A Blog by Carl Zimmer

That GMO-cancer study? It gets worse.

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]

A Blog by Carl Zimmer

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

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!

 

 

A Blog by Carl Zimmer

Darwinius versus blog power: A look back

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.

A Blog by Carl Zimmer

Evolution and the Media: Caveat Lector!

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.

A Blog by Carl Zimmer

Of Birds and Thumbs

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

A Blog by Carl Zimmer

Darwinius: Science, Showbiz, and Conflicts of Interest

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?

A Blog by Carl Zimmer

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

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. 

A Blog by Carl Zimmer

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

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.

A Blog by Carl Zimmer

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

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?

A Blog by Carl Zimmer

Science Held Hostage, Updated

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.

A Blog by Carl Zimmer

Darwinius: Named at Last!

In a remarkable feat of commenter-blogger synergy, the Loom has helped give Darwinius its name back.

As I posted yesterday, some commenters on the Loom pointed out that, amidst all the hullaballoo over the unveiling of this primate fossil (oh, don’t get me started), it looked as if the scientists who wrote the paper failed to follow the rules for naming a new species. The people who make the rules (the International Commission on Zoological Nomenclature) require paper copies of a scientific paper, not just a digital one, as was the case of Darwinius.

Today, the executive secretary of the ICZN used the Loom to confirm that, yes, Darwinius was not yet Darwinius.

But at last, it is. Here’s an update from Peter Binfield, the managing editor of Plos ONE, the journal that published the paper.

Regarding the requirements for making the name Darwinius masillae nomenclaturally available in the eyes of the ICZN, we have been in discussion with Ellinor Michel (the ICZN Executive Secretary) and have additionally consultated with Richard L. Pyle (an ICZN Commissioner). They have advised us that by doing the following, we have met the ICZN code and therefore the name should be considered nomenclaturally available.

A print-run of fifty copies of the paper has been created on May 21st. The top sheet of each copy has the following text appended to the footer: “This document was produced by a method that assures numerous identical & durable copies, and those copies were simultaneously obtainable for the purpose of providing a public and permanent scientific record, in accordance with Article 8.1 of the International Code of Zoological Nomenclature. Date of publication: 21st May 2009”

Apart from this wording, these copies are identical to the electronic version that is freely available from our web site at: http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0005723&representation=PDF

These copies are now obtainable from our offices at 185 Berry Street, Suite 3100, San Francisco, CA 94107, USA. Anyone who requests a copy, and tenders a fee of $10 (towards the cost of postage and printing) will receive a copy.

Having made the printed copies available, we have been told by the individuals named above that we have conformed with the relevant ICZN codes. They have also indicated that the proposed resolution is an interim step, which should meet the requirements of the Code until a formal amendment is published within the next few years.

We are very grateful to the ICZN for their actions to resolve this matter.

Richard Pyle of the ICZN thought that Peter’s update required a small clarification, which he just sent in:

The pending proposed Amendment to the ICZN Code for allowing electronic forms of publication (see: http://www.iczn.org/electronic_publication.html) is currently in review, as is required for all such major amendments to the Code.  This process will likely be completed within the next year, and if adopted, the amendment should go into effect at that time.

What will require “a few years” to be published is the next (Fifth) Edition of the ICZN Code (see: http://iczn.ansp.org ). Presumably, this Edition of the Code will also support the electronic publication of nomenclatural acts (especially if the proposed amendment to the existing 4th Edition of the Code is approved).

To those not steeped in species, genera, suborders and suprafamilies, all of these bylaws and codes may trigger vertigo. But keeping the world’s biodiversity in order is not for the faint of heart. With 1.8 million species on the books, and tens of thousands of new ones being added every year, taxonomists need an intricate set of rules to keep it all straight. The fact that taxonomists share a set of rules, no matter how intricate, was one of the great advances in the history of biology. (See my lecture [audio] for a sense of the chaos that came before.)

But who knows how Linneaus would have dealt with the Internet….

A Blog by Carl Zimmer

Science Held Hostage

darwinius220.jpgSometimes big movie production companies decide that they’d be better off not showing a movie in advance to the critics. They know that the reviews would probably do more harm than good. Looking back on the the Darwinius affair, I’m starting to wonder if the unveiling of this fossil was stage-managed in the same way.

I only started looking into the story after observing all the bizarre publicity around it. And as I’ve probed this strange media event, I’ve gotten some interesting information from reporters who were on the Darwinius beat. It makes for a disturbing timeline:

May 10: The Daily Mail gets wind of the fossil and the show that will be broadcast about it.

