and density have had a big impact on human development at certain pivotal points. That continues in the modern world, as young people disproportionately produce innovation, generate economic growth, and finance social support networks for the elderly...

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Date: Thursday, 18 Oct 2012 14:20
Corey S. Powell headshot

What about overpopulation?

It’s an inevitable question. Conventional wisdom says that the demands of an ever-growing number of humans will soon push our planet’s resources to the limit. Surely any discussion of “the future of population” would have to focus there. But two pieces of information steered me—and this issue—in a different direction.

One is the history of failed projections about the consequences of population growth...

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Date: Thursday, 18 Oct 2012 09:10

In antiquity what we term Tunisia and Tripolitania were part of “African province.” Just as “Asia” originally referred to the margins of what we now term Asia (regions of Anatolia), so “Africa” originally denoted a subset of the northwest fringe of the continent which became Africa. In biogeography this segment of the continent is actually not part of Africa (it is part of the Palearctic ecozone). And yet the vicissitudes of early modern cartography are such that continent had to be bounded by water on as many sides as possible, and today we clumsily make recourse to the term “Sub-Saharan Africa” to distinguish that region from the northern littoral, which is really part of the Mediterranean world.

This context is somewhat relevant when we evaluate a new PLoS ONE paper, North African Populations Carry the Signature of Admixture with Neandertals. This paper makes little sense unless you’ve read an earlier one, Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. In that paper authors make the case that a majority of the ancestry of modern Maghrebis seems to date back to before the Neolithic, from a late ...

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Date: Wednesday, 17 Oct 2012 07:46

If you have a hard time following all the Neandertal genomics findings from the last few years, and their implications, National Geographic has a really thorough piece up. It’s a good digest of all the news you can use. One thing I would like to add: from what I can tell the probability of the signals of admixture in non-Africans being genuinely Neandertal seem to be increasing as we progress. In other words, you should weight the “other side” (ancient population structure, where some African populations were closer to Neandertals before they left Africa) less than you did in 2010.

Of course one of the more inevitable aspects of the admixture story has been the humanization of Neandertals. I don’t know how I feel about this. Should our own affinity to Neandertals alter our view of their behavior or anatomy? Plenty of behaviorally anatomically modern humans were beastly after all.

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Date: Monday, 15 Oct 2012 21:38

Who to trust? That is the question when you don’t know very much (all of us). Trust is precious, and to some extent sacred. That’s why I can flip out when I realize after the fact that someone more informed than me in field X sampled biased their argument in a way they knew was shady to support a proposition they were forwarding. What’s the point of that? Who cares if you win at a particular bull-session? You’re burning through cultural capital. And not that most of my interlocutors care, but I’m likely to never trust them again on anything.

In any case, this came to mind when I ran across a James Fallows’ post at The Atlantic. Here’s a screenshot of the appropriate section, with my underlines:

The PNAS link is wrong. The correspondent is actually linking to an article in Quaternary International. And they do point out that there are possible problems with draft quality sequences due to contamination. But I didn’t find the paper too persuasive. There are two issues. First, the Denisova genome is very good quality. So you can be more ...

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Date: Saturday, 13 Oct 2012 18:39

I was recently invited to write an essay for a promising new web site that launches today, called Being Human.  It’s all about what it means to be Homo sapiens, and I chose to focus on our brain, which is so fundamental to our unique place in the natural world. In fact, we like to think of ourselves as our brains. You could, after all, imagine yourself as just a brain in a vat. It might be hard to manage, but if someone could figure out the right liquids to put in the tank and the right wires to stick into it, it “ought” to work. Hence, The Matrix.

This is actually a new notion, and in my essay, I take a look at our ideas about the brain over the past couple thousand years. Check it out.

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Date: Friday, 12 Oct 2012 19:21

Well, not really…but in some ways close enough judged against the initial reference point of where I started on certain questions. Dienekes contends:

This will help us understand both: the ancestors of non-Africans did not come forth fully formed, like Athena from Zeus’s head, having spent millennia of perfecting their craft and honing their minds by perforating shells and scratching lines in some South African cave. Instead, they may been plain old-style hunter-gatherers who stumbled into Asia by doing what they always did: following the food. At the same time, the UP/LSA revolution may not have been effected by a new and improved type of human bursting into the scene and replacing Neandertals and assorted dummies, but rather as a cultural revolution that spread across a species that already had the genetic potential for it, and was already firmly established in both Africa and Asia.

