Category: Link Love

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

By Carl Zimmer | October 25, 2011 6:47 pm

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: Read More

CATEGORIZED UNDER: Life In Motion, Link Love

#ArsenicLife Goes Longform, And History Gets Squished

By Carl Zimmer | September 30, 2011 10:00 am

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 scoundrel; the story is good as long as it’s full of human nature in all its extremes. But profiles of scientists are tricky, because science transcends any single individual scientist. To do the science justice, you may need to pull the spotlight away and get into the less human stuff, like chemical reactions and pH levels.

The story thus focuses mainly on Wolfe-Simon, with scientific critics effectively reduced to mean chair-throwers, their scientific objections dispatched in a couple lines. People and events are relevant insofar as they affect Wolfe-Simon. And in the process, Clynes writes some mystifying stuff:

What made the level of criticism so extraordinary is that the paper, in itself, is not so flawed that it should not have been published. The argument was compelling, the conclusions were measured, the data was thorough, and the paper made it through the same peer-review process as other articles in Science.

And Clynes has us believe that this barrage of extraordinary, brutal criticism (or perhaps questions from journalists) forced Wolf-Simon and her colleagues to go into witness protection:

Overwhelmed with questions from the media, Wolfe-Simon went underground. Guided by NASA’s PR team, she and Oremland and the paper’s other co-authors began citing NASA spokesperson Dwayne Brown’s position that the authors would not be responding to individual criticisms. The agency, Brown said, didn’t feel it appropriate to debate science using the media and bloggers. Discourse should occur in scientific publications.

“I wasn’t hiding, but I didn’t want to get involved in a Jerry Springer situation, with people throwing chairs,” Oremland says. “There are hundreds of blogs some viable and some off the wall, and they all want an immediate response. To try to engage in scientific commentary that way seems like a descent into madness.”

What the–?

I’ve seen this version of the arsenic life story before, and I can say (as one of the people mentioned in Clynes’s story) that it simply does not square with the facts. I really hope it doesn’t get set in people’s minds like concrete.

Let’s just run through the timeline, shall we?

Thursday, December 2: An eagerly anticipated NASA press conference, the publication of the paper in Science, front-page news in leading newspapers, with no articles I’m aware of dealing seriously with the critics.

[Update: Friday December 3: Chembark, a chemistry blogger, declares, "I am not convinced."  Jim Hu of Texas A&M writes, "Could there be arsenic-based backbone in the DNA? Maybe. But it would be extraordinary and so I would like to see better evidence." I for one missed these posts.]

Saturday, December 4: Rosie Redfield, a microbiologist with a blog she mainly uses for her class, expresses deep skepticism. It is the only such blog post I know of that presented a detailed criticism at this point in the timeline. [Update--I should say, the only blog post I was aware of.]

Sunday, December 5: Alex Bradley, another microbiologist, guest-blogs at We Beasties in a similar vein. The criticisms are harsh but deal in the scientific details of the paper.

The audience for both posts is small–an audience of fellow microbe junkies.

By Sunday afternoon, I think it’s time to write something. I’m wondering if Redfield and Bradley are saying what a lot of other scientists are thinking. I start getting in touch with leading experts in the areas that the paper touches on. In the next couple days they will get back to me, and just about all of them say the paper has serious problems, one simply declaring it should never have been published.

Naturally, it’s only fair to give the authors of the study a chance to respond. So on Sunday afternoon, I send links to the two blog posts above to Oremland and Wolfe-Simon. Oremland promptly writes back, “Sorry, but ‘nope.’”

I’m a bit surprised and email back to find out why. Here’s what I get:

It is one thing for scientists to “argue” collegially in the public media about diverse details of established notions, their own opinions, policy matters related to health/environment/science.

But when the scientists involved in a research finding published in scientific journal use the media to debate the questions or comments of others, they have crossed a sacred boundary.

