Category: Darwinius

That GMO-cancer study? It gets worse.

By Carl Zimmer | October 10, 2012 5:32 pm

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]

CATEGORIZED UNDER: Darwinius, Meta

From Darwinius to GMOs: Journalists Should Not Let Themselves Be Played

By Carl Zimmer | September 21, 2012 5:17 pm

I don’t like starting the weekend in a state of infuriation, but here we are.

On Wednesday, French scientists had a press conference to announce the publication of a study that they claimed showed that genetically modified food causes massive levels of cancer in rats.

The paper appeared in a peer-reviewed journal. That being said, outside experts quickly pointed out how flimsy it was, especially in its experimental design and its statistics. Scicurious has a good roundup of the problems at Discover’s The Crux.

But those outside experts were slow to comment in part because reporters who got to see the paper in advance of the embargo had to sign a confidentiality agreement to get their hands on it. They weren’t allowed to show it to other experts.

We’ve seen this sort of bad behavior before from scientists. In 2009, paleontologists held a spectacular press conference at the American Museum of Natural History (complete with Mayor Bloomberg in attendance) to tout a primate fossil that was the centerpiece of a big cable TV show that aired that week. The paper describing the fossil was released minutes before the conference. Only one reporter managed to get her hands on the paper earlier than that, but she had to sign a confidentiality agreement with the production company.

In both cases, the strategy was clear: prevent science writers from getting informed outside opinions, so that you can bask in the badly-reported media spotlight. Sure, the real story may emerge later, but if you get that first burst of attention, you can lock in people’s first impressions. The documentary about the primate fossil got the audience its producers were hoping for. The French scientists got the attention of the French government, and thus reinforcing opposition to genetically modified foods, although the study itself fails to make that case. Mission accomplished.

This is a rancid, corrupt way to report about science. It speaks badly for the scientists involved, but we journalists have to grant that it speaks badly to our profession, too. If someone dangles a press conference in your face but won’t let you do your job properly by talking to other scientists, WALK AWAY. If someone hands you confidentiality agreements to sign, so that you will have no choice but to produce a one-sided article, WALK AWAY. Otherwise, you are being played. Saying, “Well, everyone else is doing it” is no excuse. You do remember your mother asking what you’d do if everyone else jumped off the Brooklyn Bridge, right?

Science writing has been marred in recent weeks by plagiarists and fabulists. We need to live up to our principles, and we need to do a better job of calling out bad behavior. BBC, AFP, and Reuters: you all agreed to do bad journalism, just to get your hands on a paper. For shame.

UPDATE 9/22 1:22 pm ET: Jonathan Amos, the author of the BBC’s article, just left a comment pointing out that he did not, in fact, sign a confidentiality agreement. On Twitter, he added that the BBC was offered the paper the day before the press conference in exchange for signing the agreement and declined. To which I can only say, Good on you, and please accept my apologies. But I am left wondering why the article itself describes the confidentiality agreement that journalists had to sign, and then does not explain what Amos just explained. (Also, I am curious who else signed the confidentiality agreement. Any French journalists have some insight?)

UPDATE 2 9/22 5:13 pm ET: In the commoents, Pascale Lepointe links to an article in Le Monde, which states flat out that they agreed to keep the paper confidential. Classy.

UPDATE 3 9/25 Zen Faulkes, among others, points out that the lead scientist on the paper also has a book coming out this week on GMOs. And there’s a TV documentary that’s been in the works for a while that’s about to air. Science as marketing!

 

 

CATEGORIZED UNDER: Darwinius, Meta

Darwinius versus blog power: A look back

By Carl Zimmer | August 5, 2010 1:29 pm

Brian Switek, one of the junior members of the science-blogging-whippersnapper brigade, has written a detailed look back at the saga of Darwinius, the primate fossil that held Mayor Bloomberg captive at a press conference. It was just published in the journal Evolution: Education and Outreach and is free for the taking. Switek has kind things to say about the impact of the Loom’s coverage of the subject, although I’m pretty sure this blog–and the many others that hopped on this crazy story–won’t stop this sort of fiasco from happening again. All we can do is help set the record straight.

CATEGORIZED UNDER: Darwinius

Evolution and the Media: Caveat Lector!

By Carl Zimmer | May 10, 2010 3:29 pm

How should teachers use the media to teach students about evolution? Carefully! That’s my advice in a paper I was asked to write for the journal Evolution: Education and Outreach, where I take a look at the history of journalists writing about evolution.

