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.
Although it’s a problem that’s been around for years, the perception of the Republican party as anti-science is growing in response to presidential contender Gov. Rick Perry’s forceful embrace of climate denialism and creationism (see, e.g., pieces by Jonathan Chait, Kevin Drum, and Paul Krugman). Even a fellow Republican, presidential-contender-without-a-chance Gov. John Huntsman, tweeted “To be clear. I believe in evolution and trust scientists on global warming. Call me crazy.” Huntsman elaborated on ABC News:
The minute that the Republican Party becomes the party – the anti-science party, we have a huge problem. We lose a whole lot of people who would otherwise allow us to win the election in 2012. When we take a position that isn’t willing to embrace evolution, when we take a position that basically runs counter to what 98 of 100 climate scientists have said, what the National Academy of Science – Sciences has said about what is causing climate change and man’s contribution to it, I think we find ourselves on the wrong side of science, and, therefore, in a losing position.
When someone like Rick Perry – an avowed anthropogenic climate change and evolution denialist – is accused of rejecting science, it’s an attack on Perry’s epistemological beliefs rather than moral values. Even though the scientific consensus is clear on both questions, Perry refuses to accept both. By rejecting well-supported scientific truths on, say, theological grounds, he is implicitly denying that the scientific method (rather than, say, theological reasoning) is the best way to determine truths about the natural world. That’s what being “anti-science” is. Given that basically everything we know about the natural world comes from natural science, we can’t tell how Perry will evaluate basic scientific truths on a whole host of important issues. That’s a big deal.
[Yuval Levin] is using obscure conceptual arguments to shield genuinely ignorant people like Perry from criticism. …flat-0ut denying the theory of evolution or anthropogenic climate change. ..involves denying the fundamental epistemological values that undergird the scientific project. Little things like “science tells us more about physical and biological truths than theology.”
Although there’s much to disagree with Huntsman about on all sorts of issues (he’s very conservative), it’s a sign of how bad the Republican party has become that their pro-science candidate has next to no chance of winning the nomination, and being pro-science is part of why his chances are so slim. As Republican strategist Nick Walters put it, “That talk won’t fly in the south.”
Unfortunately for them [the thieves], staff at the Hertfordshire museum were aware of the string of thefts from other museums and auction houses, and had swapped the real rhino horns for carefully crafted fakes, almost indistinguishable from the real thing. And totally worthless.
Here’s one of the afflicted rhinos:
Black rhino (Diceros bicornis) at the Tring Musuem, from which thieves removed a fake horn. Photo issued by Natural History Museum.
The real horns are safe at the museum. The Associated Press provides a further account.
From the freethinker Magazine, we find that 200 portable, open-air confessionals have been set up in Madrid’s Retiro Park in honor of the Pope’s visit. I wonder if they’ll be used during the abortion holiday, when the Pope has granted a week of easy absolution for that mortal sin.
As the article documents, many Spanish are angry because the Pope’s visit will cost around 70 million dollars, most of it footed by pilgrims or Spanish businesses. But think how many lives that money could save if spent wisely in, say, Africa. And there will be other costs, too:
But critics are calling the claims ridiculous. Father Rodríguez [a Spanish priest who works among the poor] and others who signed the 10-page petition say the costs are always fuzzy when the Pope swans to town. They suspect that the cost of extra security, of collecting trash and of stress on health systems will add up to millions for taxpayers. For one thing, the pilgrims have been granted an 80 percent discount on public transportation, which some find particularly galling because subway fares just went up by 50 percent.
There are also reports that Spain is blocking public access to social media sites that could be used to plan counter-Pope demonstrations.
Most of you know about the threatening emails that Canadian Dennis Markuze, aka “Dave Mabus” sent to many atheists and scientists. I myself received hundreds of them, including death threats. When I asked others how to report them, I learned that Markuze had already been reported to the Montreal police, who apparently weren’t interested in messing with him so long as he sat in his mother’s basement and didn’t actually hurt anyone.
That, of course, has changed. Carl Zimmer, P. Z. Myers, and others made serious complaints, there was a petition signed to the police, and, finally, the police themselves lured Markuze into attacking their own Twitter account. Ars Technica has the whole gory tale of his capture and arrest.
And, as far as anyone could tell, the complaints went nowhere. The local authorities weren’t interested in acting, and most of Mabus’ targets didn’t even live in Canada. That eventually changed, in part due to Mabus’ lack of discretion when it came to choosing his targets. One of Zimmer’s tweets apparently caught the attention of William Raillant-Clark, who handles press for the University of Montreal. Calling the inaction “unacceptable,” Ralliant-Clark began investigating the story and placed his results on Tumblr; he also included the Montreal Police’s press account on Twitter in some of the conversation.
