The Loom » Link Love

A Hot Young Earth: My Answer to the Annual Edge Question

Carl Zimmer — Sun, 15 Jan 2012 17:47:28 +0000

Each year, literary agent and science salonista John Brockman poses a question about science and gets a slew of answers from scientists, writers, and other folks. This year’s question is

WHAT IS YOUR FAVORITE DEEP, ELEGANT, OR BEAUTIFUL EXPLANATION?

Brockman got 187 responses, totaling some 126,700 words. A book, you say! Well, if this year is like previous ones, this year’s answers will indeed become a book. But in the meantime, you can browse the answers for yourself, perhaps plucking out those of your favorite people. (Fellow Discover blogger cosmologist Sean Carroll chooses Einstein’s explanation of gravity, for example.)

I found this year’s question particularly thought-provoking. Why is it that we call an equation or a theory “beautiful”? They don’t have pretty hazel eyes. They aren’t desert landscapes. I’m not sure of the answer. Scientific explanations seem to be beautiful if they give sense to confusing complexity in a very short space. Or maybe we just like the feeling we get when we consider how our puny human brains can interpret the universe.

For a lot of physicists, the beauty of an equation seems to be a good hint that it’s ...

Words bring life to life

Carl Zimmer — Fri, 13 Jan 2012 13:58:16 +0000

Drew Berry is one of the great movie-makers of the molecular world. He makes gorgeous computer visualizations of DNA, proteins, and the various goings-on inside the cell. Last night I spent a little time watching a new TEDx talk of his just posted online. My first thought was, “Why didn’t I get to see these movies when I was learning about biology as a kid? Life is unfair.” Compared to the flat cartoons of textbooks, or even the crude animations in documentaries of yore, Berry’s work seems to come from some advanced alien civilization.

In case you haven’t seen Berry’s work before, I’ve embedded his lecture here. (You may have heard about him when he got a recent Macarthur “genius” grant.) If you have seen his stuff before, I’d suggest you watch this anyway. And this time, don’t just watch. Listen.

When I first saw Berry’s work a while back, I was immediately gob-smacked. But as I watched his synchronized swimming of molecules a while longer, I realized after a while that I didn’t understand a lot of what was going on. I didn’t know the names of the molecules I was looking at, and, more importantly, I couldn’t tell what ...

XMRV takes another step to de-discovery?

Carl Zimmer — Thu, 22 Dec 2011 17:01:54 +0000

I’ve written a few times here about the battle over a virus called XMRV, and its supposed link to chronic fatigue system. I just wanted to point this morning to a few articles by some fine writers about the latest twist: the paper that first claimed a link has been completely retracted.

Ivan Oransky in Reuters

Jon Cohen in Science

Ewen Callaway in Nature

[Image: Wikipedia]

Melville and microbes: An interview about science writing with Eric Michael Johnson

Carl Zimmer — Tue, 20 Dec 2011 22:02:41 +0000

Eric Michael Johnson, an historian of science, is also the writer behind an excellent blog, “The Primate Diaries.” The other day he gave me a call to talk about science writing. He put together a two-part Q&A that he published today (part one and part two) that ranges from the science writing in Moby Dick to the microscopic virtues of Twitter. I was particularly flattered to get a portrait done by Nathaniel Gold. Check it out!

Swans and stem cells: winners of this year’s Imagine Science Film Festival

Carl Zimmer — Tue, 25 Oct 2011 22:47:45 +0000

For the third year in a row I had the pleasure of serving as a judge for the Imagine Science Film Festival. Along with fellow judged neuroscientists David Eagelman and Darcy Kelley and documentary filmmaker Robb Moss, I watched a slew of short films that touched in one way or another on science. The awards were just announced, and so I thought I’d hunt around for some online sites where you can watch them, either as previews or in their entirety. Here’s what I found:

The Scientist Award went to the best short that depicts a scientist in an accurate and original way. We awarded it to “Chasing Birds in Beringia” by Stephani Gordon:

The Nature Scientific Merit Award went to the best short that incorporated science in a compelling narrative. The winner was
Eagleman Stag, by Mikey Pease. Here’s a trailer; the full movie is ten minutes long.

