Tag: Darwinius

New australopithecine described

April 8, 2010 • 11:26 am

by Greg Mayer

Lee Berger of the University of the Witwatersrand and several colleagues will be describing a new species of Australopithecus, A. sediba, from 1.78 to 1.95 million-year-old deposits in South Africa, in tomorrow’s issue of Science. The issue will also have a geological article on the find by Paul H.G.M. Dirks of James Cook University, Queensland, and colleagues, and a news item, all available now at Science‘s website (plus a podcast and video). The description is based on two partial skeletons, including a well preserved juvenile skull, most of the right arm and shoulder girdle, parts of the hip and leg, and various other bits.

Skull of juvenile Australopithecus sediba. Image from University of the Witwatersrand.

The new species has a long arm, but the pelvis and leg indicate that it was bipedal (i.e. it could both climb and walk upright). The general evolutionary conclusion the authors draw is the mosaic nature of the origin of Homo features: some Homo-like characters evolved before others, e.g. bipedality preceding cranial enlargement. They find specific features linking the new species to Homo, and posit it to be intermediate between earlier australopithecines and Homo:

The age and overall morphology of Au. sediba imply that it is most likely descended from Au. africanus, and appears more derived toward Homo than do Au. afarensis, Au. garhi, and Au. africanus.

Something I rather liked about the paper is that it is quite data rich, having tables of comparison of traits and measurements of the new find and several other fossil hominids. Such data-richness is unusual for papers in Science, which prefers short papers, with data often being relegated to electronic appendices or other papers; the Berger et al. paper is an unusual ten pages long.

The news has already reached media websites (e.g. the New York Times, the BBC and the Telegraph). Unlike the case of Darwinius masillae, however, in which premature press coverage, which included the name and its diagnostic characters, and web posting of the description, led to questions about the proper authorship and publication of the name, the authors and journalists in this case have done everything right. The news accounts are appearing coincident with the name being published (i.e. printed on paper), not prior to its publication. (The newspaper pieces linked to above are online now, but they won’t be published in the sense of the International Code of Zoological Nomenclature until tomorrow, when the scientific paper itself will be published.) There will thus be no questions about the publication of the name; the authors have made sure that, as the ICZN recommends, Australopithecus sediba is “self-evidently published within the meaning of the Code” (ICZN, Rec. 8B)

Darwinius, the “link” and the book

July 4, 2009 • 12:50 pm

Over at the Times Literary Supplement, paleontologist Ian Tattersall reviews Colin Tudge’s new book on Darwinius, The Link.

As you may remember if you read this and other evolution-related websites (see Greg Mayer’s post on this site), Darwinius masillae is an extraordinarily complete primate fossil that was revealed to scientists and the public in May, complete with a paper in PLoS,  overheated press releases, a movie deal on the History Channel, and, of course, Tudge’s book.  What was truly remarkable about this affair was the degree of hype: a publicity explosion that has never been equaled by any evolution-related discovery (indeed, even the completion of the human genome did not receive such fanfare).  Mayor Bloomberg was there, a press release touted Darwinius (known more familarly as “Ida”) as “a revolutionary scientific find that will change everything” (everything??), and one of the authors of the Darwinius paper, Jens Franzen, proclaimed that “When we publish our results it will be like an asteroid hitting the Earth.”

Well, hardly.  Ida turned out to be a really lovely fossil that didn’t add much to our knowledge of primate evolution.  It is almost certainly an adapiform primate, member of a group that went extinct without leaving descendants, and the early reports that Ida was a “missing link” between the two branches of primates were premature and based on incomplete and sketchy analysis by the scientists who described her.  Ida probably belongs firmly in the lemur/loris group.

Several of the science bloggers realized this immediately, although most reporters swallowed the “missing link” description uncritically (to be fair, they are not primate paleontologists).   The whole sorry affair resulted from the agreement between Ida’s discoverers and the publicists to prevent any scientists other than the “dream team” (that’s what Tudge calls them) from looking at the fossil or the research before publication, and blacking out journalists’ access to the paper until after the big press conference.  In the end, it was the bloggers like Brian Switek, and a few intrepid science journalists like Ann Gibbons and Carl Zimmer, who put Ida in the correct perspective.