I start way back, at the beginning:

Evolution has been news from the start. On March 28, 1860, The New York Times ran a massive article on a newly published book called On the Origin of Species (Anonymous 1860). The article explained how the dominant explanation for life’s staggering diversity was the independent creation of every species on Earth. “Meanwhile,” the anonymous author wrote, “Mr. DARWIN, as the fruit of a quarter of a century of patient observation and experiment, throws out, in a book whose title has by this time become familiar to the reading public, a series of arguments and inferences so revolutionary as, if established, to necessitate a radical reconstruction of the fundamental doctrines of natural history.”

If you want to read the rest of that 1860 article, you can find it here. And if you want to read the rest of my paper, check out the pdf I’ve posted over at my web site.

Of Birds and Thumbs

By Carl Zimmer | June 17, 2009 1:04 pm

limusaurus.jpgMeet Limusaurus. It is not–I repeat NOT–the missing link between anything. And yet it is still an important fossil that may help us understand how birds evolved from dinosaurs.

The recent splash about a certain fossil primate has revealed yet again just how much a lot of people (sadly, including a lot of journalists) want to cling to the notion that paleontologists are only interested in missing links–which, I guess, are supposed to be the direct ancestors of some living group of organisms that are precisely halfway between primitive forerunners and the advanced living creatures.

This notion is wrong in many ways. First of all, the entire body plan shared by, say, living birds did not leap into existence in a single ancestor. In fact, what we today consider the bird body plan actually evolved through a long series of steps. Different parts of bird anatomy evolved at different times. It’s now generally agreed that birds descend from a group of dinosaurs called theropods that includes lots of famous two-legged species like T. rex and Velociraptor. Many studies show that feathers had already evolved in forms seen on birds today on dinosaurs long before they had wings, beaks, or lots of other adaptations that all birds today have. So looking for “the” missing link for birds is ridiculous from the get-go.

The obsession about missing links is wrong-headed for another reason. Paleontologists can learn a lot about the history of a living group of organisms without unbroken chain of direct ancestors (which is fortunate, because the fossil record is far too scrappy to ever uncover such a series). That’s because the evolution of animals is, in many ways, like branches growing from a tree. So paleontologists can look at the branches of a related group of species and note which species have which traits. There are some traits that all the species share, which were already in place in their common ancestor. And there are some traits that are only found among a smaller group of related species within the tree. Those are new traits that evolved later than the earlier traits. Scientists can then mark nodes along the tree to show how new traits evolved, and how old ones got modified into new ones. And as scientists discover new fossils, they can come up with more detailed hypotheses for the pattern of this change.

wagnerbirdhand.jpgLimusaurus, which makes its debut in tomorrow’s issue of Nature, sheds light on one particularly contentious matter about the origin of birds: how the fingers in a dinosaur hand got transformed into the end of a wing. A bird wing starts out as a limb bud, inside of which tiny clusters of cartilage cells start to form. Eventually, these clusters stretch out into wrist and finger bones, which later fuse together to provide a bendable spar that can support flight feathers. (To the left here is a simple diagram of the bones in a chicken’s hand.)

2-3-4.jpgOnly three digits form in a bird limb bud. Many lineages of land vertebrates have lost one or more digits over the course of their evolution. But which digits did the birds lose?

Scientists have generally argued for one of two possibilities. One possibility is that the thumb and pinky were lost, as I’m illustrating with my own hand here. That’s the pattern that has evolved in other land vertebrates, such as in horses. And when developmental biologists look at the clusters of cells that first develop in bird limb buds, they appear where the middle three digits appear in other land vertebrates. This alternative goes by the name 2-3-4. (Scientists name the five digits of the hand or foot starting from the thumb [1] and going out to the pinky [5].)

1-2-3.jpgwagnerarchhand.jpgalligatorhand.jpg

Yet a number of paleontologists have argued that the fingers in a bird’s wing are actually 1-2-3, as I’m showing in my second self-portrait. In early birds, such as Archaeopteryx, the fingers were not yet fused. As a result, they can give a clearer look at the anatomical connections between the bones and how they compare to other land vertebrates. I’ve lined up Archeopteryx‘s three-fingered hand with the five-fingered hand of an alligator, the closest living relative of birds. That top white digit looks a lot more like a stout thumb than a slender index finger. More evidence offered in favor for the 1-2-3 hypothesis comes from how the digits of early birds and related dinosaurs make contact with wrist bones as digits 1, 2, and 3 do in other land vertebrates.

Last year scientists at Yale decided to investigate this intriguing paradox by investigating the genes that build bird wings. In all land vertebrates, the same set of genes help set the identities of the digits. They found that in both mammals and alligators, there’s a key difference in the genes that are active in the thumb and in the four other digits. In the four other digits, a gene called HoxD-11 is active late in development. In the thumb, it’s silent. That difference may be a crucial reason why thumbs are so different from other fingers.