Here’s where Mabus’ thoroughness backfired. Noticing the Twitter conversation between Ralliant-Clark and his former victims, he added the journalist to his target list. And, since the Montreal police’s Twitter account was also mentioned, it got a copy too. Mabus actually started sending diatribes to the local police force.
He’s a sick man, and I hope he gets the help he needs. But really, the Montreal Police should have taken action long before this. How many death threats does it take before someone gets investigated? Or do they have to wait until those threats are actually carried out?
After six months of languishing at Science Online Express, the “Arsenic Paper“, by Felisa Wolf-Simon et al. (full reference below), has finally appeared online. It also appears with eight “technical comments”—criticisms of the methodology and results—a response by the authors, and a note by editor Bruce Alberts (all of these are at the link, though I think there’s a paywall for the original paper).
As you remember, this paper attracted huge attention because of its claim that a bacterium growing in Mono Lake, California was able to incorporate arsenic instead of phosphorus into its DNA and proteins. This in turn led to all sorts of speculations about whether life could have evolved in places (or on planets) that had different arrays of chemicals, or even more than once on Earth. There was a press conference and a lot of hoo-haa promulgated by the authors, including a press conference and a TED talk and Glamour Magazine interview with Wolf-Simon. At the same time, a lot of critics began to weigh in with serious questions about the paper’s results, with some researchers declaring it fatally flawed. Bloggers, scientists, and journalists, such as the Philadelphia Inquirer’s Faye Flam, all noted problems with the paper. And I don’t recall anybody other than the authors defending it.
It’s extremely unusual for a paper to be delayed this long, and then to appear simultaneously with its critiques. Usually the paper is published and then the critiques (with a response by the authors of the original paper) appear in the journal a few months later. Alberts’s note doesn’t do much to clarify the situation:
The Research Article “A bacterium that can grow by using arsenic instead of phosphorus” by F. Wolfe-Simon et al. [p. 1163, (1)] was the subject of extensive discussion and criticism following its online publication. Science received a wide range of correspondence that raised specific concerns about the Research Article’s methods and interpretations. Eight Technical Comments that represent the main concerns, as well as a Technical Response by Wolfe-Simon et al., are published online with this issue . . .
. . . We hope that publication of this collection will allow readers to better assess the Research Article’s original claims and the criticisms of them. Our procedures for Technical Comments and Responses are such that the original authors are given the last word, and we recognize that some issues remain unresolved. However, the discussion published today is only a step in a much longer process. Wolfe-Simon et al. are making bacterial strain GFAJ-1 available for others (2) to test their hypotheses in the usual way that science progresses.
But what happened is pretty obvious. After the blow-up around the paper’s release, Science realized that they screwed up. Their way of making amends was to delay the paper—after all, they couldn’t reject it after it had already been accepted—and publish it simultaneously with the critiques. Having read them, and the authors’ response, you can easily see that the paper wasn’t properly reviewed in the first place. Too many questions remain about the technique, the statistics, and the results. Even I, a biologist far removed from biogeochemistry and microbiology, can see that the paper wasn’t thoroughly vetted.
Over at Slate, Zimmer weighed in again on Friday with an analysis of the scientific sociology of this paper.The big lesson he draws is that we’re entering a new era of science, in which papers can be made or destroyed by post-publication review by blogging scientists:
Redfield [Rosie Redfield, a vociferous critic of the paper] and her colleagues are starting to carry out a new way of doing science, known as post-publication peer review. Rather than leaving the evaluation of new studies to a few anonymous scientists, researchers now debate the merit of papers after they have been published. The collective decision they come to stays open to revision.
Post-publication peer review—and open science in general—is attracting a growing number of followers in the scientific community. But some critics have argued that it’s been more successful in theory than in practice. The #arseniclife affair is one of the first cases in which the scientific community openly vetted a high-profile paper, and influenced how the public at large thought about it.
I think post-publication review is all to the good. Let a thousand voices blossom—even if some of them are misguided. In the end, it’s science, and the truth will out. In the meantime, immediate online criticism is the only way to counteract the hype and p.r. that often attend the release of hot new papers—hype intensified by clueless journalists with no training in science.
The whole thing reminds me of the Darwinius affair, in which a primate fossil was touted as a missing link between the two major groups of primates. There was a lot of buzz and an authorial press conference. Science bloggers raised serious questions and, sure enough, more careful research showed that the vaunted fossil wasn’t a “link” at all. In this era of tight money and lots of scientists competing for attention, the ability to call immediate online attention to problems with high-profile research can only be a boon.
