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Date: Wednesday, 21 Nov 2012 00:15

Absence can speak volumes. The lack of sediment in a flat piece of ground—a track—can testify to the footstep of a dinosaur that once walked on it. The lack of minerals in a solid shell—a hole—can reveal the presence of parasite that was once trapped in it. The world’s museums are full of such “trace fossils”, but so are many of the world’s art galleries.

The image above is taken from a woodcut currently residing in Amsterdam’s Rijksmuseum. It was made by etching a pattern into a block of wood, so that the remaining raised edges could be dipped in ink and used to print an image. These woodcuts were the main way of illustrating European books between the 15th and 19th centuries, and were used for at least 7 million different titles.

But as you can see, the print is littered with tiny white holes. These are called wormholes, and inaccurately so—they’re actually the work of beetles. The adults laid their eggs in crevices within the trunks of trees. The grubs slowly bored their way through the wood, eventually transformed into adults, and burrowed their way out of their ...


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Date: Tuesday, 20 Nov 2012 12:57

Jad Abumrad and Robert Krulwich have a new episode of Radiolab airing this week. The theme of the show is heredity and its attendant mysteries. I had great fun telling the strange and tragic story of the early twentieth century biologist Paul Kammerer, who thought he could change the human race with the help of a midwife toad. (Some of my favorite sources about this tale and its present-day reverberations are herehere, here, here, here, and here.)

Science writer Sam Kean joins the Radiolab crew as well, along with some scientists doing fascinating work on mother rats licking baby rats, Swedes surviving harsh winters, and more.

Added bonus: my daughters Charlotte and Veronica helped read the program credits. They get their ability to pronounce “Jad Abumrad” from me.

I’ve embedded the show below–



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Date: Sunday, 18 Nov 2012 06:10

A month ago I posted Don’t trust an archaeologist about genetics, don’t trust a geneticist about archaeology, in response to James Fallows at At 5% Neanderthal, You Are an Outlier. Fallows has now put up a follow up, The Neanderthal Defense Committee Swings Into Action, where he links to my response post. This prompted the original archaeologist in question to reach out to me via email. I am posting the letter, with their permission, below.

Hello!

I’m dropping an email because I followed a link from Fallows to find my email to him highlighted negatively on your blog. I’ve emailed a few times with Mr. Fallows on various topics and had no idea he was going to post that email – he didn’t ask until after it was already up and so, yes you’re right it was a casual dashed off email and confused two different articles (both of which incidentally I have read so please no more comments on what I may or may not have done). Mea Culpa. And you’re right, I’m not a geneticist – I’m not even a lab scientist. However, I know a heck of a lot about archaeology and I work closely with ...


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Date: Friday, 16 Nov 2012 18:33

Each year I run a workshop for science graduate students at Yale, encouraging them to write clearly, compellingly, and effectively. I’m tempted next year to just cue up this video of Steven Pinker discussing his next book–a psychology-based guide to good writing–and kick back.

[via]



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Date: Friday, 16 Nov 2012 17:35

TEDYouth is in its second year of putting together an afternoon of short talks for high school students. I’ll be joining in with a quick introduction to my favorite parasite. The event, which takes place in New York City, will be live-streamed–visit this page for more information for viewing. It will run from 1 pm to 6 pm ET. I’m scheduled to talk at 2:45.



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Date: Thursday, 15 Nov 2012 17:50

In May I wrote in Discover about a major experiment in neuroscience. Ahmad Hariri, a neuroscientist at Duke, is gathering lots of data from hundreds of college students–everything from genetic markers to psychological profiles to fMRI scans. He hopes that the Duke Neurogenetics Study, as he’s dubbed it, will reveal some of the ways in which the variations in our genes influence our brain circuitry and, ultimately, our personality and behavior.

Hariri plans to collect data from over 1000 people, but he and his colleagues are already starting to analyze the hundreds of students they’ve already examined to look for emerging patterns. In the open-access journal Biology of Mood and Anxiety Disorders, they’ve just published some of their first results. While the results are, of course, preliminary, they do offer an interesting look at the future of neuroscience. Rather than pointing to some particular gene or brain region to explain some feature of human behavior, neuroscientists are learning how to find patterns that emerge from several factors working together.

