Kevin Richardson is an animal behaviorist who works on a wildlife reserve in South Africa. He’s integrated himself into a lion pride, which has led to some remarkable videos.

Now who wouldn’t want to disport himself with these giant kittehs, or fondle their cute little cubs?  But, as Roy Horn (of Siegfried and Roy) learned, these animals are still wild.  I fear Mr. Richardson’s days are numbered, but he doesn’t seem to care.

You can find more Lion Whisperer pictures and videos here, as well as on YouTube.

On a cuter note, this little guy opens his mouth to meow, but nothing comes out.  The endearing “silent meow,” well known to ailurophiles, is one of the many tactics cats use in their continuing quest to pwn humanity.

h/t: Monica

. . .but maybe they could glide and parachute out of trees.  If you’ve followed bird evolution, you know they evolved from theropod dinosaurs, and that feathers evolved before flight, probably for thermoregulation or sexual/species signalling. Some of the earliest “true” birds (and that’s a definition which is somewhat subjective), though, had feathers which were longer, superficially resembling those of modern birds.  These creatures included the famous Archaeopteryx (which lived about 145 mya), and Confuciusornis (125 mya, the first bird with a toothless beak).

There has been a lot of argument about whether these beasts, especially Archaeopteryx, could fly;  the controversy has involved scrutinizing the feathers, the structure of the wing, the bones, and the presumed muscle mass (for a summary of the arguments, go here).  The conclusion: we don’t know. Up to now the consensus seems to have been that it was a best a weak flyer.

A new paper in Science by Robert L. Nudds and Gareth Dyke (from University of Manchester and University College Dublin respectively) concludes, however, that both Archaeopteryx and Confuciusornis were non-fliers.  They arrived at this conclusion using measurements of feather characteristics (primary flight feathers) and Euler-Bernoulli beam theory, used in architecture to calculate the load-bearing ability of beams.  They measured five specimens of Confuciusornis (see Fig. 2) and one (the Munich specimen) of Archaeopteryx.

The upshot is that the rachis of the feather (the shaft) was too slender to support wing flapping, and that the wings of these birds would have buckled had they attempted powered flight.  The graph below shows how slender the shafts of the fossil species were compared to those of modern birds:

Fig. 1.  B: Plot of Feather length versus body mass (top line) and rachis diameter versus body mass (bottom line).  Black diamonds: Archaeopteryx, gray diamonds Confuciusornis; black circles: modern bird species.  The fossil birds have feathers as long as those of modern birds, but the rachis diameter is much smaller (note that data are on a log scale, which makes the differences look smaller than they really are).   C.  Plot of rachis diameter versus feather length, again on a log scale. Symbols the same for B. Fossil birds have much a much slimmer rachis for their feather length than do modern birds.

A slender feather shaft raises the danger of the feather buckling under the large stresses of powered flight, and the beam theory shows that the Confuciusornis primary feather would buckle at 1/90th of the force that would buckle the feathers of a modern bird of comparable size.  Archaopteryx feathers would have buckled at about 1/45th of that force.

The authors conclude that neither bird could fly:

With feathers structurally similar to those of modern birds, Confuciusornis and Archaeopteryx could only have parachuted with their wings held dorsally, reducing the forces acting on the primaries while providing drag to reduce descent speed. A parachuting arrangement seems incongruent with their overall wing morphologies.

The catch is “feathers structurally similar to those of modern birds.”  Modern birds have feathers with hollow shafts. It’s possible that these ancient ones had feathers with solid shafts. That, according to the authors’ calculations, would have enabled them to fly, albeit with much less of a “safety margin” for buckling than we see in  feathers of modern birds.  I’m not sure how likely it is that these feathers had solid shafts, and I suspect you can’t tell from fossils, or the authors would have mentioned it.

But this paper doesn’t completely end the controversy.  A news-and-views piece by Michael Balter at ScienceNow reports dissent from other paleontologists:

But some researchers are not ready to close the book on early flight. “I agree that Confuciusornis and Archaeopteryx were poor fliers,” says Luis Chiappe, a paleontologist at the Natural History Museum of Los Angeles County in California. “I don’t agree, however, that these birds were unable to fly by flapping their wings.” That’s because, he says, the fossilized shafts of the feathers of early birds are often not well defined, making them difficult to measure accurately.