You should begin to get worried about a paper when its authors (Wolf-Simon here, in a video for Dutch television) characterize their results, before publication, like this: “If my hypothesis proves to be true, it will fundamentally alter our understanding of being alive.” Even if the arsenic hypothesis did prove to be true—and I suspect it won’t—it will have miniscule effect on our understanding of being alive. Sheesh!
All I can say is that I didn’t make a penny, and that O.J. is now where he belongs.
I worked on many DNA-based cases in the 1990s; my expertise involved making sure that the prosecution used DNA evidence properly in its population-genetic calculations. The state often got the calculations—the “match probabilities”— completely wrong, biasing the data against the defendant. (A “match probability” must be calculated when the defendant’s DNA matches other DNA-based forensic evidence, like blood or semen at the crime scene. It involves comparing the defendant’s genotype with that of a “random” sample of the population, calculating the probability that the defendant-forensic match could have occurred just by chance. This involves principles that are common in evolutionary genetics.)
I ensured that these calculations were correct and, if I had to, took the stand to explain to judges and juries how match probabilities should be calculated. Try telling a jury of regular people, who barely know what DNA is, how to calculate Hardy-Weinberg equilibrium! That was a tough job.
My philosophy here was to make sure that my field was not corrupted by zealous prosecutors trying to secure convictions based on faulty calculations. Everyone deserves a fair trial, even rich and odious people like O.J. Almost all the cases I worked on, however, involved poor defendants who could not afford lawyers, and were represented by public defenders who were completely baffled by statistics. I took money in only the first case I dealt with, here in Illinois, and then decided that my testimony would look less “tainted” were I to work for free. So I did. But that tactic, of course, was also attacked by prosecutors: they would ask me, when I was on the stand, “Why aren‘t you taking money, Dr. Coyne? Are you on some kind of crusade or something?”
I have always thought that the hardest thing I’ve had to do in my professional life was to get on the stand in a murder trial, trying to deal with prosecutors who were more interested in convictions than truth, and who were determined to destroy my testimony any way they could. It’s nerve-wracking, for you know that somebody’s life is at stake. Next to that, a big symposium talk or a grant proposal is a piece of cake! Fortunately, I didn’t have to testify in the O.J. case.
People ask me how I could work for O.J., who seemed pretty obviously guilty. My answer is that I wasn’t concerned with his innocence or guilt, but with whether DNA data were presented properly to the jury. And of course everyone, rich or poor, deserves that kind of expertise. I worked for free on that case, too, though I could have made a pile.
Have pity on the poor defendants who can’t afford experts! One thing you quickly learn from this kind of experience is that there is different “justice” for the rich and poor.
Lizards are far and away the most species-rich group of living reptiles, with over 7000 species. One of the first things you learn if you’re a little boy interested in such creatures is that snakes are lizards. One of the other things you learn is that snakes are not the only group of legless lizards. There are, in fact, many groups of lizards with reduced or missing legs, such as the European slow worm and American glass snakes (now preferably called glass lizards). Snakes are just the most evolutionarily successful such group of lizards, comprising 3000 or so of the species of lizards. One of the most distinctive of the non-snake legless lizards are the worm lizards, or amphisbaenians, a group of about 150, mostly tropical, burrowing species. Perhaps our greatest student of the group, the late Carl Gans, thought them so distinctive that he championed a classification in which they were ranked equally with lizards and snakes within the Squamata (the taxon which includes lizards and all their derivatives, including snakes and amphisbaenians), although most other workers did not accept this ranking.
A worm lizard, Amphisbaena sp.
Gans wrote in his Biomechanics (he was a functional morphologist and physiologist as well as a systematist) that:
Unfortunately, we lack fossils intermediate between the Amphisbaenia and other groups, and can only speculate what their ancestors looked like.
A paper published in Nature today by Johannes Muller and colleagues (abstract only) goes a long ways towards constraining our speculations. In the paper, they describe a new species of lizard from the Eocene Messel shale of Germany (Messel is a famous lagerstatte: a deposit with extraordinary fossil preservation) as a transitional form from ‘normal’ lizards to the amphisbaenians.
Cryptolacerta hassiaca, holotype, from Nature 473:365.