The Visual Science Award was given to the best short that depicts a science in a visually-engaging manner. This year’s winner was “Breast Stem Cells”
by Etsuko Uno & Drew Barry. Here’s their visualization:

There were also some movies that got honorable mentions. For the Scientific Merit, here’s the trailer to the creepy, understated “The ...

#ArsenicLife Goes Longform, And History Gets Squished

Carl Zimmer — Fri, 30 Sep 2011 14:00:22 +0000

If you haven’t been tracking the arsenic life saga closely over the past ten months, check out Tom Clynes’s big feature at Popular Science. It focuses on the travails of Felisa Wolfe-Simon, the lead author on the paper, who has gone from the Olympian heights of TED talks to getting “evicted” from the lab where she’s worked for the past couple years. (Her word.)

For those of us who’ve been tracking the story for a while, that last fact popped out. Wolfe-Simon had been working in the lab of her co-author Ronald Oremland, but that’s now over. Let’s recall that her senior colleagues dubbed the intriguing microbe she studied GFAJ-1, for “Get Felicia A Job.”

It’s a good article. I won’t be forgetting the opening scene anytime soon, when Wolfe-Simon is ambivalently posing for a television crew, and she sinks into the mud of Mono Lake, where she first encountered GFAJ-1.

But I do share some of the reservations that science writer David Dobbs expresses over at his blog Neuron Culture. As a genre, the profile is one of the most addictive and enjoyable of all. It doesn’t matter if the profile is of a hero or a

The Penultimate Chapter in the XMRV-Chronic Fatigue Story?

Carl Zimmer — Fri, 23 Sep 2011 15:03:57 +0000

I’ve devoted a few posts (here and here and here) to the saga of a disputed link between chronic fatigue syndrome and a virus called XMRV. This week marks the next chapter in the story, with more evidence that the original results were at least partly due to contamination and a partial retraction of the original paper. Two great writers at Science, Martin Enserink and Jon Cohen, have put together an epic telling of this affair, from the first reports two years ago to the latest developments. The magazine has wisely put the piece out in front of their paywall. Do read it.

As Enserink and Cohen note, this is not the final word. That will probably come early next year, when a larger study led by Ian Lipkin of Columbia. We’ll see then if the link is buried at last, or lives to see another day.

Google+ invitations: Click here for one

Carl Zimmer — Mon, 08 Aug 2011 12:41:32 +0000

I learned that Google has retooled its invitation system for Google+. Instead of manually adding names into a message field, I can just drop a link into this post and offer 150 invitations. So if you want to dabble in this new experiment in social media and enforced non-pseudonymity, please click here.

Bellybutton biodiversity update: Wonderlands upon wonderlands

Carl Zimmer — Sat, 30 Jul 2011 14:31:59 +0000

Last month I contemplated the staggering diversity of microbes in my bellybutton–an experience made possible by my participation in a survey of microbiome diversity carried out by scientists at North Carolina State University. At the time, I thought I was quite the host. I was informed there were 53 species living in my navel, some of which had never been seen on skin before and some of which were altogether new to science. I was even informed that I was a “wonderland.”

Well, the project is moving forward at quite a clip, and the scientists are starting to push more of their data online. Here you can see the species from the first 60 volunteers they’ve studied. The lists are coded by number–I’m B944. I appear to have lost a species so I’m down to 52. And 52 is, I’m seeing, nothing to blog home about. So far, the diversity champion is the anonymous owner of bellybutton B1288. 107 species! Now that’s a wonderland….

Goodbye, E. coli?