According to Tattersall’s review, The Link looks as hyped-up and tendentious as were the original announcements.  The book was apparently written in only a couple of months so that it would appear the day after the press conference:

Colin Tudge’s book is part of the media blitz; and, at the risk of damning it with faint praise, I have to say that it is much the best part. It is more restrained and judicious than the other coverage; and while it does strictly hew to the party line, the hyperbolic statements it makes are always carefully attributed to others. To that extent, it is a thoroughly professional job, as one would expect of a distinguished interpreter of science to the public. . .

If The Link deserves a prize of any kind, it is for the speed with which it was written. Your reviewer has it on good authority that the television producers were still trawling around the Book of Ida project as late as January of this year; and Tudge evidently found he could not meet the almost impossibly short time constraints imposed by the TV schedule without co-opting the assistance of his colleague Josh Young. In combination with deadline pressure, this co-authorship presumably helps to explain a pattern of minor and generally harmless inconsistencies and inaccuracies throughout the book that might have been resolved with more time for reflection. It was hard, for example, to credit that the same author could have written on page 13 that “dinosaurs and mammals had coexisted briefly”, and (correctly), later on, that “the oldest known mammals could be older than the first dinosaurs”. And, in a note at the end of the book, we learn that he didn’t.

In this rather unseemly rush to publication, Tudge and Young were not alone. Speed, as well as obsessive secrecy, seems to have infected the entire Ida project from its inception. As reported by Nature, a member of the Dream Team complained that “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”. I’m sure it’s not how Colin Tudge likes to write books, either.

Let’s just say that my own opinion is along the lines of Tattersall’s, but less charitable. More about that later.

Darwinius: what’s at issue?

May 21, 2009 • 3:10 pm

by Greg Mayer

I’m leaving in a few days for Costa Rica, and Jerry is back, so this will be my last post on Darwinius, at least for awhile. At least three different issues have been debated in the blogosphere concerning “Ida“: 1) What are her phylogenetic relationships; 2) Was the media campaign excessive; and 3) Has the name been published?

Darwinius on toast1) What are her phylogenetic relationships? This is the most important one, because it is, as John Maynard Smith once put it, about the world, and not about names. Is Darwinius close to the common ancestor of monkeys, apes, and men, or is it a member of the group that includes lemurs and lorises? The question has been raised and discussed most forcefully by Brian Switek at Laelaps, who thinks the evidence presented for relationship to monkeys and apes is weak. To my mind (and I’m not a specialist in primates or even mammals), he’s got a strong point, and we can look forward to a publication by Brian (or some other critic) on this issue.

2) Was the media campaign excessive? The short answer is yes. I expressed some uneasiness over the media campaign here at WEIT, and many others have documented the extravagant claims and consequent media misunderstandings further. See especially what Carl Zimmer had at the Loom, Brian at Laelaps, and PZ Myers at Pharyngula. But by far the best (or at least funniest) take on this was Ed Yong’s satirical evisceration of the inflated media campaign at Not Exactly Rocket Science, from which I have been kindly permitted to reproduce the by now iconic “Darwinius on Toast” above. There are many unresolved questions concerning how to present science to the public, and differing views concerning how aggressive a media campaign should be, but this one was at least one step beyond.

3) Has the name been published? This is the most technical issue, and is about names (rather than the world), but it’s attracted the most attention. See the posts here at WEIT, the Loom (and here), the Lancelet, and Laelaps, including the ensuing commentary by, among others, Henry Gee, Martin Brazeau, and Larry Witmer. There are several issues, and I’ll treat them very briefly (since this is a blog post, and not a paper in the Bulletin of Zoological Nomenclature!).  For reference, The International Code is online here.

3a) Has the name Darwinius masillae been published (in the sense of the Code) in Plosone? No. Many people have noted that Art. 8.6 requires non-paper works to be deposited in 5 major libraries, and that a statement to this effect must be included in the paper. No such statement is in the paper. More importantly, although it has been noted in only one comment I’ve seen, Art. 9 goes on to specify that nothing distributed by the web counts as being published. The non-paper works envisioned in Art. 8 are things like CDs, not web postings. So, the various remedies proposed, such as reposting on Plosone with the requisite statement, would not work. To be published, a non-Web work must be made: paper, CD, DVD (the latter two requiring the fulfillment of the 5 major libraries rule), or something else which satisfies Arts. 8 and 9.

