Why Evolution is True is a blog written by Jerry Coyne, centered on evolution and biology but also dealing with diverse topics like politics, culture, and cats.
Earlier this year my friend Chris Noto and his colleagues Derek Main and Stephanie Drumheller published a paper describing injuries to turtle and dinosaur bones from the Cretaceous that show evidence that they were preyed upon by crocodiles. Besides the irresistible alliteration, their paper serves to show that we can sometimes learn much more about extinct animals than merely their skeletal morphology, and, with the right sorts of evidence, can learn about their behavior, ecology, and physiology as well.
The fossils were recovered at a site in Texas known as the Arlington Archosaur Site. Modern crocodilians feed on turtles, and also on dinosaurs, if you think of birds as dinosaurs (which, in a sense, they are). They will seize turtles side to side (as shown in the reconstruction) or top to bottom. American alligators are particularly fond of turtles, and, compared to some other crocodilians, their rear teeth are especially blunt and peg-like (sort of like molar teeth). This helps to crush the shells of turtles they are eating (which, I have been told, break with a popping sound). E.A. McIlhenny, the great naturalist of hot sauce fame, wrote:
I have seen alligators catch large terrapins and turtles of considerable size and crush their hard shells as if they were made of paper, swallowing them whole.
Tooth scars on a turtle shell (above) and a dinosaur leg bone (below).
Noto et al’s study is a nice example that shows we can learn about more than just the morphology of extinct creatures, but can also learn about thier biology and the paleocommunities they lived in, including (in other studies) ecology, behavior, and even color (see, for example, Matthew’s recent post here, and earlier posts by Jerry here and here).
McIlhenny, E.A. 1935. The Alligator’s Life History. Christopher Publishing House, Boston. (Reissued in a facsimile edition in 1976 by the Society for the Study of Amphibians and Reptiles, with a foreword by the great herpetologist and conservationist, Archie Carr.)
Noto, Christopher R., Derek J. Main, and Stephanie K. Drumheller. 2012. Feeding traces and paleobiology of a Cretaceous (Cenomanian) Crocodyliform: Example from the Woodbine Formation of Texas. Palaios 27:105-115. (abstract)
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?
1) 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 (seeArticle 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.
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.
In the latest issue of Nature is a report on a pretty amazing transitional fossil: Pulija darwini, a relative of modern seals, but one that was a “pre-seal” in that it walked on land. It was related to but not on the direct line of ancestry to modern pinnipeds. Pujila appears to have been much like a large otter. It’s already been covered amply on several other blogs, so I’ll just refer you to the official Pujila website (be sure to manipulate the three-dimensional model and the three dimensional skull), which has all the information, and a disquisition on the beast on Ed Yong’s blog Not Exactly Rocket Science.
Reconstuction of animal from Pujila website, reconstruction of skeleton from Nature paper
A semi-aquatic Arctic mammalian carnivore from the Miocene epoch and origin of Pinnipedia
Natalia Rybczynski, Mary R. Dawson & Richard H. Tedford
Summary of the article: Modern pinnipeds (seals, sea lions and the walrus) are semi-aquatic, generally marine carnivores the limbs of which have been modified into flippers. Recent phylogenetic studies using morphological and molecular evidence support pinniped monophyly, and suggest a sister relationship with ursoids (for example bears) or musteloids (the clade that includes skunks, badgers, weasels and otters). Although the position of pinnipeds within modern carnivores appears moderately well resolved, fossil evidence of the morphological steps leading from a terrestrial ancestor to the modern marine forms has been weak or contentious. The earliest well-represented fossil pinniped is Enaliarctos, a marine form with flippers, which had appeared on the northwestern shores of North America by the early Miocene epoch. Here we report the discovery of a nearly complete skeleton of a new semi-aquatic carnivore from an early Miocene lake deposit in Nunavut, Canada, that represents a morphological link in early pinniped evolution. The new taxon retains a long tail and the proportions of its fore- and hindlimbs are more similar to those of modern terrestrial carnivores than to modern pinnipeds. Morphological traits indicative of semi-aquatic adaptation include a forelimb with a prominent deltopectoral ridge on the humerus, a posterodorsally expanded scapula, a pelvis with relatively short ilium, a shortened femur and flattened phalanges, suggestive of webbing. The new fossil shows evidence of pinniped affinities and similarities to the early Oligocene Amphicticeps from Asia and the late Oligocene and Miocene Potamotherium from Europe. The discovery suggests that the evolution of pinnipeds included a freshwater transitional phase, and may support the hypothesis that the Arctic was an early centre of pinniped evolution.