But in birds, the scientists found, something odd happens. In digit 2 (corresponding to our index finger), HoxD-11 is silent. One way to interpret this result is as follows: birds really do have 2-3-4 hands. Their dinosaur ancestors lost their thumb and pinky. And they also evolved a shift in the pattern of gene activity in their hands, so that HoxD-11 stopped switching on in the index finger. As a result, it became thumbish.

limusaurushand220.jpgEnter Limusaurus. This 1.7-meter-long dinosaur was recently discovered in China. It’s interesting for a lot of reasons, such as the fact that it appears to be one of several examples of a carnivorous theropods giving up meat and becoming a plant-eater. (The simple feathery covering is inferred from discovery of feathers on other dinosaurs.) Limusaurus is also interesting for its hands, shown here. After carefully analyzing the different bones that make it up, Limusaurus‘s discoverers have concluded that it has digits 2,3, and 4–plus a tiny digit 1.

This vestigial thumb has only a single bone left, the metacarpal at its base. The scientists conclude that by the time Limusaurus evolved, some features of the bird hand had already evolved–namely, a lost pinky and a vestigial thumb. But the remaining fingers had not yet undergone further changes seen today in birds, such as the thumbiness of the index finger.

To see how the Limusaurus  hand fits into the overall hypothesis about bird evolution, you can take a look at the tree the authors publish in their paper, reproduced below. Limusaurus belongs to the branch marked Ceratosauria. All living birds belong to Neornithes at the top. It will take future fossil discoveries to put this hypothesis to the test. But it’s already a fascinating synthesis, showing how an ordinary five-fingered hand evolved over millions of years into many new forms, including one three-fingered arrangement that you can see soaring overhead today.

Update: Co-author Jim Clark gets into some of the details of the research in his comment on my post. Thanks, Jim.

Reference: Xing Xu et al, “A Jurassic ceratosaur from China helps clarify avian digital homologies,” Nature 459:940 doi:10.1038/nature08124

Images: Limusaurus hand and tree from Nature paper. Hand diagrams from Vargas et al, PLOS One 2008. Limusaurus reconstruction by Portia Clark Sloan.

birdhandtree.jpg

CATEGORIZED UNDER: Darwinius, Evolution

Darwinius: Science, Showbiz, and Conflicts of Interest

By Carl Zimmer | June 10, 2009 2:37 pm

The story of Darwinius masilae continues…

In our previous chapter, we noted that the scientists who described this fossil claimed “no competing interests exist,” ignoring the fact that the fossil was the center of a spectacular media circus that included a heavily financed TV documentary. I contacted Peter Binfield of PLOS One, where the paper was published, and asked for a comment. He said he was contacting the authors and would get back to me.

He has.

The paper is going to be formally corrected, and in the interim the following statement has been posted to the comment section on the paper’s website:

“The authors wish to declare, for the avoidance of any misunderstanding concerning competing interests, that a production company (Atlantic Productions), several television channels (History Channel, BBC1, ZDF, NRK) and a book publisher (Little Brown and co) were involved in discussions regarding this paper in advance of publication. However, to clarify, none of the authors received any financial benefit from any of these associations and these organizations had no influence over the publication of this paper or the science contained within it. The Natural History museum in Oslo will receive some royalty from sales of the book, but no revenue accrues to any of the scientists. In addition, the Natural History Museum of Oslo purchased the fossil that is examined in this paper, however, this purchase in no way influenced the publication of this paper or the science contained within it, and in no way benefited the individual authors.”

I’m no expert in the ethics of fossils and museums, and so I’ll need to ponder this statement a while before commenting. In the meantime, let me throw this one out to those in the know. What do you think? Is this kosher?

CATEGORIZED UNDER: Darwinius, Meta

A Darwinius Carnival (Plus Some History of "Missing Links")

By Carl Zimmer | June 2, 2009 1:49 pm

It’s now been a bit over a week since Darwinius Day, and the sky, for the moment at least, still remains blue. It’s a good moment to look back and take stock of that hallucinatory ride through the media-science funhouse, and Brian Switek–a remarkable undergraduate who took to the Times of London to help people think straight about this fossil–has assembled a blog carnival just on this topic. In particular, check out the post that looks at a brief but questionable statement in the Darwinius paper: “The authors have declared that no competing interests exist.” I asked PLOS One about whether that was true, and they said they’re getting in touch with the authors. Stay tuned.

