On May 20 of last year, at a remarkable press conference in New York, a group of researchers announced—with much ballyhoo—that they’d found a 47-million-year-old primate fossil named Darwinius masillae (nicknamed “Ida”).  Ida, the finest fossil primate in existence, was touted loudly as the missing link between the two major branches of primates, the Haplorhini (anthropoids [apes and monkeys] and tarsiers), and the Strepsirrhini (lemurs and lorises; see figure below). Concurrent with the press conference was a History Channel documentary and a book about Ida, Colin Tudge’s The Link, that proclaimed, with much heavy breathing, that Ida was, as one of the earliest primate ancestors of our own species, an earthshaking discovery (see my review of the book here).

The description of Ida was eventually published in a paper by Franzen et al. in the journal PLoS ONE, a journal that doesn’t exercise stringent scientific review of submitted papers.  The reaction of both bloggers and scientists was very critical, with many pointing out that Ida didn’t look like a missing link at all, but may have been only an adapiform primate, a representative of a lineage within the Strepsirrhini that went extinct without leaving descendants.  The phylogenetic analysis of the PLoS paper, they claimed, was cursory and incomplete.  A later paper in Nature by Seiffert et al. cast further doubt on Ida’s status, suggesting that the features that led Ida’s discoverers to lump her with the haplorhines were convergent—that they had evolved independently in haplorhines and adapiforms and thus could not serve as evidence for Ida’s anthropoid ancestry.

Well, a paper just out in the Journal of Human Evolution, by Blythe Williams et al. (including my Chicago colleague Callum Ross), appears to drive the final nail in Ida’s coffin—at least regarding her status as a missing link between the major branches of primates.  Summarizing all the evidence in a cladistic framework (combining, as Williams et al. say, “hundreds of dental, skull, limb-bone, embryological, physiological and molecular characters of living and fossil primates”), they come up with two conclusions:

1. First, the Eocene adapids (of which Ida was one) were not, as Franzen et al. implied, more closely related to anthropoid primates than to lemurs and lorises.  Rather, the adapids were stem strepsirrhines that lived well after that group diverged from the haplorhines  (our own ancestors).

2.  Second, detailed study of Ida’s mandibles, teeth, orbit, leg bones and other traits show that she possesses no clear synapomorphies (shared derived traits) with haplorhines, but rather is clearly an adapiform.  All the evidence, then (more will soon be published in Proceedings of the National Academy of Sciences) puts Ida far from the haplorhines and anthropoids, and firmly in the now-extinct adapids.  Franzen’s failure to recognize this apparently rests partly on their unaccountable failure to use any fossil haplorhines in their original phylogenetic analysis.

Figure 1 from Williams et al. shows where Darwinius sits in the primate phylogeny (we’re with the crown Anthropoidea):

Science Daily gives a precis of the paper here.

Well, in science you win some and lose some, and all of us are familiar with being wrong. But it’s something else to be wrong when you’ve rushed prematurely into print, proclaiming earth-shattering conclusions from a slipshod analysis. A win for the bloggers, who called Franzen et al. out within days of their announcement.

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Williams, B. A., R. F. Kay, E. C. Kirk, and C. F. Ross. 2010.  Darwinius masillae is astrepsirrhine—a reply to Franzen et al. (2009).  J. Human Evolution, online.

Franzen, J.L., Gingerich, P.D., Habersetzer, J., Hurum, J.H., von Koenigswald, W., Smith, B.H., 2009. Complete primate skeleton from the middle Eocene of Messelin Germany: morphology and paleobiology. PLoS ONE 4, e5723.

Erik R. Seiffert, Jonathan M. G. Perry, Elwyn L. Simons & Doug M. Boyer. 2009.  Convergent evolution of anthropoid in Eocene adapiform primates.  Nature 461:118-1122.