The former position, that the Out-of-Africa population were genetically endowed supermen who blitzkrieged other humans ~50,000 years ago was probably the most common position ~10 years ago. It’s outlined by Richard Klein in The Dawn of Human Culture. A contrasting argument was put forth at about the same time by Stephen Oppenheimer in

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Date: Thursday, 11 Oct 2012 07:39

The always informative Ann Gibbons has a piece in Slate, The Neanderthal in My Family Tree. There is almost nothing new for regular readers of this weblog, but it’s rather awesome that Slate is now publishing stuff like this. Many people are simply unaware of the new paleogenomics. Case in point, a good friend who has a doctorate in chemical physics, and was totally unaware a year after the seminal Science paper on Neandertal admixture of the likelihood of Neandertal admixture!

Nevertheless, I think it is important for me to be repetitive and highlight a disagreement I have with the Gibbons’ piece. She says:

…But the differences in the genomes of Denisovans, Neanderthals, and modern humans are also revealing the genetic traits that set us apart from them—the traits that made us human. “I’ve been comparing it to the pictures of Earth that came back from Apollo 8. The Neanderthal genome gives us a picture of ourselves, from the outside looking in,” says paleoanthropologist John Hawks of the University of Wisconsin in Madison, in his blog on paleoanthropology, genetics, and evolution. “We can see, and now learn about, the essential genetic changes that make us human—the things that made ...

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Date: Wednesday, 10 Oct 2012 21:32

Last month I blogged about the unsavory practices of French scientists who unveiled a study purporting to show that genetically modified corn and herbicide cause cancer in rats. Not only was the study weak, but the scientists required reporters to sign an oath of secrecy to see it in advance. As I explained to the NPR show On the Media, this strategy raised the odds that all those pesky questions about statistical significance from meddling outsiders would be absent from the first wave of reporting.

In Nature today, Declan Butler continues his great reporting on the affair, unearthing additional disturbing parts of the story. My favorite was this passage from the agreement that some reporters–incredibly–agreed to sign:

“A refund of the cost of the study of several million euros would be considered damages if the premature disclosure questioned the release of the study.”

Who knew that doing basic science reporting could land you catastrophically in debt? Well, aside from Simon Singh…

[Update: Link to Nature fixed]

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Date: Tuesday, 09 Oct 2012 13:55
William Jungers illustration by Zina Saunders

The smallest human species that ever lived, Homo floresiensis, was astonishing in several ways. It thrived on an isolated Indonesian island from at least 95,000 until 17,000 years ago, outlasting even the burly Neanderthals; nicknamed the hobbit, it stood only about three feet tall and had a puny brain, yet it hunted and crafted stone tools. Fossils of H. floresiensis, discovered in 2003, contradicted the accepted theory that size and strength steadily increased as humans evolved. Physical anthropologist William Jungers of Stony Brook University in New York is now studying the remains of these hobbit people.

In November 2006, at Indonesia’s Archeological Institute, it was blistering hot and I was dripping sweat on the spectacular bones of the tiniest human ever to walk this earth. My job was to analyze their anatomical affinities with other human ancestors and use medical imaging to look inside them. We concluded the hobbit was indeed a human ancestor.

Two years later I was invited to join continuing excavations at Liang Bua, the cave on the island of Flores where the hobbit had been discovered...

Illustration by Zina Saunders

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Date: Tuesday, 09 Oct 2012 02:49

A few months ago someone asked me (via email) which populations I would love to get typed (genetically that is). There is one population which did not come to mind at the time: the Sumerians. Why? Because these are arguably the first historic nation. The first self-conscious ethnic group which operated by the rules which we define as the fundamentals of literate civilization. Strangely, they are an ethno-linguistic isolate. My own assumption until lately has been that this is not too surprising, in that prior to the rise of expansive civilizations (Sargon of Akkad) there was much more linguistic and ethnic diversity than we currently see around us. Or, was evident even in the early Iron Age. In other words, the ancient Fertile Crescent may have resembled the highlands of Papua, with Hurrians, Akkadians, Gutians, Elamites, Sumerians, etc., all speaking mutually unintelligible dialects which diverged very far back in the mists of antiquity.