For their new study, Hariri and his colleagues looked in particular at problem drinking. They hoped to find factors that ...



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Date: Thursday, 15 Nov 2012 09:58

Your cry is heard!


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Date: Wednesday, 14 Nov 2012 16:00

The American Association for the Advancement of Science has just announced this year’s Kavli Awards for Science Journalism. I’m pleased to report that I won in the category of newspapers with a circulation of 100,000 or more.

The award was for three stories I wrote for The New York Times. They didn’t have much in common, which is how I like it:

A Sharp Rise in Retractions Prompts Calls for Reform (April 17)–The scientific enterprise is getting dysfunctional. The fact that this article received 341 comments suggests to me that it hit a nerve.

Studies of Microbiome Yield New Insights (June 19)–I explore the emerging concept of medical ecology, in which we look at our bodies as wildlife parks to be managed, rather than battlegrounds to be carpet-bombed.

Evolution Right Under Our Noses (July 26)–My editor at the time, James Gorman, came across a cool paper on the rapid evolution of fish in the Hudson River. I said, “It’s nice, but it’s not unique by any means. I mean, evolution’s going on all over New York.” Gorman, with that sharp editorial nose of his, said, “Really? Then write about that.” So off I went to ...



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Date: Monday, 12 Nov 2012 00:04

While I was at Spencer Wells’ poster at ASHG I was primarily curious about bar plots. He’s got really good spatial coverage, so I’m moderately excited about the paper (though I didn’t see much explicit testing of phylogenetic hypotheses, which I think this sort of paper has to do now; we’re beyond PCA and bar plots only papers). That being said, Spencer was more interested in me promoting the Scientific Grants Program. Here’s some more information:

The Genographic Project’s Scientific Grants Program awards grants on a rolling basis for projects that focus on studying the history of the human species utilizing innovative anthropological genetic tools. The variety of projects supported by the scientific grants will aim to construct our ancient migratory and demographic history while developing a better understanding of the phylogeographic structure of world populations. Sample research topics could include subjects like the origin and spread of the Indo-European languages, genetic insights into Papua New Guinea’s high linguistic diversity, the number and routes of migrations out of Africa, the origin of the Inca, or the genetic impact of the spread of maize agriculture in the Americas.

Recipients will typically be population geneticists, students, linguists, and other researchers or scientists interested ...


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Date: Sunday, 11 Nov 2012 21:54

As most readers know I was at ASHG 2012. I’m going to divide this post in half. First, the generalities of the meeting. And second, specific posters, etc.

Generalities:

- Life Technologies/Ion Torrent apparently hires d-bag bros to represent them at conferences. The poster people were fine, but the guys manning the Ion Torrent Bus were total jackasses if they thought it would be funny/amusing/etc. Human resources acumen is not always a reflection of technological chops, but I sure don’t expect organizational competence if they (HR) thought it was smart to hire guys who thought (the d-bags) it would be amusing to alienate a selection of conference goers at ASHG. Go Affy & Illumina!

- Speaking of sequencing, there were some young companies trying to pitch technologies which will solve the problem of lack of long reads. I’m hopeful, but after the Pacific Biosciences fiasco of the late 2000s, I don’t think there’s a point in putting hopes on any given firm.

- I walked the poster hall, read the titles, and at least skimmed all 3,000+ posters’ abstracts. No surprise that genomics was all over the place. But perhaps a moderate ...


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Date: Sunday, 11 Nov 2012 16:00

Over the past few weeks, I’ve been dipping into a project called “Moby Dick Big Read.” Plymouth University in England is posting a reading of Moby Dick, one chapter a day. The readers are a mix of writers, artists, and actors, including Tilda Swinton.  They are also posting the chapters on SoundCloud, which makes them very easy to embed. Here is one of my personal favorites, Chapter 32, “Cetology.”

When I was an English major in college, I read Moby Dick under the guidance of English professors and literary critics. They only paid attention to a fraction of the book–the fraction that followed Ishmael on his adventures with Captain Ahab. This was the part of the book that they could easily compare to other great novels, the part they could use for their vague critiques of imperialism, the part–in other words–that you could read without having to bother much with learning about the particulars of the world beyond people: about ships, about oceans, and, most of all, about whales. How many teachers, assigning Moby Dick to their students, have told them on the sly that they could skip over great slabs of the book? How many students have missed ...