Monday, December 6: Wolfe-Simon emails back at 12:42 AM, a few hours after I emailed her. She cc’s all her co-authors and administrators at NASA, including the director of the astrobiology program:

Mr. Zimmer,

I am aware that Dr. Ronald Oremland has replied to your inquiry. I am in full and complete agreement with Dr. Oremland’s position (and the content of his statements) and suggest that you honor the way scientific work must be conducted.

Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated. You can see many examples in the journals Science and Nature, the former being where our paper was published. This is a common practice not new to the scientific community. The items you are presenting do not represent the proper way to engage in a scientific discourse and we will not respond in this manner.

Regards,
Felisa

In the morning I get busy on my story. That evening, the CBC comes out with a story focused on Redfield’s complaint, relaying NASA’s statement that it’s not appropriate for scientists to debate each other in the media. I scratch my head and get back to work.

Tuesday, September 7: I publish a story in Slate about arsenic life, describing the detailed criticisms of a number of scientists (which I’ve posted in full on the Loom). I quote the no-comments of Oremland and Wolfe-Simon.

—Now, we can have a fine debate about whether journalists should ask scientists to respond to criticism from other scientists about their work. Oremland and Wolfe-Simon may truly believe that this crosses a sacred boundary. I say it doesn’t. It’s standard practice. Science, where the arsenic life paper was published, lets reporters get their hands on papers early, and reporters regularly seek out other scientists for comments on those papers before publishing their articles. If two scientists post their thoughts on public blogs, there is no difference in asking authors of a paper to respond to their critiques. Trying to make such a distinction is pointless.

I’ve been doing this kind of thing for a long time, and I have never encountered a response like this one from the hundreds of scientists I’ve interviewed. And that includes scientists who work for or are sponsored by NASA, despite the claims that popped up that NASA policy forbids such open debate. In fact, the scientist who gave me the headline for my story–”This Paper Should Not Have Been Published”–is herself part of NASA’s astrobiology team. Did she say, “Mister, you’ve crossed a sacred boundary”? Nope. She wrote me a long, detailed explanation of why she thought the paper failed.

In other words, I’m pretty sure I’d win that debate.

But the story you get from Clyne and others is not that Oremland and Wolfe-Simon had some a priori policy never to deign to comment on criticism that weren’t published in a scientific journal. It’s that they were overwhelmed by Jerry Spinger-grade hordes of unseemly scientist bloggers and relentless journalists–so overwhelmed that they had to vanish. They were victims.

But for this version of events to be true, the hordes must have stormed their lab in a single day–at some point between Saturday, when Redfield posted her critique, and Sunday, when the scientists told me they wouldn’t comment for the story. As far as I can tell, there were just two blog critiques published during that time, and a CBC news article. If someone can point to any evidence of this alleged horde that I’ve somehow missed–perhaps the gnawed bones of some graduate student left in its trail–I’d love to see it.

Otherwise, this just seems like one of those stories that sounds good in hindsight. And if any good is going to come out of this strange saga, we should strive to get all its stories straight.

[Update: Clynes responds.]

CATEGORIZED UNDER: Arsenic life, Link Love, Top posts

The Penultimate Chapter in the XMRV-Chronic Fatigue Story?

By Carl Zimmer | September 23, 2011 11:03 am

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

By Carl Zimmer | August 8, 2011 8:41 am

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.

CATEGORIZED UNDER: Link Love

Bellybutton biodiversity update: Wonderlands upon wonderlands

By Carl Zimmer | July 30, 2011 10:31 am

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….

CATEGORIZED UNDER: Link Love, Microcosm: The Book

Goodbye, E. coli?

By Carl Zimmer | July 8, 2011 10:18 am

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.)