In their continuing effort to enslave humans, cats made us invent the cat door, or catflap, so they wouldn’t have to wait at the door and meow.  Now, a German cat has forced its owner to construct a cat elevator:

This is an evolutionary step forward from the previous, low-tech version that actually required a human operator:

A few weeks ago both P.Z. Myers and I were interviewed by David Sharfenberg, a journalist for the Boston Phoenix.  Sharfenberg said he was working on a piece about Kenneth Miller, had read my website, and wanted to discuss my views on Miller, on his faith, and on how he reconciled science and his Roman Catholicism.  I talked to him a while, taking care to mention both the good things that Miller does (namely his anti-creationist activities and his widely-used biology textbooks) as well as my disagreements with his conflation of science and faith.  I remember telling Sharfenberg that I thought that, along with Eugenie Scott, Ken Miller was America’s most valuable asset in fighting creationism.

So what did Mr. Sharfenberg do? He publishes a piece that completely omits the praise that both P.Z. and I had for Miller, concentrating entirely on our problems with Miller’s blurring faith and science.  And he calls the piece “Ken Miller Just Can’t Win.”

Well, journalists can slant a piece any way they want, and of course P.Z. and I have been vocal critics of Miller’s accommodationism (see P.Z.’s take on this here), but it would have been nice had Sharfenberger mentioned briefly that both P.Z. and I had nothing but plaudits for Miller’s battle against Intelligent Design.  I think it would only have been fair for a journalist to add that, in one very important respect, we’re on his side.  But you won’t find a single mention of that in his piece. Like many journalists, Sharfenberg has a hook for his story, and anything that blunts that hook is bad.

But:  Ken Miller can’t win?  LOL! What can’t he win?  He’s a primo fighter for evolution, a professor at Brown, an author of several widely used textbooks, which I assume has made him fairly well off, and also an author of  two popular anti-creationist books, Finding Darwin’s God and Only a Theory.  The only thing he hasn’t “won” is the unstinting respect of certain atheists. That’s not very much to lose!

Nor does he deserve that respect.  If Miller kept his faith to himself, neither P.Z. nor I would say a word about it. If he wants to go to Our Lady of Mount Carmel Church every Sunday, more power to him.  But when he decides to write books about his faith, and, more important, about how he sees a way to reconcile that faith with science, then he lays himself open to public criticism.  Why should that reconciliation, which after all involves religion, science, and philosophy, be immune to scrutiny? Why should those of us who feel differently have to keep silent?

And it’s the reconciliation itself, not Miller or his personal religious views, that I’ve gone after.  Miller is, after all, a nice guy, and his ideas are far, far less of a problem than those of, say, William Dembski.  So when Sharfenberg says that I “wrote a lengthy essay in The New Republic last year attempting to dismantle Miller and his intellectual ally Karl W. Giberson,” that’s not precisely true.  The point of the essay was not to take apart Miller and Giberson themselves (to whom I offer encomiums in my piece), but to critically examine their views, and related views, that try to forge a harmony between faith and science.

Those who say that I should mute even that non-personal form of criticism don’t understand that my goal (and presumably the goal of P.Z. and other “new atheists”) is not just to defend evolution, but to stick up for science in its purest form, unsullied by superstition, and to defend rationality, of which science is only one branch.  Mixing science and faith can confuse people.

Sharfenberg himself is a good example of how Miller’s finding-God-in-science arguments promotes that confusion:

But the cell biologist [Miller] also makes explicitly scientific arguments: maintaining, for instance, that quantum indeterminacy — the ultimately unpredictable outcome of physical events — could allow God to intervene in subtle, undetectable ways.

If that’s an “explicitly scientific argument,” then the King James Bible is a biology textbook!  How many others have come away from Miller’s books or lectures buying his arguments that the “fine-tuning” of physical constants, or the inevitability of human evolution, are scientific indicators of the divine? (One of the chapters of Only a Theory is called “The World that Knew we Were Coming.”)

I do have one beef with a statement by Miller appearing in the Phoenix piece:

This sort of sly intervention [God acting through quantum indeterminacy], he [Miller] argues, is vital to the Creator’s project: if God were to re-grow limbs for amputees, for instance — if God were to perform the sort of miracles demanded by atheists as proof of his existence — the consequences would be disastrous.