Philip Currie, a paleontologist at the University of Alberta in Canada, says that although the paper provides the “most convincing evidence yet” that these birds did not do well in the air, he also questions the authors’ conclusions that they were capable of only gliding or parachuting. The birds’ fossils have been found both in marine and lake sediments, Currie says. “If they were only dropping out of trees, how did they end up so far from shore?”

Fig. 2. One of the Confuciusoris specimens analyzed in this study.  The primary feather measured is indicated by the black bar.  White scale bar is 2 cm.

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Nudds, R. L. and G. J. Dyke.  Narrow primary feather rachises in Confuciusornis and Archaeopteryx suggest poor flight ability.  Science 328:887-889.

I visited The University of British Columbia at Vancouver a few weeks ago, but couldn’t post my pictures until now. That’s because one of the subjects was embargoed until this week. That was the skeleton of a blue whale that was being prepared and installed in the university’s Beaty Biodiversity Center, adjacent to the biology department.  It’s open for viewing now, and so I can show it.

The blue whale (Balaenoptera musculus) is the largest animal (by body volume) that ever lived—larger than any dinosaur.  Females can weigh up to 150 tons! (For comparison, that’s as heavy as 50 Hummers.) Because they’re so large and can provide so much oil, they were mercilessly slaughtered in the last century, and now only about 10,000 individuals are left.

A blue whale beached itself on Prince Edward Island twenty years ago, and, after it died, was promptly buried with bulldozers to reduce the stench.  Decades later scientists unearthed the beast, and found that nearly the whole skeleton was intact. It was a remarkable specimen, and was installed hanging from the ceiling of the museum.  Here, embargoed until today, is a photograph of the installation:

Notice that the vestigial pelvis and leg bones are missing. I asked the preparator (the guy up on the scaffold) if they had recovered them.  He said, “Yes, indeed!” and fetched them from the back. (They were to be installed at the end.)  I love vestigial pelvises of whales because they’re one of the most obvious and incontrovertible proofs of evolution.  They let me pose with the bones; those white nubs pointing downward from the tips are the vestigial femurs:

My host at UBC was Dolph Schluter, who’s famous for his work on adaptation and evolution in stickleback fish.  He managed to pry $3 million out of the Canadian government to build a series of experimental ponds, in which he studies selection and speciation in the two “morphs” of sticklebacks, benthic and limnetic.  Here’s Dolph and his setup:

Vancouver’s Museum of Anthropology, part of the University, is a hidden gem—one of the best museums of any sort I’ve been in.  It’s a lovely building set on the coast with a background of sea, mountains, and conifers.  The collection of northwestern native art is simply astounding, but there are artifacts, art, and clothing from cultures around the world.  The totem poles are fantastic. Here’s some native art:

And since we’ve been discussing interspecific love, here’s a doll made for an Inuit child:

Here are Dolph and I at the Vancouver airport, demonstrating the very close link between evolution and atheism before catching a puddle-jumper to Portland.  We traveled back to Chicago together because Dolph gave a seminar at Chicago the day after I left Vancouver.  I was reading Victor Stenger’s The New Atheism on the plane, but then a priest sat next to me and, a coward, I put it away.  It turned out that the priest was not a nice guy: he was brusque, unfriendly, and, when he had to visit the bathroom, simply looked at me and shouted, “I have to get up!”, expecting me to rise from my aisle seat let him past.  No “please” and no “thank you”. I realized then that I’d always retained a sort of vestigial faitheism, assuming that anybody wearing a clerical collar would be nice and friendly simply by virtue of their overt faith.  It was a shock to realize that priests could be as unpleasant as anyone else.

Finally, a note on the door of St. John’s College, where I stayed at UBC.  Educational discrimination against chiropterans!

I suppose we all thought that the Obama administration would be better then the Bush administration at protecting the environment.  So I was depressed when Obama announced opened up a lot more areas to offshore drilling, which seemed like a dangerous sop to Republicans and to industry.

But it’s even worse than that.  As reported in today’s New York Times, the Minerals Management Service (MMS), an agency of the U.S. government that issues permits for companies to drill offshore oil wells, has regularly ignored the warnings of biologists about the possible impact of drilling on endangered species. What’s more, the MMS violated federal regulations by not making oil companies get required environmental-impact permits from the National Oceanic and Atmospheric Administration, an agency that is responsible for protecting marine life.  The latest disaster also involved a well drilled without those permits:

Those approvals, federal records show, include one for the well drilled by the Deepwater Horizon rig, which exploded on April 20, killing 11 workers and resulting in thousands of barrels of oil spilling into the gulf each day.