Ann Gibbons, a Science correspondent, wants to get her hands on the paper.  “I struggled in vain all last week to get a copy of the article,” she emailed me this morning. PLOS will not give her the paper, which will not be published until May 19, the same day as a major press conference on the fossil.

May 15: The Wall Street Journal gets a fairly long interview with one of the co-authors of the Darwinius paper (who apparently thought the conversation was off the record)

May 16: Gibbons, having failed to get the paper from PLOS, convinces the producers of the the documentary on  Darwinius, Atlantic Productions, to give it to her. In order to get it, she signs a non-disclosure form agreeing not to show it to anyone until 10:30 am on May 19, the day of the press conference. But she does not get the paper until Monday.

May 18: Gibbons finally gets the paper Monday afternoon, the day before the press conference. But she cannot show it to any experts due to her non-disclosure agreement.

May 19: At 10:40 am, I (and many other reporters) get a press release from PLOS about Darwinius. The press release has a link that lets us download the paper, and there is no embargo on it. In other words, we can start writing about it right away. But the email arrives right before the press conference at the American Museum of Natural History where Darwinius is unveiled to a swarm of reporters. The web is almost immediately flooded with reports on Darwinius, based only on the press conference.

As the day progresses, I am puzzled by the lack of outside commentary in articles on Darwinius. The articles I encounter only have quotes from the co-authors of the paper saying how important it is, and television producers telling us how this is going to change everything. (On a related note, the sky is still blue today.)

Not realizing the kind of constraints reporters like Gibbons were under, I decide to get in touch with experts myself and see what they think. Short answer: cool fossil, not a “missing link,” and a paper with some shortcomings.

In the comments section of my own post, AP science reporter Malcolm Ritter had this to say today:

As the reporter who covered this story for The Associated Press, I’d like to point out two things: 1. Major journals generally make upcoming papers available to reporters a few days ahead of publication so we can get independent comment for our stories. But PLoS ONE withheld the Darwinius paper until 10 minutes after the Hurum press conference began (judging by the time stamp on the PLoS email to me). So reporters had nothing to show outside experts to solicit some perspective before Hurum et al. started talking. 2. Carl, you said you never found a news story that had comments from independent experts. I’m not sure when you checked, but my story quoting both Beard and Fleagle went out at 4:40 p.m. (It replaced a preliminary version that I’d written off the press conference. I’d contacted both men beforehand an arranged to speak after we’d all seen the paper).

Indeed, by the time Malcolm updated his article, I had given up hope of finding comments from indepentent experts and was doing my own blogging. I apologize for implicitly kicking dirt on the work of Ritter and other diligent journalists.

So, to recap: it appears that both PLOS and Atlantic Productions did not give journalists any time to consult with outside experts before launching a major press conference with a huge blitz of media attention. In other words, science writers who were trying to do their job well and responsibly were actively hindered. Those who declared ridiculous things, such as claiming that human origins were now solved once and for all, were not.

I have a hard time even imagining how this behavior could be justified. I’ve sent emails to the contacts listed in the PLOS press release on Darwinius both at PLOS and Atlantic Productions to ask why they took this course of action.

I’ve yet to get a response.

Update #1: This article in the Australian was brought to my attention after I published this post, with quite a quote from co-author Phil Gingerich:

“There was a TV company involved and time pressure. We’ve been pushed to finish the study. It’s not how I like to do science.”

Update #2: Peter Binfield from PLOS has responded:

I am the Managing Editor of PLoS ONE. This paper was originally submitted to us on March 19th 2009 and underwent appropriate scrutiny by an Academic Editor (named on the published article) and three expert peer reviewers. Peer review comments were returned to the authors who revised their paper accordingly and the paper was ultimately accepted on May 12th 2009. These dates are available on the paper itself.

Once the paper was accepted we made a strenuous effort to publish the article in time for the Press Conference which was happening on May 19th – only a week later. We were not involved in the Press Conference, but felt it was clearly in the public interest to have the article publicly available in time for that conference. Our production team managed to get the article published more than two weeks quicker than normal, so that it would be ready for the 19th. However, it was only on the afternoon of the 18th May that we knew the paper would definitely be available in time and until that point, no final copy of the paper was available.