CATEGORIZED UNDER: Link Love, Microcosm: The Book

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

By Carl Zimmer | July 6, 2011 2:17 pm

[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 with the DNA itself. In all living things, DNA is naturally composed of four compounds, adenine, cytosine, guanine, and thymine. Thymine, shown in the upper left panel here, is a ring of carbon and nitrogen atoms, with oxygen and hydrogens atoms dangling off the sides. Since the 1970s, some scientists have tried to swap thymine for other molecules, such as the one show to the lower left here. This compound is called 5-chlorouracil, the “chloro-” referring to the chlorine marked here in red. No natural DNA contains chlorine.

A team of German scientists recently published the details of an experiment that has taken them a long way towards E. coli that live only on chlorouracil. They didn’t simply sit down and type out a new sequence for E. coli’s genome–we just aren’t smart enough to make such predictions. Instead, they harnessed evolution. The scientists fed a population of E. coli chlorouracil, supplementing their dieet with a little thymine to keep them from starving to death. Bacteria that picked up mutations that allowed them to use some chlorouracil instead of thymine were favored by natural selection. They lowered the thymine levels to increase the pressure on the bacteria to evolve more.

After five months of this evolution, the E. coli underwent a noticeable change. For one thing, they changed shape. They started out in the normal capsule shapes in the top photo, turned into the worm-like shapes below, and then later became capsule-shaped again. The scientists also found that the bacteria were slurping up chlorouracil. Ninety percent of the thymine in their DNA was replaced by chlorouracil. As Lowe writes, the scientists found that the bacteria were still incorporating some thymine into their DNA through a pathway no one had discovered before (which just shows how marvelously mysterious E. coli remains after a century of intensive study). The scientists shut down this new pathway, and found that the bacteria still grew happily. But now they only had 1.5% thymine in their DNA.

This E. coli is different from ordinary E. coli, with over a thousand mutations that enable it to take up chlorouracil. But it is not quite yet off the grid. If it is fed thymine and no chlorouracil, it can switch back to a conventional way of life. So now we’ll see if scientists can further evolve the bacteria so that they can only live on chlorouracil, and starve on thymine.

I checked in with Steven Benner, a chemist who has raised a lot of concerns about the arsenic-life research last year. What did he think of the new research?

“It looks true,” he said.

Benner also pointed out that using chlorine in DNA is a pretty modest changed compared to what would have been required to substitute arsenic for phosphorus in the backbone of DNA. Swapping in chlorine doesn’t change how the compound reacts with other compounds, doesn’t change its size much, doesn’t change its stability much, and so on.

On the other hand, it appears to have the advantage of being real.

[Update: Rosie Redfield, an outspoken critic of the arsenic-life research, just got back to me with nice things to say as well:

"This looks quite solid to me (I read it quickly). The technology is nice, very appropriate for the project. No red flags at all."]

De-discovery round-up (plus a correction)

By Carl Zimmer | June 30, 2011 1:30 pm

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 and is not unique to this journal,” he said.

In fact, JPSP has received only one submission reporting failed replications of Bem’s studies. I did reject that paper based on the reason your column stated.

And to put that in context, I also rejected another submission to the journal that reported successful replications of some of Bem’s studies, on the same grounds.

I believe that a published correction is warranted; the difference between one and three papers is quite meaningful in this context.

Best regards,
Eliot Smith

I’ve passed on Smith’s message to my editor at the Times, and I’ll also take this opporunity here to apologize for the error.

I’m not sure how meaningful it is in the context of my essay, since my point was that policies against publishing replication studies get in the way of science’s self-correction. But a mistake is a mistake.

Discovering my microbiome: "You, my friend, are a wonderland"

By Carl Zimmer | June 27, 2011 11:09 am

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 of a Petri dish in which some of the bacteria from my bellybutton were thriving. Then Hulcr and Lucky got down to the serious work of identifying the species in the navels of their volunteers (90 and counting).

Yesterday, Dunn sent me a spreadsheet detailing my own results. “You, my friend, are a wonderland,” he wrote.