3ai) Can the name be made available by publishing a short paper (on paper) with a bibliographic reference to the Plosone posting? No, because availability by bibliographic reference must be by reference to a published work (Art. 13.1.2), and anything on the Web is not published (Art. 9.8).

3b) Has the name been published elsewhere? I hope not, but fear it may have been. I pointed out that the various newspaper articles may count as publication, because they meet the various criteria for publication (obtainability, simultaneity, etc.; Art. 8), and also contain 1) the name, and 2) are “accompanied by a description or definition that states in words characters that are purported to differentiate the taxon” (Art. 13.11), and even follow Recommendation 13A: “a summary of the characters that differentiate the new nominal taxon from related or similar taxa.” Many newspaper articles, in addition to a general description, included explicit differentia– incisors, grooming toes– from related taxa, thus providing a diagnosis.

3bi) Can newspapers provide a public and permanent scientific record? In my post, I considered that the newspaper articles might be discounted, because perhaps they had not been issued “for the purpose of providing a public and permanent scientific record” (Art. 8.1.1). Some commenters have taken the position that this is self-evidently the case, but it’s not crystal clear to me.  The Code has always been loath to mandate specific formats of publication, specifying rather general properties (availability, simultaneity, identity, etc.) that a variety of formats might fulfill.  Historically, a huge variety of things have counted as publications (although no newspaper examples come to mind). Some newspapers have science sections, some are “papers of record”; I think the spirit of the Code is to approach each case on its individual merits. That is why the Code urges authors and editors to avoid anything that might make the situation murky, but it does so through recommendations (see my previous post for the specific recommendations).

3bii) Doesn’t the Code try to avoid “accidental” publication? Yes it does, as several commentators have pointed out. It has added meeting and symposium abstracts to the list of formats that are not permissible (Art. 9.9) to help avoid what the Code calls “unintentional publication”; but newspapers, as such, are not mentioned. The Code also now requires that the intention to establish a new name be explicit (Art. 16.1). This article is intended to prevent new names, especially a replacement name (nomen novum) to be introduced without mention, en passant if you will. Unfortunately, the newspaper articles make it absolutely clear that a new nominal taxon has been discovered and is being given a new name, and that this is the intention of the authors (on which, see next paragraph).  The Daily Mail article even uses the word “christened”. The Code urges authors to use “sp. nov.” or some other appropriate indication (Rec. 16A), but, again, does not require it. The Code recommends that any appearance of a new name in a work prior to its intended publication be accompanied by a disclaimer, making the new name unavailable (Art. 8.2 and Rec. 8D). The Daily Mail article contains the phrase “a scientific study to be published”: this might be taken to be such a disclaimer, and while it’s not as clear as one might want, it’s perhaps the most straightforward way of discounting the Daily Mail article. Such phrases may (or may not) appear in the other newspaper articles.

3biii) If it has been published elsewhere, who is the author of the name? The Code provides that when it is clear from the contents of a publication that the name and the conditions that make it available other than publication (i.e. the description or diagnosis) are the work of a person(s) other than the author of the publication, then the author of the name is the other person (Art. 50.1.1). In this case, the newspaper articles make clear that the name and its description were provided by someone else, many mentioning Jorn Hurum and Phil Gingerich. They (or whoever is mentioned in the earliest article published) are thus the authors.  This is a good thing, because it gives credit to at least some of the people actually involved in the work. The newspaper reporter would not be the author of the name.

To summarize the question of publication, the name has not been published in Plosone, but it may have been published in a newspaper. I hope the latter is not the case, and perhaps the Commission could issue a clarifying opinion (following an appropriate application) on the status of names published in newspapers (the problem may be distinguishing newspapers from newsletters from cheaply printed bulletins, and so on).

There are some other issues that have been discussed– the merits of paper vs. the web, the nature of peer review– but these go well beyond the particulars of Darwinius, although it might provide a case study for some of these issues. But one of the take home lessons here is that the recommendations of the Code should be taken to heart, and authors and editors should ensure that works affecting nomenclature are “self-evidently published within the meaning of the Code“(Rec. 8B), and that new names should not appear in works prior to their intended publication, or, if they do, they should “contain a disclaimer (see Article 8.2), so that new names published for the first time therein do not enter zoological nomenclature unintentionally and pre-empt intended publication in another work” (Rec. 8D).