I think I’ve been able to figure out why chemist Philip Skell’s attack on Jerry in Forbes was so unresponsive to what Jerry actually wrote: he probably wrote most of it before seeing Jerry’s article! P.Z. Myers noted a piece in the Eugene, Oregon, Register-Guard by teacher Stuart Faulk rebutting Skell’s arguments. Addressing Skell’s claim that evolution is irrelevant to medicine, Faulk (who is Skell’s son-in-law!) does some research:
The contention that evolutionary science is not useful is easily shown false by counter-example. The necessary research is accomplished by walking the five feet to my coffee table and picking up the March edition of Scientific American magazine, in which the article “New Tactics Against Tuberculosis” describes progress against the spread of drug-resistant TB….As the authors state of one promising approach, “It allows us to harness the power of natural selection in our quest to thwart (drug-resistant TB).”
He also notes that Skell’s claim that for evolution to be relevant to medicine, then paleontology must drive its research agenda, is an “absurd idea”, “introduced by Skell, not evolutionary scientists.” Faulk goes on to note that Skell’s real concerns are religious, not scientific, as “any Web search will show”.
That Skell’s arguments are easily rebutted is not surprising; what is surprising is that Faulk was responding to something Skell wrote in the Register-Guard that appeared February 12, the same day as Jerry’s piece in Forbes, and 11 days before Skell’s piece in Forbes. The Register-Guard piece is only available on the web as an excerpt, but it seems to be much the same as what appeared in Forbes. You compare:
The Register-Guard, Feb. 12: “Darwin was great, but too often he’s oversold”
In 1942 Nobel Laureate Ernst Chain wrote explicitly that his discovery (with Florey and Fleming) of penicillin, and the development of bacterial resistance to that antibiotic, owed nothing to Darwin’s and Alfred Wallace’s evolutionary theories. The same can be said about a variety of other 20th century discoveries: that of the structure of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; and various new surgeries.
Forbes, Feb. 23, “The dangers of overselling evolution”
In 1942, Nobel Laureate Ernst Chain wrote that his discovery of penicillin (with Howard Florey and Alexander Fleming) and the development of bacterial resistance to that antibiotic owed nothing to Darwin’s and Alfred Russel Wallace’s evolutionary theories.
The same can be said about a variety of other 20th-century findings: the discovery of the structure of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; new surgeries; and other developments.
I can understand why Jerry found Skell’s Forbes piece off-point:
The curious thing is that Skell’s piece is not, as it pretends to be, a critique of what I said in Forbes, but merely a repetition of the argument, which he has been making for years, that evolution is of no practical use for humanity and of no use to experimental biology
The one thing I would add to these critiques of Skell is to point out his curious use of the phrase “experimental biology”, and his disdain for what he seems to consider unobservable or uncertain knowledge. He seems to imply that chemistry and “experimental” biology, are good science, because they are observable; other sorts of biology (i.e. evolution), and (if the apparent criterion is to be applied uniformly), geology and astronomy are not, because we have not seen a live trilobite, or Gondwanaland, or a star moving along the main sequence. Thus creationists seek not just to eliminate biology, but much of the rest of science as well. All knowledge in empirical science, including chemistry, is tentative; and the changes in the kinds of plants and animals you see as you travel up slope on a fossiliferous exposure are much more observable than any chemical bond.