We do regularly help PLoS ONE authors with the distribution of press releases under an embargo, as do many other journals, but when we do this we only ever issue that information on a date that is acceptable to the authors. The authors of this paper requested that we did not issue a press release, or reveal any other information about this paper, until 10.30 EST on the 19th May (the time of the press conference). We respected their wishes, and at the time of publication also issued our own press release about this article.

We are delighted to have published this work, which has clearly captured the imagination and attention of researchers, the media and the public. The paper has been discussed, scrutinized, praised and criticized, and is a terrific example of why open access to research is so beneficial.

I’m curious what scientists, journal editors, reporters, and other readers think of Binfield’s response. Other prominent journals don’t leave these matters up to the scientists (or their television producer pals). They inform the scientists of which issue a paper is scheduled for, and they put the paper on a press list a few days earlier.

Now, I know that PLoS ONE is unusual in a lot of ways. For one thing, they don’t reject papers for not being of sufficient importance. They state, “Judgments about the importance of any particular paper are then made after publication by the readership (who are the most qualified to determine what is of interest to them).” But does that mean they should also go along with an embargo from their authors that hinders good reporting on the papers?

In any case, I have yet to hear from the television producers. Given PLoS One’s response, I’m more curious than ever to hear from them.

Update #3 (Friday morning):

Still no word from Atlantic Productions. But, as a consolation prize, here’s quite a tale from journalist Mark Henderson of the Times of London (Note: Atlantic Productions is based in Britain):

…the PLoS paper WAS made available under embargo to the press — but only to selected individuals and under very unusual restrictions. I was invited to read it by Atlantic Productions on Tuesday morning (I’m Science Editor of The Times in London), but I had to go to their offices to read it and wasn’t allowed to take a copy away. I also had to sign a non-disclosure agreement, which meant I wasn’t able to approach anyone else for comment until the embargo lifted. The Guardian also had advance access (they got to see more in advance than we did, and earlier). So — obviously because they bought the film rights — did the BBC. But other UK papers (Independent, Telegraph etc) got nothing. This is a very weird (and in my experience unprecedented) way to manage the release of published science.

Update #4: Ann Gibbons sent in this point of clarification as a comment, but for some reason comments have stopped being posted. (I’m on it…)

In response to Hank Campbell, no. 6, PLOS and Atlantic didn’t withhold the paper from me as a backlash to AAAS, which publishes Science. They withheld it from all reporters, and in fact, Atlantic Productions did me a small favor–they called me at home on Saturday night, 5/16 to respond to my request for the paper and after signing a non-disclosure agreement, I was given a copy the evening before the embargo lifted, which helped me a bit. In the meantime, like Carl, I called the authors and other leading paleontologists to find out what they knew. But I was prevented by the embargo from printing details that I gleaned about the paper, and no self-respecting researcher will comment about a paper without reading it. We wrote two blogs about the hype last week, but could not post a story with independent scientists’ reactions until Tuesday afternoon and the 29 May issue of Science (see: http://sciencenow.sciencemag.org/cgi/content/full/2009/519/1)

A Blog by Carl Zimmer

Does Darwinius Exist, Revisited: The Official Word Is…Not Yet.

Yesterday I blogged about how Darwinius, the famous fossil primate that will change everything, may not actually have a published named yet. The trouble is that the official rules seem to indicate that a paper in an electronic journal is not enough. Paper is required. A spirited discussion among scientists blossomed in the comment thread, which has morphed into a conversation about Science 2.0.

To get an official comment, I contacted the organization that oversees the naming of new species, the International Commission on Zoological Nomenclature. This morning I got the following message from the Executive Secretary, Ellinor Michel.

1. The names are not nomenclaturally available from  the electronic version of the  publication. 
2. The journal has contacted us for advice on how to ensure these names  are nomenclaturally available, which we provided, saying that a  separate print edition must be produced by a method that assures numerous identical and durable copies, and that those copies must be obtainable free of charge or for purchase.

3. If the publisher does what we recommended, then the names will be nomenclaturally available from the date of the paper publication.

4. This is a provisional arrangement as the ICZN is working on a proposed amendment to the Code allowing nomenclatural availability of names published in electronic-only journals. The proposed amendment is available here: http://www.iczn.org/electronic_publication.html and we encourage public input in this important discussion.

5. There are >1.8 million named species in the world, with approximately 16,000-25,000 new nomenclatural acts each year in zoology alone. Managing the scientific names indexing of this biodiversity requires rules promoting stability. The International Commission on Zoological Nomenclature, representing the taxonomic community and users of zoological names, works to uphold stability but also to develop the rules to accommodate technological development.