Carl Zimmer — Fri, 08 Jul 2011 14:18:25 +0000

Lucas Brouwers, one of the new bloggers at Scientific American’s snazzy new blog network, takes a look at an intriguing paper (free pdf). The authors of the paper in examined many different strains of E. coli and come to a remarkable conclusion: they’ve been splitting apart so far that they may soon no longer be a single species. Check it out. (And, if you have a lot of time to spare, check out the rest of Scientific American’s fine line-up of bloggers.)

Last year: Arsenic life. This year: Chlorine life?

Carl Zimmer — Wed, 06 Jul 2011 18:17:27 +0000

[Note: Some folks don't like the phrase "chlorine-based life." I welcome suggestions in the comments for a better shorthand descriptor]

Last year, a team of NASA-funded scientists claimed to have found bacteria that could use arsenic to build their DNA, making them unlike any form of life known on Earth. That didn’t go over so well. (See my two pieces for Slate for a quick recap: #1, #2.) One unfortunate side-effect of the hullabaloo over arsenic life was that people were distracted from all the other research that’s going on these days into weird biochemistry. Derek Lowe, a pharmaceutical chemist who writes the excellent blog In the Pipeline, draws our attention today to one such experiment, in which E. coli is evolving into a chlorine-based form of life.

As I wrote in Microcosm, scientists have been contorting E. coli in all sorts of ways for years now to figure out what the limits of life are. Some researchers have rewritten its genetic code, for example, so that its DNA can encode proteins that include amino acids that are not used by any known organism.

Others have been tinkering ...

De-discovery round-up (plus a correction)

Carl Zimmer — Thu, 30 Jun 2011 17:30:33 +0000

It’s been very gratifying to listen to the conversation that’s been triggered by my essay in this Sunday’s New York Times on scientific self-correction. Here, for example, is an essay on the nature of errors in science by physicist Marcelo Gleiser at National Public Radio. Cognitive scientist Jon Brock muses on how to get null results published.

I also got an email from Eliot Smith, the editor of the Journal of Personality and Social Psychology who accepted the controversial clairvoyance paper I described in my essay. I wrote that three teams of scientists failed to replicate the results and that all three studies were rejected by the journal because they don’t accept simple replication studies.

Mr. Zimmer

Your recent Times column stated the following:

Three teams of scientists promptly tried to replicate his [Bem's] results. All three teams failed. All three teams wrote up their results and submitted them to The Journal of Personality and Social Psychology. And all three teams were rejected — but not because their results were flawed. As the journal’s editor, Eliot Smith, explained to The Psychologist, a British publication, the journal has a longstanding policy of not publishing replication studies. “This policy is not new ...

Discovering my microbiome: “You, my friend, are a wonderland”

Carl Zimmer — Mon, 27 Jun 2011 15:09:59 +0000

Some people get a thrill from getting their genome sequenced and poring through the details of their genes. I’m a bit off-kilter, I guess, because I’m more curious about the genomes of the things living in my belly button. And let me tell you: it’s a jungle in there.

I first became curious about my navel in January. I was in Durham, North Carolina, to attend a meeting, and as I walked out of a conference room I noticed a cluster of people in the lobby handing out swabs. They were asking volunteers to stick the swabs in their belly button for the sake of science. Our bodies are covered with microbes, and scientists are discovering weirdly complex patterns to their biodiversity. From fingers to elbows to chin to forehead, different regions of our skin are dominated by different combinations of species. But the bellybutton remained terra incognita.

I happily donated my microbiome to the study, which is being conducted by Jiri Hulcr and Andrea Lucky, two post-doctoral researchers in the laboratory of Rob Dunn at North Carolina State University. After a few weeks, Hulcr sent me a photo ...

Darwin+Hip Hop+Off Broadway=Baba Brinkman

Carl Zimmer — Tue, 14 Jun 2011 14:30:10 +0000

During the World Science Festival, I met Baba Brinkman, who performs hip hop about, among other things, evolution. He let me know that his “Rap Guide to Evolution” will be opening this Friday at the SoHo Playhouse in New York. Here are details about the venue and getting tickets.