In today’s issue of Science, Matthew Bennett and eleven colleagues from Britain, America, Kenya and South Africa report on the discovery of ancient footprints:
Here, we report hominin footprints in two sedimentary layersdated at 1.51 to 1.53 million years ago (Ma) at Ileret, Kenya,providing the oldest evidence of an essentially modern human–likefoot anatomy, … The Ileret prints show that by 1.5 Ma,hominins had evolved an essentially modern human foot functionand style of bipedal locomotion.
Although there were no directly associated fossils, the most likely maker of the prints was Homo erectus. In WEIT, Jerry discussed the famous 3.75 million year old Laetoli, Tanzania footprints, which established that our ancestors had walked bipedally since at least that time. The Laetoli prints, however were made by Australopithecus afarensis, and the newly announced prints are the oldest known for our genus, Homo (we are Homo sapiens), and Bennett et al. discuss the ways in which the Ileret prints indicate their makers had a more modern foot morphology than the makers of the Laetoli prints. Homo erectus had a smaller brain than we do, so we see a general pattern in the fossil record exemplified: mosaic evolution– different characters evolving at different rates. In this instance, we see an essentially modern foot, with a brain that is intermediate between Australopithecus and modern Homo. And, we see, once again, that intermediate forms occur at the times, and in the places, we expect them to on the hypothesis of descent with modification.
Update: A reader asks are the new prints from Homo erectus or Homo ergaster, two very closely related fossil species of Homo. Bennett et al. don’t claim one or the other, writing:
The large stature and mass estimates derived from the Ileretprints compare well with those of Homo ergaster/erectus on thebasis of postcranial remains and are significantly larger thanpostcrania-based stature and mass estimates for Paranthropusboisei and Homo habilis (table S3) (19–21), suggestingthat the prints at FwJj14E were made by Homo ergaster/erectusindividuals.
In media reports, other scientists, for example Daniel Lieberman of Harvard (quoted in the New York Times), have referred to the prints as from erectus. My own view is that the species taxonomy of fossil hominids is probably oversplit; if there is to be one name, it would, by priority, be erectus. The great Ernst Mayr wrote a paper in 1951 entitled ‘Taxonomic categories in fossil hominids’ (Cold Spring Harbor Symposia on Quantitative Biology 15:109-118), and it’s worth rereading; see also what Jerry had to say in chapter 8 of WEIT.
Phil Gingerich and his colleagues at the University of Michigan, the Geological Survey of Pakistan, and the University of Bonn have just described a brand new and intriguing pair of whale fossils in the journal PLoS ONE, which you can find here. Tis whale Maiacetus inuus, lived about 47.5 million years ago, which puts it roughly at the time of the fossil whale ancestor Rodhocetus (see pp. 50-51 of WEIT). Rodhocetus was probably an amphibious creature, living on both sea and land, and this is almost certainly true of the new find as well.
The really intriguing thing about Maiacetus is that the female fossil contained an embryonic individual, apparently near term. This is the first known example of a fossil embryonic whale. What’s more, the embryo was positioned with its head facing the rear, so that it would be born head first. That birth position is characteristic of land-dwelling animals (probably an evolutionary feature to allow the embryo to start breathing as soon as possible), but is not found in marine mammals. In the latter group, babies are born tail first, probably so that a.) they won’t drown during birth and b.) so that they are born in the right position to immediately bond with and start following their mother.
There are other interesting features of this whale, too, like the permanent first molar teeth in the fetus, indicating precocial development
From the structure of its limbs and body, Maiacetus obviously lived on both sea and land, since the hind limbs are still substantial but reduced. The position of the fetal whale shows that it did, however, give birth on the land. Just another link in the ever-growing chain of fossils documenting the evolution of whales.
1) 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 