I’ve contacted PLOS and the authors and am waiting to hear where things stand now that the official word has been released.

Update: Darwinius is now Darwinius.

A Blog by Carl Zimmer

Does Darwinius Exist?

Darwinius has achieved the ultimate triumph of pop-culture consciousness, having become for the moment the background image on the main Google search page. But some of the commenters in my post yesterday on the head-slapping hype around this fossil pointed out something I thought deserving of its own post: Darwinius may not actually exist.

By this I mean that the name Darwinius may not be valid officially published. I first became aware of this from Nature editor Henry Gee’s twitterings. The problem has to do with the fact that the journal where Darwinius was pubished, PLOS One, is only online.

Today Martin Brazeau laid out some details here at the Loom, citing the International Committee on Zoological Nomenclature, which sets the rules for naming new species:

 …it isn’t named yet. This is starting to pop up in various comments now, surprisingly slowly, however.

According to ICZN:

Article 8.6 Works produced after 1999 by a method that does not employ printing on paper. For a work produced after 1999 by a method other than printing on paper to be accepted as published within the meaning of the Code, it must contain a statement that copies (in the form in which it is published) have been deposited in at least 5 major publicly accessible libraries which are identified by name in the work itself.

If, in fact, these conditions have not been met by this electronic publication, then “Darwinius” has not officially been published…

Larry Witmer of Miami Ohio University chimed in…

You’re absolutely right, Martin. Henry Gee (Nature) also has pointed to Article 8.6 (in a Facebook entry) and posted the link to the International Code of Zoological Nomenclature, for those that want to check out the rules: http://www.iczn.org/iczn/index.jsp. Article 8.6 is in Chapter 3.

The Code has a copyright of 1999, so one has to wonder how they’ll rule on online-only names, such as Darwinius. And Darwinius is only one of a growing number of cases. I’m sure the Commission is looking at the whole issue. In fact, maybe one benefit that may come from the unprecedented over-the-top attention given to “Ida” is that it may bring this whole taxonomic issue to the fore.

I’m part of a group that had been looking at PLoS ONE as a potential venue for our manuscript (mostly because of the ability to include more graphics and movies), but we decided against it for precisely this reason. Would the new name be valid?

While these rules may seem a bit esoteric to most people, taxonomists take them as seriously as a heart attack. I’ll be curious to see how this story develops. How strange would it be for the most famous fossil of the day to be rendered nameless.

Update: I asked John Hawks, the editor of the paper, and he deferred to the PLOS office. I’ve dropped an email with Michael Eisen, too. In the meantime, Hawks pointed me to this blog post, which may clear things up…or not.

Update #2: Michael Eisen, a co-founder of PLOS and a member of the board of directors, kindly left this comment:

In the past, PLoS has gone to great lengths to ensure that taxanomic papers published in PLoS One meet the ICZN standards. Last year PLoS One published a paper describing a revision of several ant genera.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001787

Cognizant of the ICZN standards, PLoS One ensured that print copies of the article were deposited in appropriate libraries. This was described explicitly in the paper.

In accordance with section 8.6 of the ICZN’s International Code of Zoological Nomenclature, we have deposited copies of this article at the following five publicly accessible libraries: Natural History Museum, London, UK; American Museum of Natural History, New York, USA; Museum National d’Histoire Naturelle, Paris, France; Russian Academy of Sciences, Moscow, Russia; Academia Sinica, Taipei, Taiwan. The three new species names established herein have been prospectively registered in ZooBank [6]–[8], the official online registration system for the ICZN. The ZooBank publication LSID (Life Science Identifier) for the new species described herein can be viewed through any standard web browser by appending the LSID to the prefix “http://zoobank.org/”.

As various people have pointed out, this language not appear in the Darwinius paper. I’m no expert on ICZN standards, and have to say that I think the print requirement is out of date, but it would appear that the omission of this language alone would disqualify the paper as an official taxonomic description.

I don’t know whether this was an oversight, or whether efforts were simply not made by the authors to conform to ICZN standards. I’ll let you know what the people at PLoS say about whether copies were deposited.

