Tigers r born

May 20, 2011 • 4:46 am

Nine days ago three Malayan tiger cubs were born at the Palm Beach Zoo, and this video, showing the birth and some postnatal solicitude, is already up.  It’s touching (and adaptive) to see the care with which that big, fanged maternal mouth picks up the newborns.

This subspecies, Panthera tigris jacksoni, is one of the six tiger subspecies that remain on the planet; until recently there were three others, but we’ve driven them to extinction.   This one lives, as the name indicates, only on the Malayan peninsula, and, like all tiger subspecies, is highly endangered.  Wikipedia gives this sad note:

Recent counts showed there are 600–800 Malayan tigers in the wild, making it the most common tiger subspecies other than the Bengal and perhaps also the Indochinese tigers. It is, nevertheless, still an endangered subspecies.

Six to eight hundred?  Most common? (Other estimates are as low as 500.) What have we done to our planet?  There may come a time—perhaps in our children’s lives—when tigers no longer live freely in the wild.

h/t: Michael

Burrowin’ lizards, Batman!

May 19, 2011 • 1:42 pm

by Greg Mayer       (Update below)

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.

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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)

Giberson hints that accommodationism is doomed

May 19, 2011 • 10:59 am

Uncle Karl has left Biologos (and his university), but is still writing for PuffHo.  His latest piece, “The anointed leaders of the religious right,” is largely about amateur historian David Barton and similar rabble-rousers who, says Giberson, are infecting American evangelical Christians with a debased populism.  But his piece is also permeated with defeatism: a defeatism that evangelical anti-intellectualism is refractory to cure.  And that includes Christians’ rejection of evolution:

Unfortunately Barton shares the Right’s academic stage with discouragingly similar leaders in other fields. In The Anointed, Stephens and I note the degree to which American evangelicalism has created its own set of homegrown academic “experts” who preach comforting messages at odds with generally accepted understandings of the modern world.

Many evangelicals get their ideas about origins from Ken Ham, architect of the Creation Museum in Kentucky, which features stunning dioramas of Adam and Eve interacting with dinosaurs. The result is that most evangelicals think the earth is a few thousand years old and that evolution is a conspiracy. When Republican presidential hopefuls are asked if they believe in evolution, they dare not answer yes, for fear of offending their antievolutionary base. Unfortunately, most of them don’t even want to answer yes. And this, despite the highly visible presence of Francis Collins at the helm of the NIH. Collins is thoroughly evangelical and, as he and I have argued in our recent book, The Language of Science and Faith, there is simply no reason why evangelicals need to reject evolution in favor of the fanciful tales told by Ken Ham and other creationists. But Collins exerts no more influence on the science of the religious Right than Noll does on its history.

Look at that last sentence: it’s a pretty explicit admission that the mission of BioLogos, which is to turn evangelical Christians toward evolution, has failed.  (The organization was founded by Francis Collins.)  But of course that mission was doomed from the outset, for asking evangelicals to accept evolution is asking them to not only reject Biblical literalism (though not all evangelicals embrace this view), but also to see humans not as the apex of creation, but as only one branch of a ramifying and materialistic process.

I suspect, but don’t know for sure, that evangelical resistance to accommodationism explains why Giberson is no longer at BioLogos.

Math argot

May 19, 2011 • 8:25 am

There’s a lovely picture on the cover of the Proceedings of the National Academy of Sciences this week:

And a description of what it depicts, which is intriguing:

Cover image: Pictured is a modern version of the Borromean rings, a topological arrangement of three interlocked symmetric rings that owes its name to the Borromeo family of Italy on whose coat of arms the rings appear. Although the three rings cannot be pulled apart, no two of them are linked—a fact that becomes apparent when one of the rings is hidden from view. Jim Conant, Rob Schneiderman, and Peter Teichner derived this particular realization of the link from their theory of Whitney towers, where it represents the Jacobi identity, or IHX-relation. See the article by Conant et al. on pages 8131–8138, which is part of the Special Feature on Low Dimensional Geometry and Topology. Image courtesy of Jim Conant, Rob Schneiderman, and Peter Teichner.