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Date: Thursday, 08 Nov 2012 02:25

Our skin is encased in a snug microbial suit, from our scalps to the tips of our toes. Bacteria begin to colonize our skin from the moment we are born, and they continue to coat us throughout life. They do us many favors. They moisturize our skin to keep it supple; they unleash anti-microbial toxins to ward off pathogens that might make us ill. Scientists know that our skin is home to many species, but they can’t yet say exactly how many–or why some species are found more often on the elbow than on the chin.

Two years ago at a conference in North Carolina, I ran into Rob Dunn, a biologist who was conducting a survey of this menagerie. He was interested in the life found in one particular spot on the human body: the belly button. At the conference, he was handing out Q-tips people could use to swab their navels, which he and his colleagues could then study to tally up the species dwelling there.

Five months later, Dunn sent me a preliminary report: “You, my friend, are a wonderland.” I was the proud host of 53 different types of bacteria, including some decidedly weird creatures, such as ...



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Date: Wednesday, 07 Nov 2012 14:25
Horseshoe CanyonThe 4,000 year-old pictographs at Horseshoe Canyon in Utah may have been inspired by the spectacular acoustics there.

When priests at the temple complex of Chavín de Huántar in central Peru sounded their conch-shell trumpets 2,500 years ago, tones magnified and echoed by stone surfaces seemed to come from everywhere, yet nowhere. The effect must have seemed otherworldly, but there was nothing mysterious about its production. According to archaeologists at Stanford University, the temple’s builders created galleries, ducts, and ventilation shafts to channel sound. In short, the temple’s designers may have been not only expert architects but also skilled acoustical engineers.

The findings add to a growing body of research suggesting that sound meant more to our ancestors than archaeologists once realized. We live in a sound-saturated society, full of iPods, thunderous special effects in movies, and thousand-watt car stereos. New discoveries in the young field of acoustic archaeology hint that just as we create elaborate sonic environments with our electronics, the ancients may have sculpted their soundscapes as well. Like many artistic endeavors, their efforts may have been rooted in an attempt to reach the divine.

Portals to the Spirit Worlds


Some of the first research on the importance of acoustics to prehistoric peoples was done by Iegor Reznikoff, an anthropologist of sound at Université Paris Ouest, who in the 1980s visited cave paintings and carvings in southern France that are about 25,000 years old, among the oldest known human art. A number of them are so far underground that scientists were puzzled as to why anyone would have gone there. Reznikoff, who has a habit of humming whenever he enters a space, noticed that in parts of the caves, his voice resonated as effectively as in any cathedral. He and a colleague mapped several caves and found...

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Date: Monday, 05 Nov 2012 06:32

Scott Jackisch (a.k.a., “Oakland Futurist Guy”) has a post up with the title, Jersey Shore is better than cat burning. Provocative? Yes. Timely? No. Jersey Shore is so 2010. We live in the age of Honey Boo Boo. This is clear from Google Trends. The red line represents searches for Honey Boo Boo, and the blue for Jersey Shore.

Mama June farting up a storm is still superior to cat burning. But about the Sistine Chapel, I’ll leave you with Mr. Jackisch’s ruminations on that and genital mutilation:

Take genital mutilation. That’s cultural. I place it right along side of the Sistine Chapel as an example of culture. Most of the Mills Students agreed that we need to take the good and leave the bad behind in regard to the old cultures. But I wonder how divisible cultural artifacts truly are. Is the Sistine Chapel integrally linked to oppression and Inquisition? Can the beauty really be expunged of the horrors that funded it and the message it inheres? Some things were lost with the passing of Culture. Some horrible things along with the great.

The question of modularity and contingency ...


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Date: Wednesday, 31 Oct 2012 19:51

Evolution: Making Sense of Life, the textbook Doug Emlen and I have just published, is now evolving into a full-blown app for the iPad. Once you get the free app, you can download some of the book’s chapters. We’ve now got the first eight chapters in the iTunes store. Chapters 1 (the introduction) and Chapter 8 (natural selection in the wild) are available for free. Chapters 2-7 can be purchased individually for between $4.99 and $9.99. The full book will be available December 1st, 2012; all 18 chapters will be priced at $80.