Update #3: I just got a new comment from Peter Binfield, the managing editor of PLOS One

PLoS is aware of the problem with the ICZN not recognizing species names that are announced in online only journals. The issue specifically relates to us being online-only (which more and more journals will become in the future) and therefore not conforming to Sect 8.6 of their code (http://www.iczn.org/iczn/index.jsp?article=8&nfv=true ) which states:

“8.6.  Works produced after 1999 by a method that does not employ printing on paper. For a work produced after 1999 by a method other than printing on paper to be accepted as published within the meaning of the Code, it must contain a statement that copies (in the form in which it is published) have been deposited in at least 5 major publicly accessible libraries which are identified by name in the work itself.”

The issue comes down to what is meant by “the form in which is it published” for an online-only title and therefore whether or not there is any point to including the statement about 5 libraries until the ICZN has made a determination on the topic.

There has been a lot of debate at ICZN on this topic (specifically how any online only journal can meet their code) but to date there has been no resolution. As the largest online-only journal in the world, this is obviously important to us and so we have been in active discussion with the ICZN (for some time) as to how we can conform.

It is worth noting that all our content is archived in several industry standard locations – PubMedCentral and LOCKSS (http://www.lockss.org/lockss/Home – which deposits an archive copy of every paper in hundreds of libraries worldwide, all named at: http://www.lockss.org/lockss/Libraries ) are two important examples, and we are in the process of being archived at the Royal Dutch Library (as well as being stored on the hard drives of millions of readers, due to our Open Access nature).

We make it clear to authors that publishing in any online only journal (of which PLoS ONE is just one example) is a problem as regards the ICZN recognition of a new taxonomic descriptions. The authors of this paper were aware of this problem but chose to publish the paper with us regardless (as have the authors of several other taxonomic papers published by PLOS ONE). We have also advised the authors to register their name at Zoobank.

Obviously we hope that this issue will be resolved sooner rather than later and that all these names will be recognized retrospectively. In order to make this happen we are actively investigating potential solutions with the ICZN (and have been for many months). Once ICZN has made a determination then we will correct the paper to reflect the approved practice and wording.

Peter Binfield

I’ve put in a few emails to officials at ICZN for comment. I’ll get back with a response from them as soon as I get one.

Update #4: Ugh! Over at Why Evolution Is True, Greg Mayer rightly points out that Darwinius has been published in paper form already: in the newspapers that ran stories before the PLOS One paper was published. As early as May 10, the Daily Mail had a piece. I’m wondering if this has ever happened before, and have newspapers ended up being cited as the original publication for other species names?

Update #5: The ICZN Executive Secretary has given me the official word. Read here for the details.

Update #6: Darwinius is now Darwinius.

A Blog by Carl Zimmer

Darwinius: It delivers a pizza, and it lengthens, and it strengthens, and it finds that slipper that's been at large under the chaise lounge for several weeks…

darwinius440.jpgIf the world goes crazy for a lovely fossil, that’s fine with me. But if that fossil releases some kind of mysterious brain ray that makes people say crazy things and write lazy articles, a serious swarm of flies ends up in my ointment.

On Friday, a reporter at the Wall Street Journal got a scoop on a new paper on a 47-million-year-old primate fossil that was published today in PLOS One. The story mentioned that the discovery would be revealed at the American Museum of Natural History. It did not mention that the fossil was also the ceneterpiece of a show on the History Channel, along with a big web site and a book–all called “The Link. Yesterday and today there have been a torrent of news articles on the new primate, dubbed Darwinius masillae. Publications that normally wouldn’t give two picas to paleontology, such as New York Magazine and Gawker jumped on the bandwagon.

So what made this primate worth all the attention? Well, reporters who attended a press conference this morning heard things like this (courtesy of the Guardian)

Nancy Dubuc of the History Channel that will be showing the film said Ida “promised to change everything that we thought we understood about the origins of human life”….

Dr Jorn Hurum, the scientist at the heart of the project, made the most exotic parallels. He screened photographs of the Mona Lisa and the Rosetta Stone, without elucidation, though the implication was clear. He variously described the fossil as the Holy Grail of paleontology and the lost ark of archeology.

I watched this media event balloon as I tried to do other work, but I kept getting distracted. I kept waiting to see an article that sought out some opinions from experts who were not involved in the discovery and analysis of the fossil, which might corroborate that this was indeed the Holy Grail of paleontology, or perhaps something just a wee bit more Earthbound than that. I never found one.

It finally got to the point where I found myself dispatching emails to two prominent primatologists–John Fleagle of SUNY Stony Brook and Chris Beard of the Carnegie Museum–to see what they thought.