But when you go to the paper, you’ll see that its abstract is so opaque to a non-mathematician that it might as well be written in Martian:

We show how to measure the failure of the Whitney move in dimension 4 by constructing higher-order intersection invariants of Whitney towers built from iterated Whitney disks on immersed surfaces in 4-manifolds. For Whitney towers on immersed disks in the 4-ball, we identify some of these new invariants with previously known link invariants such as Milnor, Sato-Levine, and Arf invariants. We also define higher-order Sato-Levine and Arf invariants and show that these invariants detect the obstructions to framing a twisted Whitney tower. Together with Milnor invariants, these higher-order invariants are shown to classify the existence of (twisted) Whitney towers of increasing order in the 4-ball. A conjecture regarding the nontriviality of the higher-order Arf invariants is formulated, and related implications for filtrations of string links and 3-dimensional homology cylinders are described.

(Presumably “Arf invariants” don’t refer to the unchanging vocalizations of a dog. )

This shows how far removed mathematics is from even other scientists.  Or are our own biology abstracts just as opaque to mathematicians?

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Conant, J., R. Schneiderman, and P. Teichner. 2011.  Higher order dimensions in low level topology.  Proc. Nat. Acad. Sci. USA 108:8131-8138.

h/t: Matthew Cobb

What made Darwin sick?

May 19, 2011 • 5:44 am

If you’ve read anything about Charles Darwin (and I’d recommend Janet Browne’s two-volume biography), you’ll know that he was plagued with illness his whole adult life.  He had terrible stomach pains, digestive problems, nausea, eczema, bouts of vomiting and—a trade secret among evolutionists—chronic flatulence.  On May 20, 1865, when he was 56, Darwin wrote down his own symptoms (extract from John Bowle’s biography):

For 25 years extreme spasmodic daily & nightly flatulence: occasional vomiting, on two occasions prolonged during months. Vomiting preceded by shivering (hysterical crying) dying sensations (or half-faint). .  ringing in ears, treading on air and vision. (focus and black dots) . . . (nervousness when E. [Emma] leaves me)—What I vomit intensely acid slimy (sometimes bitter) consider teeth.

If you visit Down House, Darwin’s home in Bromley (formerly Kent), you’ll see in his study a screen, behind which stands a basin.  When I asked about it, I was told that that was where Darwin would go to hurl if he felt nauseous during his lucubrations.

Darwin repeatedly sought remedies for his illness, including the famous “water cure” of Dr. Gully.  His doctors prescribed a bland diet, a copy of which used to be on display in Down House. It included broth and a boiled chicken wing.  I once hoped to write about this diet under the title “On the Origin of Feces,” but never got to use it (you’ve seen it first.)  Nothing worked well, and Darwin was in bad health until his death from heart disease at 73.  It’s amazing, considering his chronic and severe illness, that the man was able to achieve so much!

You may also know that ever since Darwin’s death, doctors have speculated on what made him so ill.  When I was younger, the prime candidate was Chagas disease, a debilitating and sometimes fatal illness endemic to the Neotropics.  Chagas is caused by a trypanosome parasite, itself transmitted by the bite of a reduviid bug (a “true bug,” by the way).  The roster of candidate afflictions is now much longer: Wikipedia lists 14 possible maladies.

Faye Flam,  evolution columnist at the Philadelphia Inquirer, takes up Darwin’s illness in her latest piece, “Darwin’s mysterious disease.” (The column, “Planet of the Apes,” may be America’s only weekly newspaper column on evolution: Olivia Judson used to write one for the New York Times, but she’s gone now.)

The most likely diagnosis now seems to be “cyclic vomiting syndrome” (CVS), a disorder that has many of the symptoms that plagued Darwin, including digestive problems, nausea, vomiting, and dizziness.  It may be caused—and this is disputed—by defects in the mitochondrial DNA (mtDNA): Flam notes that Darwin’s mother had similar symptoms, and of course mtDNA is inherited from the mother.  Chagas disease may also have been involved, but since Darwin had many of his symptoms before he arrived in South America on the Beagle (remember his “terrible seasickness”?), something else might have been going on.