“Suppose that it was common knowledge that if you were a righteous person and of great faith and prayed deeply, all of a sudden, your limb would grow back,” he says. “That would reduce God to a kind of supranatural force . . . and by pushing the button labeled ‘prayer,’ you could accomplish anything you wanted. What would that do to moral independence?”

So let me get this straight.  Some miracles are ok (Miller apparently believes in the Resurrection and the divinity of Jesus), but they can’t be too numerous?  Or too obvious? It’s ok for Jesus to heal the lame, or get rid of Parkinson’s disease (see here), but growing back a limb? No, no, that’s WAY too obvious.  Unlike healing the lame, regrowing a limb would completely ruin moral independence?  How, exactly, is that supposed to happen?  And what about the alternative explanation for why prayer can apparently cure paralysis, deafness and cancer but not excised limbs (no, it’s not that God hates amputees)? Could Miller’s ideas about amputation be making a virtue out of necessity?

Only a theologian could buy Miller’s argument.  Any smart twelve-year old could see right through it.

And that’s what’s so ironic about accommodationists and their religious allies. They’re always accusing atheists of having an unsophisticated understanding of theology.  But when religious scientists like Miller, Giberson, or Francis Collins spout the most juvenile and transparently self-serving kind of apologetics, well, that’s just fine.

. . . because there’s no snow in Saudi Arabia.

From the BBC:

Police in the US state of New Jersey have ordered a family to cover up their snow sculpture of the famous nude Venus de Milo after a neighbour complained.

Eliza Gonzalez sculpted the snow-woman with her son and daughter on her front lawn in Rahway following a snowstorm.

Many people praised their creation, but a police officer told them a neighbour had found it too risque, she said.

When given the option of covering the sculpture up or knocking it down, she dressed it in a bikini top and sarong.

“We didn’t want to have any problem with the police so we covered it up,” Ms Gonzalez told the AFP news agency.

But she now thinks the snowy Venus looks “more objectified and sexualised” than it did before the authorities intervened.

Fig. 1.  Eliza Gonzalez and the bowdlerized snow-woman.

The phylogeny of arthropods has always been messy.  One reason is that studies trying to discern their evolutionary relationships often use too few taxa (this is, after all, the most species-rich of all animal groups), and, especially, too few genes.  Conclusions have been based, for example, on only 18S and 28S rRNA and mtDNA (the latter is, of course, effectively one gene).  And this has led to conflicting conclusions, some of which contravene morphologically-based systematics.

For example, morphology seems to define a group called the “mandibulata”: all those arthropods that have mandibles.  But some molecular work has lumped the myriapods (centipedes and millipedes), which have mandibles, together with the chelicerates, which don’t have mandibles but a nonhomologous biting structure called chelicerae. (Chelicerates include spiders, horseshoe crabs, pycnogonids, and the like; see Fig. 1 below).

Now, a new paper in Nature by Regier et al. has come up with a near-definitive family tree of arthropods that resolves many of the questions that arose from studies using lesser resolution.  In their work, Regier et al. used many arthropod species (75, to be exact), and 62 single-copy genes that were orthologous in species from flies to humans.  This is a huge genetic sample, allowing for a good, well-supported tree based on 41 kilobases of DNA sequence.

We needn’t go into the messy details, but there are three quite important findings.

1.  Insects (“Hexapoda”) are not a sister group of crustaceans, as was indicated by some molecular studies. Nor are they the sister group of myriapods, the traditional arrangement supported by morphology.  Instead, insects are nested within crustaceans (see Figure 1).  In the same sense that birds are dinosaurs, then, insects are crustaceans.

2.  The sister group of insects within crustaceans comprises two rather obscure taxa that were long thought to be primitive: the cephalocarids and the remipedes.  Regier et al., however, find these two groups (see below) belong to the monophyletic clade called Xenocarida.  Their “primitiveness” is thus deceptive.  Now the fact that some crustaceans, like the Xenocarida, are more closely related to insects than to other crustaceans means that the group “Crustacea” is paraphyletic, since, by not including insects, it doesn’t include all descendants of the common ancestor.  If we want to be punctilious taxonomists, we’d have to dump the name “Crustacea”, or else reclassify insects as crustaceans.