I am no longer quite so sure about this model. That is largely due to the possibility that there was a great deal of demographic change between the Mesolithic and the Bronze Age, with successive waves ...

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Date: Sunday, 07 Oct 2012 13:42

On Tuesday I’ll be in Hartford to participate in the Science on Screen series. It started in Boston last year, and now it’s spreading across the country. Each evening consists of a science-themed movie paired with a talk about some of the science involved. On Tuesday, Real Artways in Hartford will be screening the virus-zombie movie, 28 Days Later. And I’ll talk about what real viruses can do to their hosts. Details here.

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Date: Friday, 05 Oct 2012 06:35

On occasion it is useful to outline definitions and frameworks. One thing that I often hear (i.e., I am constantly told) is that beauty is a subjective, and culturally defined, construct. In particular it is common for me to listen to explanations of “Eurocentric Western” beauty standards, as if they are sui generis. These views do not emerge in a vacuum. Rather, they grasp upon a real phenomenon: that beauty standards are malleable and vary across time and place. But like Classical Greeks who may have promoted a converse view, that beauty is an objective aesthetic reflection of innate characteristics of human value, modern subjectivists ignore the empirical reality in favor of a clean and simple narrative.

From where I stand it strikes me that Western intellectuals who engage in a discourse which engages the construction of the non-Western Other sometimes forget that the non-Western Other is itself a social construct with only constrained utility. To unpack it in more plain language, non-Western societies are diverse across themselves, and can not be bracketed as  singular non-Western Other in a deep sense. And, they exhibit strong similarities to each other, and Western ...

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Date: Wednesday, 03 Oct 2012 21:59

It’s getting close to two years now since a NASA-funded team of scientists announced they had found a form of life that broke all the rules by using arsenic to build its DNA. It’s become something of an obsession for me. If you want to follow the saga, click here and start back at the earliest post. In July I live-blogged the announcement that other scientists had replicated the experiment and failed to find the same results. In some ways, that was the logical end to the story

My fascination with this story has been tempered from the start by a creepy feeling. As a science writer, I most enjoy reporting on advances in biology: the research that opens up the natural world a little bit wider to our minds. The “#arseniclife” affair was less about biology than about how science gets done and the ways it goes wrong: the serious questions it raised about peer review, replication, and science communication. That fierce debate did some collateral damage. The microbe in question, known as GFAJ-1, went from being the species that would force us to rewrite the biology textbooks to yet another ...

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Date: Wednesday, 03 Oct 2012 06:02

Fifteen years ago John Horgan wrote The End Of Science: Facing The Limits Of Knowledge In The Twilight Of The Scientific Age. I remain skeptical as to the specific details of this book, but Carl’s write-up in The New York Times of a new paper in PNAS on the relative commonness of scientific misconduct in cases of retraction makes me mull over the genuine possibility of the end of science as we know it. This sounds ridiculous on the face of it, but you have to understand my model of and framework for what science is. In short: science is people. I accept the reality that science existed in some form among strands of pre-Socratic thought, or among late antique and medieval Muslims and Christians (not to mention among some Chinese as well). Additionally, I can accept the cognitive model whereby science and scientific curiosity is rooted in our psychology in a very deep sense, so that even small children engage in theory-building.

That is all well and good. The basic building blocks for many inventions and institutions existed long before their instantiation. But nevertheless the creation of ...

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Date: Monday, 01 Oct 2012 19:35

A new look at retracted papers since 1975 paints a picture that’s none too pretty. Retraction rates are zooming up, and most of those retractions, a new study finds, are due to misconduct such as fraud and plagiarism. I write about the study in tomorrow’s New York Times. Check it out.

Author: "--" Tags: "Scientific Method"
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