The Minerals Management Service, or M.M.S., also routinely overruled its staff biologists and engineers who raised concerns about the safety and the environmental impact of certain drilling proposals in the gulf and in Alaska, according to a half-dozen current and former agency scientists.

Those scientists said they were also regularly pressured by agency officials to change the findings of their internal studies if they predicted that an accident was likely to occur or if wildlife might be harmed.

The concerns of government scientists were brushed aside:

Managers at the agency have routinely overruled staff scientists whose findings highlight the environmental risks of drilling, according to a half-dozen current or former agency scientists.

The scientists, none of whom wanted to be quoted by name for fear of reprisals by the agency or by those in the industry, said they had repeatedly had their scientific findings changed to indicate no environmental impact or had their calculations of spill risks downgraded.

“You simply are not allowed to conclude that the drilling will have an impact,” said one scientist who has worked for the minerals agency for more than a decade. “If you find the risks of a spill are high or you conclude that a certain species will be affected, your report gets disappeared in a desk drawer and they find another scientist to redo it or they rewrite it for you.”

And, just as in the bad old days, the Minerals Management Service is stonewalling:

Kendra Barkoff, a spokeswoman for the Minerals Management Service, said her agency had full consultations with NOAA about endangered species in the gulf. But she declined to respond to additional questions about whether her agency had obtained the relevant permits.

Heads should roll at the MMS. And, at the least, Obama should address the country on how the BP disaster will affect the future of offshore drilling and his plan to make great swaths of our coasts vulnerable to spills.  As far as I know, he hasn’t said anything about this issue.

UPDATE:  Obama has spoken out, harshly criticizing BP and the drill-rig owners for their internecine finger pointing, and promising to fix the broken permit process:

Reacting to reports that federal regulators allowed extensive offshore drilling without first demanding the required environmental permits, the White House and the Interior Department said on Friday that there would be a review of all actions taken by the Minerals Management Service, the agency responsible for offshore rigs, under the National Environmental Policy Act, or NEPA.

Now let’s see if he closes off the coastal areas that he opened for drilling two months ago.

Another tour de force by the unknown artist.

We all know the Burgess Shale fauna from Steve Gould’s book Wonderful Life, which described it as a group of fantastic animals lacking any affinity with modern-day animals.  Gould suggested that they went extinct without issue in the Cambrian, about 505 million years ago, but could easily have given rise to modern animals if the “tape of life” had been rewound.

Later work by Simon Conway Morris and others, of course, showed that the Burgess Shale fauna, although weird, did have affinities with modern groups like arthropods, lobopods (Onychophora) and annelids. Indeed, some of the fauna could have been ancestors of modern groups, although there still seem to be bizarre forms—called the “problematica”—without affinities to modern animals.

Related to the Burgess Shale fauna is the even better collection of animals in the Chengjiang Fauna of China, also in the Cambrian but earlier—about 525 mya.  Here we see clear representatives of echinoderms, arthropods, annelids, sponges, and even what seems to be a chordate.

The Burgess Shale fauna did disappear from the fossil record about 505 mya.  Maybe they suddenly went extinct, or perhaps they lived on but just weren’t preserved, since many of them were soft bodied and wouldn’t have fossilized easily. The next major fauna we see is in the Ordovician period (488-443 million years ago), whose beginning shows mostly shelly or hard-bodied creatures: trilobites, echinoderms, gastropods, brachiopods, and, hard-shelled arthropods like barnacles.  What happened to the Burgess shale animals?

A new paper in Nature by Peter Van Roy et al. gives the answer: those animals were there all along.  They didn’t go extinct in the Cambrian, as long thought, but hung on for at least twenty million years more, perhaps giving rise to more forms that were ancestral to modern life.  Their disappearance in the later Cambrian reflected not extinction but poor preservation.

Van Roy et al. describe a remarkably preserved fauna from a valley in southeastern Morocco (the “lower Fezouata Formation”) that dates to the lower Ordovician.  Remarkably, the Fezouata fauna contains not only Burgess-Shale type creatures (Fig. 1), but also later and typical Ordovician creatures (Fig. 2)  Clearly, the Burgess fauna persisted for millions of years after they were supposed to have gone extinct.