3.  The Mandibulata, mandible-carrying arthropods, is now confirmed as a real monophyletic group, since the myriapods now join all the other mandible-bearing beasts, as they should.

Maybe this seems arcane to those who aren’t interested in arthropods, but it really does seem to settle long-standing questions about where the insects came from.  And it sets the standard for the numbers of species and genes that should be included in a good phylogenetic analysis.

Figure 1 (from Regier et al.). The phylogeny of arthropods.

Fig. 2.  Speleonectes tulumensis, a marine crustacean, a remipede, and a member of Xenocarida, the sister group of insects

Fig. 3.  A cephalocarid, also a member of the Xenocarida

h/t: Phil Ward, Cliff Cunningham

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Regier, J. C.  J. W. Shultz, A. Zwick, A. Hussey, B. Ball, R. Wetzer, J. W. Martin and C. W. Cunningham. 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463:1079-1083.

Today’s New York Times reports on how religious people and conservatives are adopting the same teach-the-controversy strategy they’ve employed with evolution.  A bill is pending in Kentucky, a similar resolution just passed in South Dakota, and Texas mandates that teachers present “all sides of the evidence on evolution and global warming.”

What’s next?  Teach the “controversy” about Western medicine? After all, lots of people believe in homeopathy, spiritual healing and the like.  How about vaccination?  And shouldn’t history classes debate the controversy about whether the Holocaust actually took place, or whether the Turks committed genocide against Armenians?

The Times reports that, according to a Pew survey, “white evangelical Protestants were among those least likely to believe that there was ‘solid evidence’ that the Earth was warming because of human activity. Only 23 percent of those surveyed accepted that idea, compared with 36 percent of the American population as a whole.”

A sentence from the resolution of the South Dakota legislature gives you the tenor of the debate:

Carbon dioxide is not a pollutant, but rather a highly beneficial ingredient for all plant life.

But how about those animals?

We’ve talked a bit about the tragedy at SeaWorld, where the orca Tillikum dragged his young keeper underwater, mauling and drowning her.  Animals that killed people used to be executed, sometimes quite gruesomely (see the sad tale of Mary the Elephant).  But I think most readers of this forum wouldn’t want Tillikum executed.  Putting a wild, free-swimming carnivore in a small tank is bound to pose dangers for people who take care of it, and, unlike cases in which free-roaming predators may develop a taste for humans, it would be relatively easy for people to avoid dangerous interactions with Tilly in the future.

But one group feels otherwise.  The Rightly Concerned website, an arm of the religious, right-wing American Family Organization, has called for not only the execution of the orca, but death by stoning.  Why? Because the Bible says so:

Chalk another death up to animal rights insanity and to the ongoing failure of the West to take counsel on practical matters from the Scripture. . .

If the counsel of the Judeo-Christian tradition had been followed, Tillikum would have been put out of everyone’s misery back in 1991 and would not have had the opportunity to claim two more human lives.

Says the ancient civil code of Israel, “When an ox gores a man or woman to death, the ox shall be stoned, and its flesh shall not be eaten, but the owner shall not be liable.” (Exodus 21:28)

So, your animal kills somebody, your moral responsibility is to put that animal to death. You have no moral culpability in the death, because you didn’t know the animal was going to go postal on somebody.

But, the Scripture soberly warns, if one of your animals kills a second time because you didn’t kill it after it claimed its first human victim, this time you die right along with your animal. To use the example from Exodus, if your ox kills a second time, “the ox shall be stoned, and its owner also shall be put to death.” (Exodus 21:29)

Right Christian of these folks.  But hey’d need a crane and one big boulder to do the proper Biblical job on Tiliikum!

Fortunately, SeaWorld is not full of these loons.  As HuffPo reports dryly, “Sea World has no plans to execute Tilly.”

h/t: Daniel Matute