Here are a couple videos from Baba…

Here’s a one called, “Performance, Feedback, Revision”:

Here’s Baba at TEDxKids:

Time to vote for the 3 Quarks Daily Science Prize

Carl Zimmer — Sun, 05 Jun 2011 04:51:19 +0000

The folks at 3 Quarks Daily are winnowing down the entrants for the best science blog post of the year. They want you to help select the finalists by voting for your favorite post from the 87 nominees. (The Loom makes an appearance at #76 with “The Human Lake.”) You can vote till June 8, 11:59 PM EST.

CreatureCast presents the baroque life on a lobster

Carl Zimmer — Mon, 09 May 2011 14:07:17 +0000

The folks at CreatureCast have created a new animation about the weirder corners of zoology. Behold Symbion pandora, an animal that clings to the mouthparts of lobsters, where it engages in the weirdest sex life I’ve ever heard of.

Darwin meets the citizen scientists

Carl Zimmer — Fri, 29 Apr 2011 15:54:52 +0000

Charles Darwin was the original crowd-sourced scientist. He may have a reputation as a recluse who hid away on his country estate, but he actually turned Down House into the headquarters for a massive letter-writing campaign that lasted for decades. In her magisterial biography of Darwin, Janet Browne observes that he sometimes wrote over 1500 letters in a single year. Darwin was gathering biological intelligence, amassing the data he would eventually marshall in his arguments for evolution. In the letters he wrote to naturalists around the world, Darwin asked for details about all manner of natural history, from the color of horses in Jamaica to the blush that shame brought to people’s cheeks.

Given the skill with which Darwin used the nineteenth-century postal system, I always wonder what he would have done with the Internet. A new paper offers a clue: he might have enlisted thousands of citizen scientists to observe evolutionary change happening across an entire continent.

Darwin used his Victorian crowd-sourcing to collect evidence that was consistent with his evolutionary theory; he didn’t expect that he could actually document evolutionary change happening in his ...

Frontiers in dark matter, and comics

Carl Zimmer — Thu, 28 Apr 2011 19:02:10 +0000

Via fellow Discover blogger Sean Carroll, I came across Jorge Cham’s podcast/comic/video about cosmology. I’m embedding it here, not just because it’s a very good summary of where we stand in understanding the stuff of the cosmos, but because Cham–he of PhD comics–has done something fascinating here. He has combined three different media into something new. I think, on the whole, it works very well. It moves a bit too fast for my eye sometimes, and can get a little herky jerky. But a living comic illustration of a scientist talking? Me likes.

Dark Matters from PHD Comics on Vimeo.

Today at the Browser: I talk about five books on the strangeness of life

Carl Zimmer — Thu, 28 Apr 2011 13:17:45 +0000

The Browser, one of my favorite sites for gathering interesting reads I can wield in my perpetual battle on behalf of procrastination, has a great feature called FiveBooks. From time to time, they ask a writer to select five of their favorite books on some particular topic, and then interview them about their choices. I was honored to be interviewed for today’s FiveBooks (just after Ian McEwan–yikes!). I chose the theme of “the strangeness of life” and then scanned my bookshelves for some favorite books that deal with it in one way or another. If you have any interest in good writing on natural history (including human natural history), I’ll wager you’ll like them all. Check it out.

Great science books for high school students: The hive-mind speaks

Carl Zimmer — Mon, 28 Mar 2011 21:31:41 +0000

Over the weekend, I was contacted by Melissa Townsend, an Arizona high school teacher, with this question:

Getting ready to assign spring reading to my students. What are your favorite non-fiction science books a HS kid can handle?

It’s an excellent question–there are some books that can open up the mind of a teenager, and leave an impression that lasts a lifetime. But when I got Townsend’s request, I was traveling to Washington to talk on a panel about blogging, so I was a bit scatter-brained. I therefore tossed the question out to the hive mind. When I read the responses, many of them made me think, “Yeah, what she said!”

Here is a selection of the answers. Add your own in the comment thread; I can update the list here accordingly.