Both researchers agreed that it was a lovely fossil, in terms of its exquisite preservation. “It’s really wonderful,” Fleagle said. It’s got bones, fur, and even its last meal in its stomach. Fleagle observed that it will be possible to learn many details about the biology of early primates from Darwinius, down to the stages by which it teeth erupted.

But does this “change everything”? Is it, as the Sun claims, “the missing link in human evolution”?

Actually, I didn’t ask Beard or Fleagle those questions. That would be a bit ridiculous. No scientist, including the co-authors of the Darwinius paper, would ever pretend that they had found a single fossil that was “the” missing link. For some reason reporters (and apparently television producers) are obsessed with the idea, as I wrote about long ago when another primate fossil was touted in a similar fashion. Newly discovered fossils are important instead in helping to resolve the order in which traits evolved, and how groups of species are related to one another. And the more fossils that are discovered, the clearer these pictures become.

Instead, I asked what Fleagle and Beard thought about the actual argument in the paper, which has to do with where humans, apes, and monkeys (known as anthropoids) fit in the primate family tree. Some of the co-authors on the new paper have argued in the past that an extinct group of primates called adapiforms gave rise to anthropoids. Others have favored a common ancestry with small primates known as tarsiers. (Laelaps has a nice history of the debate.) The authors of the new paper argue that Darwinius is an adapiform, but it also has traits that link it with  anthropoids. So, according to them, it’s an early relative of our own anthropoid lineage.

Both Fleagle and Beard were not impressed with this argument. Fleagle observed that, ironically, most of the evidence presented in the paper is old news. Except for the ankle and a few other traits, most of the traits offered to link adapiforms to anthropoids “have been known for decades,” said Fleagle. It’s nice to have those traits all in one primate fossil, but they don’t advance the debate. Fleagle is intrigued by the anthropoid-like ankle of the fossil, but he also notes that it’s “roadkill,” flattened down to a 2-millimeter pancake. He wonders whether their interpretation of the ankle will hold up to scrutiny.

Beard has similar things to say via email.

I’ve been deluged today by journalists regarding this. It is a marketing campaign for the ages. The fossil is nice because it is so complete, but it is a rather vanilla-flavored adapiform that does not differ appreciably from other members of that well-known group of Eocene primates…

Beard was also puzzled that the authors did not compare Darwinius to an important early anthropoid fossil Beard found, known as Eosimias. In fact, he was underwhelmed by the entire comparison of Darwinius to other primates (a phylogenetic analysis):

The phylogenetic analysis is not very complete, and I would certainly interpret many of the characters they do cite very differently than they do. But one of the most shocking things of all about the technical paper is that they found room to cite 89 references, but there is not one mention of Eosimias to be found there. This is bizarre indeed. In a paper that purports to tell us something about anthropoid origins, the authors have conveniently ignored the single most significant fossil that has been published to date. Incomprehensible.

We certainly haven’t heard the last of Darwinius–on that, even the critics agree. But let’s hope that we’ve heard the last of the Holy Grail.

[Title from the great Tom Waits: lyrics, video]

[Image: PLOS One]

Update: In response to comments from Kilian and Brett, I thought I’d add a little more detail here on the evolutionary relationships the authors argue for in the paper. Scientists have long split the primate order into two suborders: strepsirrhines and haplorhines. Strepsirrhines included lemurs, galagos, and a few other species, which all share certain traits, such as a wet nose (the root of the name strepsirrhine). Monkeys, apes, and tarsiers are typically included in the Haplorhines. The Darwinius team argues that their new fossil, Darwinius, is more closely related to haplorhines (which includes monkeys and apes) than it is to strepsirrhines. Therefore, it (and other adapiforms) are ancient relatives of monkeys and apes.

Brett wondered whether there was a tree in the paper. There is, and thanks to PLOS’s open access policy, I can post it right here:

darwinius-tree440.jpgA couple points here:

1. They need to fix the typo in Strepsirrhini.

2. This is what Beard would call “not very complete.” Three branches makes for a pretty bare tree, especially when you consider that there are a fair number of early primate fossils known at this point. Fleagle pointed out to me that there are some early anthropoid fossils that lack some of the traits that supposedly join Darwinius to anthropoids. This could all be sorted out with a detailed phylogenetic analysis, which no doubt someone will carry out. The authors of the study get kudos from Fleagle for providing so much anatomical detail and high-resolution images of the primate, because that will enable lots of scientists to take their own stab at placing Darwinius in the primate tree.