The CVS hypothesis was first suggested in 2009 by John Hayman in a short paper in the British Medical Journal (free); it’s well worth reading if you’re a Darwinophile.  Of course, there’s not much we can do now to test Hayman’s theory, or the other theories, short of exhuming Darwin from Westminster Abbey and looking at his DNA.  And since CVS might not be caused by lesions in mtDNA, that idea is a nonstarter.  All we can do is speculate.  Regardless, though, we must admire Darwin all the more for producing so many works of genius while laboring under terrible physical adversity.

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BTW, Flam has a “blog” associated with her column, also called Planet of the Apes. Last week I wrote about her column on the Catholic Church’s non-acceptance of the modern theory of evolution; this week on her “blog” she’s published some angry responses from Catholic readers, including this gem:

The sun definitely circles the earth as proved by Ptolomy [sic] in the 2nd Century.  All science followed him for 14 centuries until Copernicus proved him wrong.  Einstein showed that the stars in the sky were fixed in place until Hubble proved they are moving.  Anything science proves today could be right but the chances are it could be wrong.  Remember that Evolution, the science, requires as much faith as creationism and both could be wrong.

Sloth crosses road: insert joke here

May 18, 2011 • 1:51 pm

The poor beast can’t help it: the species evolved before there were roads!

The video describes this as “a sloth attempting to cross a busy road in Manuel Antonio, Costa Rica.”  This looks to me like the brown-throated sloth (Bradypus variegatus), of which I saw many during a summer in Costa Rica. Note the algae growing in its fur; one sloth expert describes its biological significance:

What I find most interesting about the three-toed sloth is the symbiotic relationship it has with other organisms. One effect of the sloth’s languid pace of life is that it can’t be bothered to groom itself. This turns out to be beneficial to several varieties of algae and mold that grow inside the sloth’s hollow hairs. The algae effectively turn the sloth green, giving it excellent camouflage among the leaves. The camouflage is crucial to the sloth’s survival, because its inability to move quickly makes it an easy target for the harpy eagle.

But the symbiosis doesn’t end there. The algae in the sloth’s fur provides food for a great many insects. (I should point out, incidentally, that sloths have extremely long fur, making them appear much larger than they really are.) Beetles have been found by the hundreds living on a single sloth. Another insect that calls the sloth home is a type of moth—Bradipodicola hahneli (or “sloth moth” to most people). The sloth’s fur provides both food and protection for the moth. Not only does it feed on the algae, but it also deposits its eggs in the sloth’s droppings, where they pupate and hatch, and then fly off to look for another sloth to live on.

h/t: Matthew Cobb

David Brooks and the evolution of human altruism

May 18, 2011 • 10:05 am

David Brooks, New York Times columnist and author of The Social Animal, has never met an evolutionary psychology argument he didn’t like.  I haven’t read his book, but I did read a long excerpt in The New Yorker and found it credulous, tedious, and lame.  P.Z. Myers, who reviewed the book, had the same opinion.  So did philosopher Thomas Nagel, who, reviewing the book in the New York Times, pretty much ripped it apart, noting that “Brooks seems willing to take seriously any claim by a cognitive scientist, however idiotic. . ” (It’s quite unusual for the Times to publish bad reviews of books by their own columnists.)

In yesterday’s New York Times, Brooks writes about recent scientific “advances” in the understanding of human altruism.  And he signs on to the idea that altruism evolved by group selection.

I disagree, and see Brooks as ignorant about the true scientific issues.  If true altruism (which I define here) is indeed a trait that’s deleterious to an individual’s reproductive fitness, then it could, as Brooks envisions, evolve only by the differential survival and reproduction of groups.

That form of evolution would work like this: although genes for altruistic behavior would be constantly weeded out of populations (for altruists, by definition, sacrifice their own genetic heritage for others), those genes might survive if groups that contained higher proportions of altruists were the groups that persisted, giving rise to descendant groups more often than groups lacking altruists.  (The idea here is that groups without altruists wouldn’t flourish very well.)  That’s group selection, and it’s how Brooks sees altruism as evolving:

In his book, “The Righteous Mind,” to be published early next year, Jonathan Haidt joins Edward O. Wilson, David Sloan Wilson, and others who argue that natural selection takes place not only when individuals compete with other individuals, but also when groups compete with other groups. Both competitions are examples of the survival of the fittest, but when groups compete, it’s the cohesive, cooperative, internally altruistic groups that win and pass on their genes. The idea of “group selection” was heresy a few years ago, but there is momentum behind it now.