The Immortal Life of Henrietta Lacks, by Rebecca Skloot. (This one was mentioned so often Townsend decided to go with it.)

Wonderful Life: The Burgess Shale and the Nature of History, by Stephen Jay Gould

The Diversity of Life, by Edward O. Wilson

Under a Lucky Star, by Roy Chapman Andrews

The Double Helix: A Personal Account of the Discovery of the Structure of ...

Crowd-sourcing the swimming eyeball

Carl Zimmer — Tue, 15 Mar 2011 14:26:09 +0000

Last week I wrote in the New York Times about a fascinating new paper in which scientists described a lamp shell embryo that is, in effect, a swimming eyeball. The paper itself, however, comes in two parts. Along with the part on the swimming eyeball, the scientists also described a later stage of the lamp shell embryo in which it developed simple eyes connected to neurons. It’s primitive version of our own eyes that reveals some interesting things about evolution–particularly about the different photoreceptors that evolved over half a billion years ago for sensing light. At the time, I was struck by the fact that this one paper had two newsworthy insights. So I was glad to see PZ Myer takes up the other half of the story in excellent detail over at Pharyngula. Check it out.

World Science Festival TV: Another afternoon shot

Carl Zimmer — Fri, 25 Feb 2011 18:59:51 +0000

I really do have work to do. So I’m profoundly resentful (in the best way possible) that the World Science Festival has launched a video site called WSFtv. Here’s seven minutes of neuroscientist Giulio Tononi (subject of my recent New York Times profile) talking about his theory of consciousness. There is a lot more where that came from.

How The Simpsons make us human

Carl Zimmer — Thu, 17 Feb 2011 16:12:29 +0000

If you’re interested in language, computers, and human cognition, check out my brother Ben’s first piece for the Atlantic, in which he pops the hype balloon that has inflated around the Watson computer’s performance on “Jeopardy.” Suddenly, my stash of Simpsons trivia has become profound!

When plants become ultrafast killers, it’s time to slow the camera down

Carl Zimmer — Wed, 16 Feb 2011 19:01:30 +0000

In my National Geographic article last year on carnivorous plants, I mentioned one particularly swift killer, the bladderwort. This aquatic plant grows little suction traps that can be triggered by passing animals. In a new paper in the Proceedings of the Royal Society, French researchers take the closest look yet at these ultrafast killers. They find that the door to the traps buckles like a popped bubble of chewing gum–but can then almost immediately swing back shut. Along with the new study on jumping fleas I wrote about last week, this is evidence of how far we’re just starting to explore the world of quick biology.

Science News has a nice write-up, and here is an excellent YouTube video provided by a co-author of the study, Philippe Marmottant, a physicist at Joseph Fourier University in Grenoble, France–complete with computer simulation, rubber-cap demos, and groovy soundtrack.

NASA on Flickr: Your afternoon is now officially shot

Carl Zimmer — Sat, 12 Feb 2011 22:27:48 +0000

NASA has selected some great pictures for Flickr. Here’s the caption for the image above, “The Original Seven”:

In this 1960 photograph, the seven original Mercury astronauts participate in U.S. Air Force survival training exercises at Stead Air Force Base in Nevada. Pictured from left to right are: L. Gordon Cooper, M. Scott Carpenter, John Glenn, Alan Shepard, Virgil I. Grissom, Walter Schirra and Donald K. Slayton. Portions of their clothing have been fashioned from parachute material, and all have grown beards from their time in the wilderness. The purpose of this training was to prepare astronauts in the event of an emergency or faulty landing in a remote area. Forty-five years ago today on May 24, 1962, Scott Carpenter went on to fly the second American manned orbital flight. He piloted his Aurora 7 spacecraft through three revolutions of the Earth, reaching a maximum altitude of 164 miles. The spacecraft landed in the Atlantic Ocean about 1,000 miles, about 1,609 kilometers, southeast of Cape Canaveral after the 4 hour, ...