Here are figures from the Nature paper showing both the Burgess fauna and more typical Ordovician fauna.  They’re lovely fossils, colored from the oxidation of the pyrite that infused them:

Fig. 1.  Burgess-Shale type organisms from the Fezouata fauna.  a, b Demosphonges; c, annelid; d, halkieriid?; e), armored lobopod?; f, g, and h, arthropods; i, arthopod appendage.

Fig. 2.  Ordovician elements of the Fezouata fauna.  a and b, arthropods; c, stalked barnacle?, d, Xiphoshuran (chilcerate resembling modern horseshoe crabs); e, another Xiphosuran.

Now this finding is not “revolutionary” in the sense of telling us more about the ancestry of modern phyla.  That revolution occurred back when Simon Conway Morris et al. realized that, contrary to Gould’s—and Conway Morris’s own initial— suggestion, the Burgess creatures were not one-offs with no affinities to modern life, but belonged to extant groups.  What the new finds show is simply that there wasn’t a mass extinction that destroyed Cambrian life, but a more gradual replacement that lasted millions of years. And it leaves the Burgess Shale creatures as good candidates for ancestors (or at least relatives) of many modern groups.

Fig. 3.  Workers in the Draa Valley.  Left to right:  Jakob Vinther, Peter Van Roy, and Derek Briggs. Photo copyright Patrick Orr.

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P. Van Roy, P. J. Orr, J. P. Botting, L. A. Muir, Jacob Vinther, B. Lefebvre, K. el Hariri, and D. E. G. Briggs.  2010.  Ordovician faunas of Burgess Shale type.  Nature 465:215-218.

The good:

At New Humanist, Anthony Grayling skewers Terry Eagleton’s latest lucubrations on evil:

No one not brought up a Catholic or a Calvinist would even remember the concept of Original Sin, let alone bring it into a discussion of evil. But Eagleton does, and at length. For those not subjugated to the outlook only within whose terms can the doctrine appear to make any sense, Original Sin seems a doozy of an idea. Compare: a pharmaceutical company tells us that we are all born with a disease that requires that we buy their product all our lives long, and that if we do it will cure us after death. This reminds me of the joke about Bernie Madoff, that his big mistake was promising returns in this life; he should have taken his cue from the religions.

At Evolution: Education and Outreach, Carl Zimmer discusses the benefits, and problems associated with how the media teaches the public about evolution.  Surprise—he doesn’t lament a dearth of popular-science reporting, and never once does he blame the scientists!  Indeed, Zimmer sees a glut of popular writing about evolution and, when that writing is misleading, as in the case of the primate fossil Darwinius, Zimmer blames a collusion between an uncritical media and scientists who are overeager to sell their work to the public.

At Greta Christina’s Blog, she demolishes the Argument from Fine Tuning.

The bad:

In  Tuesday’s New York Times, Robert Wright, , who previously blamed the murderous rampage of Major Hasan not on Islamic doctrine, but on America’s war on terrorism, manages to reach an identical conclusion when analyzing the recent terrorist episode in Times Square.  It’s social difficulties, mental illness, financial problems, and American depredations in the Middle East—anything but religion.  Wright continues to earn the sobriquet bestowed by Christopher Hitchens, “the leading liberal apologist for the faith-based.”

At The Chronicle of Higher Education, Michael Ruse laments the fact that nobody is buying and reading his newest book, Science and Spirituality.  And he complains about a bad review—on Amazon!

In his syndicated column of last Thursday, the vile and and anti-Semitic Pat Buchanan complains that there are too many Jews on the Supreme Court:

Not since Thurgood Marshall, 43 years ago, has a Democratic president chosen an African-American. The lone sitting black justice is Clarence Thomas, nominated by George H. W. Bush. And Thomas was made to run a gauntlet by Senate liberals.

Indeed, of the last seven justices nominated by Democrats JFK, LBJ, Bill Clinton and Barack Obama, one was black, Marshall; one was Puerto Rican, Sonia Sotomayor. The other five were Jews: Arthur Goldberg, Abe Fortas, Ruth Bader Ginsberg, Stephen Breyer and Elena Kagan.

If Kagan is confirmed, Jews, who represent less than 2 percent of the U.S. population, will have 33 percent of the Supreme Court seats.

Is this the Democrats’ idea of diversity?