Update. While I was writing this, Carl Zimmer got a reply from the Executive Secretary of the ICZN. She confirms that posting on Plosone does not make a name nomenclaturally available. The issue of the newspaper publication was not addressed; I’m not sure if Carl asked about this. I’m leaning myself toward the idea that inclusion of the statement that the study is going to appear somewhere else could be construed as a disclaimer, thus avoiding newspaper publication of the name (I’m still not sure that all newspaper articles included such a statement).

Update 2. Carl Zimmer at the Loom has a nice account of the PR run-up to the press conference, which he titles “Science Held Hostage“. And, also from Carl, Plosone has today printed a 50 copy paper edition. If we can dismiss the newspaper versions (which, as I indicate in my first update, I think we can because they can be plausibly interpreted to have a disclaimer), then the name is now published with the intended authorship; the date of publication is 21 May 2009 (not 19 May, which is when it was posted to the web). Carl also succinctly explains why the nomenclatural rules are necessary:

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.

Has the name Darwinius masillae been published? And if so, by who?

May 20, 2009 • 1:27 pm

by Greg Mayer

In a previous post on the hype surrounding the online posting of a paper on ‘Ida’, the Eocene primate from the Messel Lagerstatte, I noted that the

from Hurun et al. 2009. Plosone. www.plosone.org
from Franzen et al. 2009. Plosone. http://www.plosone.org

authors had made a nomenclatural faux pas in allowing the name and a description to be published before their paper appeared, thus making the authorship and date of publication of the name murky. At Laelaps, cromercrox (comment 35 here and comment 16 here), and at the Loom, Martin Brazeau and Larry Witmer (comments 27 & 29) have also noted nomenclatural problems, since online posting does not constitute publication under the International Code of Zoological Nomenclature, unless copies “have been deposited in 5 major publicly accessible libraries which are identified by name in the work itself”, (ICZN 8.6), which didn’t happen. As posted by Plosone, the paper is not published for nomenclatural purposes.

My concern was not that the name was unpublished, but that it had already been published, in one or more of the newspapers or perhaps even magazines that covered the pre-press conference hoopla. In the Code, Article 8 defines publication, Articles 10 and 11 cover general conditions of availability of a name, and Article 13 gives the particulars for names published after 1930 (the rules are stricter after 1930). The requirements may be summarized by saying that a proper new name must be published (sensu Article 8), and must “be accompanied by a description or definition that states in words characters that are purported to differentiate the taxon” (ICZN 13.1.1). I fear these requirements have been met by some of the pre-press conference articles.

The earliest one I have found is the one in the Daily Mail from May 10 (there may be earlier ones– I haven’t looked very hard). (I also don’t have a paper copy, and am assuming the web article appeared in the paper.  If it didn’t, I could illustrate the exact same points for the New York Times, for which I do have paper copies.) In the article, by Sharon Churcher, the name appears:

Christened Darwinius masillae, it belonged to an extinct group of primates which lived in rainforests.

It also includes characters that are purported to differentiate the taxon:

The study’s authors insist that the fossil can’t be a lemur because it lacks two features: the ‘toothcomb’, a set of lower front teeth used to groom fur; and ‘toilet claws’, toes on the hind feet used for scratching.

The Mail is also mass produced in identical copies obtainable for free or by purchase, publicly available, and permanently archived in many libraries. So it looks like the name has been published.  The one possible out is that you could argue that the Mail isn’t issued for the purpose of providing a scientific record, but purposes are slippery things. Does a newspaper with a science section (which is of course quite purposeful) meet the requirement, but perhaps one without doesn’t? I don’t know. That’s why it’s murky. It is to avoid murkiness that the Code makes Recommendation 8B:

Authors and publishers are strongly urged to ensure that a new scientific name or nomenclatural act is first published in a work printed on paper.

also Recommendation 8D:

Authors, editors and publishers have a responsibility to ensure that works containing new names, nomenclatural acts, or information likely to affect nomenclature are self-evidently published within the meaning of the Code. Editors and publishers should ensure that works contain the date of publication, and information about where they may be obtained. (emphasis added)

and Recommendation 8E:

Editors and publishers should avoid including new names and the information that might appear to make the names available, or new nomenclatural acts, in works that are not issued for public and permanent scientific record (such as pre-symposium abstracts, or notices of papers to be delivered at a meeting). They should ensure that such documents contain a disclaimer (see Article 8.2), so that new names published for the first time therein do not enter zoological nomenclature unintentionally and pre-empt intended publication in another work. (emphasis added)

But it looks to me like the Mail (or the Times, or whoever published it first) is the first valid publication of the name. The Code provides that the author of a name need not be the author of the work:

However, if it is clear from the contents that some person other than an author of the work is alone responsible both for the name or act and for satisfying the criteria of availability other than actual publication, then that other person is the author of the name or act. If the identity of that other person is not explicit in the work itself, then the author is deemed to be the person who publishes the work. (ICZN 50.1.1; emphasis added)

Jorn Hurum and Phil Gingerich are mentioned in the article as people who did the work, with Hurum given precedence.  So what’s the proper citation of this new taxon? It’s

Darwinius masillae Hurum and Gingerich in Churcher 2009.

Paleontology and the media

May 19, 2009 • 12:15 am

by Greg Mayer

The New York Times is reporting some major media event at the American Museum of Natural History on Tuesday concerning a 47 million year old primate fossil from Germany.  There’re reports of secrecy, exclusivity, and high priced documentaries. It seems a tad curious, since by available reports, the American Museum has nothing to do with the research or the fossil, which is in the collection of the Natural History Museum in Oslo, and the fossil was already reported on by the Times a few days ago and by the Daily Mail over a week ago. The fossil is from the Messel shale an important lagerstatte. Keep an eye out for the reports later today.

(PS The American Museum has what seems to be a really neat new mammal exhibit, reviewed here.  If you’re in New York, go see it.)

Update. The press conference has been held. The BBC has a few videos here. The specimen is a very well preserved, nearly complete, articulated skeleton, with remnants of fur and stomach contents (as is often the case in specimens from the Messel Lagerstatte), of a basal higher primate (i.e. near the ancestry of monkeys, apes, and man). The authors of the paper made a taxonomic faux pas in allowing the name of the new creature, along with a description, to be published prior to the appearance of their paper. The authorship of the name, and its date of publication, are now murky.

Update 2. As I feared, a big media roll out is not always conducive to getting the story right.  Just now on the Rachel Maddow Show, the features reporter said that the new primate might be the missing link between man and ape. It is of course nothing of the sort, and the authors never said it was, but using the term “missing link” as the key descriptor of the find (see the Daily Mail link above for an example) was bound to lead to some such misunderstanding. He also stressed that it could be “upright”, which many may take to mean bipedal, but, of course, it wasn’t. Laelaps and PZ concur about the doleful effects of the media hype. More from Laelaps here. The hype is even more overheated than I realized: from the promoters: “WORLD RENOWNED SCIENTISTS REVEAL A REVOLUTIONARY SCIENTIFIC FIND THAT WILL CHANGE EVERYTHING | Ground-Breaking Global Announcement”. Money quote from Laelaps:

I have the feeling that this fossil, while spectacular, is being oversold. This raises an important question about the way scientific discoveries, particularly fossil finds, are being popularized. Darwinius is just the latest is a string of significant fossils to be hyped in the media before being scientifically described (or at least before that information is released to the public). Other recent examples include “Dakota” the Edmontosaurus, the pliosaur “Predator X“, and “Lyuba” the baby mammoth. I am glad that these finds are stirring excitement, but I am a bit put off by the way they are presented.

Update 3 (May 20). Carl Zimmer and Ed Yong add to the critical pile on. A sample of Ed Yong’s wonderful satirical evisceration:

Around the world, signs that everything has changed have already begun to appear. Jeanette Gould from Stoke-on-Trent was shocked to discover the outline of Darwinius emblazoned on her morning toast. “Well, it ruined breakfast,” said Ms Gould, failing to appreciate the detail of the creature’s stomach contents outlined in bread crumbs. “I couldn’t very well spread raspberry jam over the direct ancestor of my children, could I?”

There is a wonderful accompanying illustration of the piece of toast.