Let’s be clear about what biologists really know about group selection and altruism.  If true human altruism has a genetic basis, it is individually disadvantageous and could have evolved only by differential propagation of groups. That’s very unlikely, since it requires that the rate at which altruist-containing groups reproduce themselves must be high enough to counteract the substantial rate at which altruism genes disappear within groups.  It’s unlikely because groups reproduce much less often than do individuals!  Further, once a group consists entirely of altruists, any non-altruistic genes would rapidly invade it, as their carriers reap the benefits of altruism without sacrificing their reproduction.

Now if we’re talking about apparent altruism, in which individuals appear to sacrifice their reproductive interests but actually reap hidden genetic benefits, then we don’t need group selection to explain it.  As I’ve written in a longer post on this topic, kin selection (“inclusive fitness”) can do it, as can simple individual selection based on reciprocity or, simply. selection for the advantages of cooperation, as in hunting lions.

Humans, after all, evolved in small social groups, which provide the ideal environment for the evolution of “reciprocal altruism” (“I scratch your back and you scratch mine”).  That kind of altruism, which isn’t “true” altruism in the sense of hurting one’s reproductive prospects, evolves most readily in small groups where individuals know and recognize each other, and have a big brain for remembering and reciprocating good deeds.  Living in groups, particularly of kin, facilitates the evolution of apparent altruism, but that is not group selection since it doesn’t require differential propagation of groups.  Genes that are selected in groups based on relatedness or individual advantage will spread throughout a species without requiring differential reproduction of groups.  That is, selection occurs in the context of groups, but doesn’t occur through selection among groups.

What do we know about human altruism? First of all, we don’t know whether true altruism, in which individuals behave in ways that help others by hurting their own reproductive prospects (firemen are one example), has any genetic basis in human society.  True altruism like that isn’t known in any other species, and I suspect that, to the extent it occurs in ours, it’s an epiphenomenon: a byproduct of our general social cooperativeness.  As far as whether we are genetically cooperative (rather than truly altruistic), that seems quite likely, but it doesn’t require group selection.  It requires selection that occurred in groups, which is different.  And we almost certainly have some behaviors that evolved by kin selection, parental care being the most obvious.

So Brooks misrepresents the views of biologists in his piece.  There really isn’t much momentum in the evolution community behind the idea of “group selection.” There is increasing realization that selection can occur in groups, that being in groups can affect how selection operates on genes, and that there can be group effects (“multilevel selection”) that influence the evolution of genes.  But there is no general feeling that “group selection” is widespread or important.  And there is no widespread agreement that true altruism, or even apparent altruism, evolved by the differential propagation of groups.

In short, we know nothing about the evolution of true human altruism except that it probably didn’t evolve.  And we don’t know much more about the evolution of human cooperation.  It almost certainly has a genetic basis—we’re social animals, after all—but we’re ignorant about the form of natural selection that favored such cooperation, and about the social and environmental circumstances that promoted that selection.

Brooks makes one more biological error, asserting that the evolution of cooperation necessarily entails evolved morality.

But the big upshot is this: For decades, people tried to devise a rigorous “scientific” system to analyze behavior that would be divorced from morality. But if cooperation permeates our nature, then so does morality, and there is no escaping ethics, emotion and religion in our quest to understand who we are and how we got this way.

Cooperation also permeates the nature of honeybees, termites, naked mole rats, and lions, but they don’t have morality.  Morality is the result of having a big brain that, in a social species, can remember other individuals and make calculations about their intentions.  Whether that “result” is genetic, so that our moral feelings are encoded in our DNA, or simply an epiphenomenon, in which we’re taught rules that enable us to function, is an open question. I suspect that some of it is genetic, but we just don’t know.