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Date: Wednesday, 31 Oct 2012 09:52

As many of you know around the year 2000 the analyses of Y chromosomal human lineages became a pretty big deal. The reason these lineages are important and useful is that they record the uninterrupted ancestry of males, from father to son, along the Y chromosome. Instead of the complexities of the whole genome, as with mtDNA you have a simple and elegant phylogenetic tree to interpret. The clusters along this tree are defined as broad haplogroups, united by derived states from a common ancestor. One of the largest haplogroups is R1a1a. It happens to be my paternal lineage, as well as Dr. Daniel MacArthur’s and Dr. Zack Ajmal’s.

The map above illustrates the peculiarity of R1a1a: it is geographically enormously expansive. How to explain this distribution? A naive response might be that this distribution is surprising similar to that of the Indo-European languages. Unfortunately this runs up against the conundrum that low caste South Indian groups, relatively untouched by Indo-Aryan culture (at least until the past few hundred years), also manifest high frequencies of R1a1a.

To make a long story short it seems that R1a1a is an ...


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Date: Monday, 29 Oct 2012 18:22

In June, a writer named Jonah Lehrer got busted for recycling material on a blog at the New Yorker. Lehrer, who specialized in writing about the brain, had been writing a blog called The Frontal Cortex for six years at that point; having just been appointed a staff writer at the New Yorker, he moved it to their web site, where he promptly cut and pasted material from old posts, as well as from magazine and newspaper pieces.

At the time, I just thought he was squandering a marvelous opportunity. When I was asked to comment on the situation, I wrote that some of the things Lehrer had done were uncool, while some were fairly harmless. But Lehrer himself acknowledged that what he was done was stupid, lazy, and wrong. So I figured he’d gotten the sort of school detention that wakes you up and keeps you from getting expelled.

Four months later, I’m struck by how wrong I was.

I’m quoted in the latest of a long string of articles about Lehrer’s misdeeds, a feature in this week’s issue of New York by Boris Kachka. Kachka talked to me for a long while, and it’s clear that he talked to ...



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Date: Saturday, 27 Oct 2012 13:17

I recently gave a talk in San Francisco about the future of viruses, based in part on my book, A Planet of Viruses. I talk about how deadly new outbreaks may emerge, how we may harness viruses for technology and medicine, and just how many viruses there are out there (hint: 10000000000000000000000000000000).

Author Carl Zimmer: Our Viral Future from Singularity Institute on FORA.tv



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Date: Tuesday, 23 Oct 2012 16:00

Last Friday, a group of volunteers gathered in the Royal Society in London to edit female scientists into the history books—or at least, into Wikipedia. Their goal was to start fixing the online encyclopaedia’s comparatively thin information about women in science and technology.

I attended the “edit-a-thon”, reporting for Nature. Before I turned up, I wondered about the rationale behind holding a specific event to edit Wikipedia, which can be done at any time and place. I also wondered how much the editors could accomplish in just 3.5 hours. Both concerns were addressed on the day, and in the piece. Take a look. Also, there was an Ada Lovelace/Wikipedia cake.


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Date: Tuesday, 23 Oct 2012 08:07

There is a high likelihood that you know of which ABO blood group you belong to. I am A. My daughter is A. My father is B. My mother is A. I have siblings who are A, O, B, and AB. The inheritance is roughly Mendelian, with O being “recessive” to A and B (which are co-dominant with each other, ergo, AB). It is also generally common knowledge that O is a “universal donor,” while A and B can only give to individuals within their respective blood group and AB.

Because ABO was easy to assay it was one of the earliest Mendelian markers utilized in human genetics. In the first half of the 20th century while some anthropologists were measuring skulls, others were mapping out the frequency of A, B, and O. Today with much more robust genetic methods ABO has lost its old luster as a genetic marker, especially since there is a strong suspicion that the variants are strongly shaped by natural selection. This makes them only marginally useful for systematics, which rely upon loci which are honest mirrors of demographic history.


But there’s another aspect of ...


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