And the cute:

More interspecific love.  Mother Chihuahua brings up abandoned kitten.

The story of Homo keeps getting weirder and weirder.  Just as I was getting used to the idea that Neandertals and more modern Homo sapiens may have made the beast with two backs,  somebody calls my attention to yet another lineage of Homo that may have coexisted with both of them.  This conclusion comes from DNA extracted from a single bone and described in a paper by Krause et al. (and, of course, Svante Pääbo) in the April 8 issue of Nature.

First, a wee bit of background.  We now know (or at least think) that there were three migrations of our relatives out of Africa:

The first migration of Homo erectus from Africa throughout Eurasia (and maybe to Indonesia), beginning 1.9 million years ago. H. erectus seems to have vanished without leaving descendants, though we’re not sure about this. And the “hobbit,” H. floresiensis, which lived in Indonesia until only 12,000 years ago, may have come from this migration.

The migration that gave rise to Neandertals, beginning about 500,000 years ago. We now think that these individuals went extinct without leaving descendants, but left a few of their genes by hybridizing with members of the third migration.

The final migration that took place about 60,000 years ago, giving rise, so we think, to all modern humans.

But the new paper suggests that there may have been a fourth out-of-Africa migration.  The genetic data suggesting this comes from a single finger bone found in a cave in the Altai Mountains in southern Siberia (see circled location in Fig. 1 below). While the cave may have been sporadically occupied by hominins starting 125,000 years ago, the bone comes from a stratum dating between 30,000 and 48,000 years ago.

Fig. 1.  Locations of specimens used in DNA analysis.  Modern humans in gray, Neandertals in blue, Denisova individual circled in red.

After extracting the DNA from this bone (and again let us remember how remarkable an achievement this is), the authors sequenced the entire mitochondrial genome.  They then compared its sequence to that of several modern human populations, some already-sequenced Neanderthal mtDNAs, and a bonobo and a chimp as outgroups.  What they found, as seen in Figure 2 below, is that the Denisova sample was an outgroup to Neandertals and modern humans; that is, it diverged from the (Neandertal + modern human) lineage roughly a million years ago, well before the divergence of the Neandertal and modern human lineages from each other.

Fig. 2.  Mitochondrial DNA phylogeny of modern humans (gray), Neandertals (blue) and the individual from Denisova (red)

What this means is that this individual could not have been part of either of the last two out-of-Africa migrations, nor could it have been part of the earlier migration 1.9 million years ago, since it diverged from our own lineage well after our lineage diverged from the ancestors of Homo erectus.  This tentatively suggests that there was yet another migration out of Africa—a fourth—that gave rise to the Denisova individual and the population to which it belonged.

Further, this “species” could have been a contemporary of Neandertals and modern humans.  The authors note that individuals with Neandertal-like mtDNA lived only 100 km away from Denisova at about the same time, and other artifacts suggest that “modern” humans also lived in the region around 40,000 years ago.  It’s possible, then, that there could have been three evolutionarily independent species of hominins living in the same area of Asia at about the same time. (We already know a similar situation held for earlier species of hominins in Africa).  More opportunities for hybridization!

Now this conclusion is tentative, for it’s based on mitochondrial DNA from a single individual. It’s possible that there was simply an ancient mitochondrial DNA kicking around in the Neandertal genome, and this individual was simply a Neandertal that had it.  This can be resolved by looking at both other individuals and at the nuclear DNA of Denisova samples. (I don’t know if there are enough bones to provide this).

And of course we can’t yet tell if this individual was a member of a new species of Homo.  That’s hard to tell from mitochondrial DNA, although zoologists often blithely (and, I think, erroneously) diagnose new species of animals based on an observed difference in mtDNA sequences.

Steve Gould once wrote that when he taught human evolution each year, his first job was to throw out all the lecture notes from the preceding year.  With our remarkable ability to recover and sequence DNA from our ancestors and relatives, and the use of “phylogeography” to trace human movement using present-day genetic patterns, the field is moving even faster now.   I am certain there are big surprises in store.

Fig. 3.  Altai Mountains of Siberia, a view from just above the cave at Denisova where the new specimen was found (Photo by J. Krause, from Nature).

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J. Krause, Q. Fu, J. M. Good, B. Viola, M. V. Shunkov, A. P. Derevianko and S. Pääbo.  2010.  The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464:838-839