I also want to add a couple extra posts to the carnival. Henry Gee, editor at Nature, was inspired by all the claims of Darwinius being a missing link to blog about the history of the phrase “the missing link.” In response to Henry’s twitter for help, I put my lexicographer brother Ben on the case. He did some research of his own, which you can find in his latest “Word Routes” column. 

CATEGORIZED UNDER: Darwinius

Big Ratings For Darwinius Day. So How Was It, Cable-Viewers?

By Carl Zimmer | May 27, 2009 9:20 am

Monday night, Darwinius masilae (a k a Ida) had her television debut on The Link, which aired on the History Channel. A lot of people saw it, says Broadcasting & Cable in a surprisingly accurate article, which managed to do a better job on the scientific side of the story than a lot of regular media outlets:

Controversy Helps ‘The Link’ Boost History–Draws 2 million viewers Monday night

By Alex Weprin — Broadcasting & Cable, 5/26/2009 1:39:59 PM MT

The Link, a History special about the recently revealed 47 million year old fossil Ida, drew 2 million viewers Monday night, according to Nielsen Fast Cable ratings. That is up 67% compared to History’s prime average.The special also drew 904,000 P25-54 and 756,000 P18-49.

Ida–and the History special–was announced just a few weeks ago at the American Museum of Natural History in New York City and in journal PLoS One. Since then, the fossil, which could be the earliest known mammalian ancestor of man, linking Anthropoids (a group which include humans) with earlier groups of primates, has been extensively covered in the media.

While the History special is dubbed The Link, implying the fossil is a so called “missing link” in human evolution, many science journalists have criticized that interpretation, arguing that there cannot be a single “missing link” and that at best the fossil adds to the already strong literature on human evolution, and at worst may not be a part of humanity’s evolutionary history at all.

I gave up cable some years ago, a bit like an alcoholic going clean and sober. So I was not among the two million who saw the show Monday, and I haven’t seen it turn up on the web since then. I’ve been trying to get a sense of it from other people’s reactions on the web. But it’s hard to judge the show based on the reactions of people who are already steeped in paleontology. After all, television, like newspapers, should be directed to the public at large. I think it’s good if a show about science makes scientists or science buffs a bit impatient or bored.

The catch is that in trying to reach as wide an audience as possible, television producers sometimes start making stuff up. Certainly the hype ginned up last week over Darwinius was packed with plenty of nonsense. But sometimes a show and its publicity are very different. What’s the case here?

Update: When I say “big ratings,” I realized after posting this, I may be suffering the soft prejudice of low expectations. Two million is a high number for the History Channel, but not for Nova on PBS. And it’s really low compared to “Jon and Kate Plus Eight,” which aired the same night as “The Link.” The most important fossil ever ever ever can’t compete with a screwed up family, I guess.

CATEGORIZED UNDER: Darwinius, Meta

May 25 Is Darwinius Day, The Most Important Day IN 47 MILLION YEARS!

By Carl Zimmer | May 22, 2009 11:20 am

A friend passed on this ad that aired for “The Link,” the show about Darwinius on May 25. Take a look.

Yep. That’s right. May 25 will be more important than 9/11. Than Pearl Harbor. Than every date in human history. Pre-human, too.

Let this be the starting point from now on for all discussions of science hype.

Update: A commenter asked if this was a spoof. It’s not. This is a real ad for the show.

Update #2: The TV producers who passed on this video to me are now wondering if this particular piece is actually some kind of mash-up, using an original teaser ad and encrusting it with even more over-the-top-itude. Are there any YouTube-ologists who can parse such things? Take a look at this and this and this and, in particular, this, which was posted by someone who suspected it was a semi-hoax.

If I had to guess, the original ad, which aired on or around May 14, was a series of historic dates (including 9/11–classy!) with voiceovers, ending with Darwinius Day (which from now on will be the day I celebrate beautiful fossils by hyperventilating into a paper bag).

Then somebody decided the ad was so ridiculous that he or she had to take it up an extra crazy notch–grafting some of the original design from the History Channel web site. If my hypothesis is correct, there is one seriously funny amateur video editor out there.

Question: did anyone see the original on TV?

CATEGORIZED UNDER: Darwinius, Evolution, Meta

Science Held Hostage, Updated

By Carl Zimmer | May 21, 2009 10:40 pm

Just a quick note–I’ve updated my post on the Darwinius affair. The journal where the paper was published has responded to my enquiries. They say the authors of the paper were responsible for the secrecy over the paper.

CATEGORIZED UNDER: Darwinius, Evolution, Meta
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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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