To catalog the biodiversity of bellybuttons, Hulcr and Lucky are extracting the genetic material from their collection of swabs. They then compare these fragments of DNA to the millions of sequences that are stored in public databases. (They limited themselves to DNA from bacteria, so for now they’re not cataloging the fungi, viruses, and other creatures that may be lurking in our navels.)

Some fragments of navel DNA precisely match the DNA of a known species of bacteria. In other cases, they’re close enough to a species for Hulcr and Lucky to assign them to a genus, a family, a class, or  some higher unit of classification. In a few cases, the bacterial DNA is so exotic that all they can say for sure at this point is that it is bacteria.

Hulcr, Lucky, and Dunn had lots of questions about the things that dwell in the human omphalos. Are they different from the species that live in other parts of the skin? Do they differ from one person to the next? Is there a core set of species found in all navels? To address these kinds of questions, they tallied up the number of volunteers who carried each species, and investigated how each species makes a living.

All told, I now discover, my belly button harbors at least 53 species of bacteria. This, Dunn informs me, is a “whopping” number.

I’m not sure whether to feel good or bad about this revelation. On the good side, I know that diversity can make ecosystems work better. One of the most important services that our microbial ecosystem performs for us is protecting us from pathogens. They can outcompete invaders, kill them with poisons, and otherwise ward them off. Scientists have run experiments to test the effect of diversity on infections. They manipulated mice so that some had no resident bacteria, and others had low levels of diversity. The researchers found that pathogens did a better job of invading low-diversity mice than high-diversity ones.

So perhaps my belly button is especially well-defended. Still, I can’t help but wonder if I ought to scrub it with some steel wool. There are some very exotic things in there. Only a small fraction of my belly button bacteria were common among the other 89 volunteers. The microbes I share with most other volunteers tend to be ordinary skin dwellers that are typically harmless (although sometimes they can turn nasty and cause problems ranging from acne to staph infections).

But out of 53 species, 35 were present in only 10 or fewer other volunteers. And 17 species in my navel didn’t show up in anyone else. In the column for notes in Dunn’s spreadsheet, he’s annotated these species with scientific descriptions like “weird one” and “totally crazy.”

Several species I’ve got, such as Marimonas, have only been found in the ocean before. I am particular baffled that I carry a species called Georgenia. Before me, scientists had only found it living in the soil.

In Japan.

When I learned this, I emailed Dunn to let him know I’ve never been to Japan.

“It has apparently been to you,” he replied.

While I may be a bit of an outlier in the belly button department, I’m not a freak. Among all 90 belly buttons Dunn and his colleagues have studied so far, they have found 1400 species of bacteria, a number of which have never encountered on human bodies before. These species are probably not so out of place as they may seem, however. The diversity of the world’s microbes is vast–far bigger than the whole animal kingdom combined. For the most of the history of microbiology, scientists have focused most of their attention on bacteria that make humans sick–ignoring the huge number of species that don’t harm us, or that live elsewhere in the world. Many species are turning out to have a much wider range than scientists have previously appreciated. Bacteria have also evolved to leap from one niche to another to another. Take Pantoena–a lineage Hulcr and Lucky have only found in my belly button and that of one other subject. Most species of Pantoena infect plants. But a few lineages have shifted from plants to people. As scientists add more branches to the tree of life, they will probably find more such transitions.

In ancient Greek mythology, Zeus release a pair of eagles to find the center of the world–the “omphalos,” which means belly button in Greek. Several statues, like the one shown above, were built around the Mediterranean to mark the supposed place where the eagles landed. It’s wonderful to be part of an experiment that gives a new meaning to this ancient word. Each of us carries a biological omphalos: a small, lint-clogged center of the microbial world.

(For more information, check out Dunn’s new book, The Wildlife of Our Bodies, for which I happily provided a cover blurb.)

[Image: University of Kentucky]

Darwin+Hip Hop+Off Broadway=Baba Brinkman

By Carl Zimmer | June 14, 2011 10:30 am

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:

CATEGORIZED UNDER: Evolution, Link Love
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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.
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