Ever since Charles L. Camp’s 1923 classic, “Classification of the lizards”, amphisbaenians have bounced around a bit in terms of who their closest relatives are (this proposal being the most heterodox), but recent molecular work (summarized here and here by Blair Hedges and Nicolas Vidal) has connected them to the Lacertidae, a group of typical-looking Old World lizards (‘lacerta’ is Latin for ‘lizard’). In describing the new species, known from a single, well-preserved, and nearly complete specimen, Muller and colleagues write that the species shows “a mosaic of lacertid and amphisbaenian anatomical characters”. The skull, like that of amphisbaenians, is strongly constructed, and evidently adapted for a semi-fossorial life, while the limbs, though well developed proximally, are fairly short and have miniaturized digits. The body is not elongated. Morphometric comparison to modern lizards show that Cryptolacerta was likely a cryptic, leaf litter dwelling form.
Thus, the burrowing head evolved before the fully fossorial life style, while the body was as yet unenlongated, and the limbs still fairly well developed. We should not be surprised to find limbs in a transitional form from the well-limbed lacertids, but it is also the case that three extant species of worm lizards, the members of the Mexican genus Bipes, retain short front legs. Though very short, the limbs are well-developed for mole-like burrowing.
Amphisbaena sp. (left) and Bipes biporus
The New York Times has a story on this, which gets the gist of the story right, but the headline (“Fossil Sheds Light on the Lizard-Snake Divide”) and lede (“The origin of snakes is a perplexing matter”) are way off: the paper concerns the origin of amphisbaenians, not snakes.
h/t: Matthew Cobb
UPDATE: Burrowing lizards seem to be all the rage this week, as alert readers Dominic and James C. Trager have pointed out two other burrowing lizard events in the comments below. First, a new species of blind skink, Dibamus, has been described by Thy Neang and colleagues in the journal Zootaxa (BBC piece here). There are about ten species of dibamids, which lack forelimbs, but have flap-like hindlimbs. Like amphisbaenians, they have bounced around a bit in their classification; the latest work (see papers by Hedges and Vidal below) places them as the earliest branch within the lizards. I’m not sure why this new species merited news coverage, except insofar as all new species are newsworthy. One of the authors of the new species is Lee Grismer, whose alpha taxonomic exploits we’ve noted here at WEIT before.
The second item is a paper by Steve McAlpin and colleagues at Macquarie University in Plosone, describing heretofore unknown complexity in lizard social behavior (NY Times piece here). I’ll let the abstract speak for itself:
Here we provide the first example of a lizard that constructs a long-term home for family members, and a rare case of lizards behaving cooperatively. The great desert skink, Liopholis kintorei from Central Australia, constructs an elaborate multi-tunnelled burrow that can be continuously occupied for up to 7 years. Multiple generations participate in construction and maintenance of burrows. Parental assignments based on DNA analysis show that immature individuals within the same burrow were mostly full siblings, even when several age cohorts were present. Parents were always captured at burrows containing their offspring, and females were only detected breeding with the same male both within- and across seasons. Consequently, the individual investments made to construct or maintain a burrow system benefit their own offspring, or siblings, over several breeding seasons.
Complex social behavior is well known in crocodilians and, of course, birds (which are glorified reptiles), but this is a unique case for squamates (so far). They don’t seem to be eusocial though, which, in addition to overlapping generations, requires cooperative care of the young (there is at least some indirect parental care here), and a reproductive division of labor. The skinks involved are burrowing, but well-limbed.
A social skink, Liopholis kintorei, from Australia. Adam Stow,via NY Times.
Camp, C.L. 1923. Classification of the lizards. Bulletin of the American Museum of Natural History 48:289-481. (pdf)
Hedges, S. B. and N. Vidal. 2009. Lizards, snakes, and amphisbaenians (Squamata). Pp. 383-389 in S. B. Hedges and S. Kumar, eds., The Timetree of Life, Oxford University Press, New York. (pdf)
McAlpin, S., P. Duckett and A. Stow. 2011. Lizards cooperatively tunnel to construct a long-term home for family members. Plosone 6(5):e19041, 4pp. (pdf link)
Muller J., C.A. Hipsley, J.J. Head, N. Kardjilov, A. Hilger, M.Wuttke and R.R. Reisz. 2011 Eocene lizard from Germany reveals amphisbaenian origins. Nature 473:364-367. (abstract)
Neang, T., J. Holden, T. Eastoe, R. Seng, S. Ith, and L.L. Grismer. 2011. A new species of Dibamus (Squamata: Dibamidae) from Phnom Samkos Wildlife Sanctuary, southwestern Cardamom Mountains, Cambodia. Zootaxa 2828:58-68. (abstract)
Vidal, N. and S. B. Hedges. 2009. The molecular evolutionary tree of lizards, snakes, and amphisbaenians. Compte Rendus Biologies 332:129-139. (pdf)
