Mad cow

Transmissible spongiform encephalopathies like Creutzfeldt-Jakob disease in humans and bovine TSE, better known as mad cow disease, have certainly caused their share of misery, as well as capturing public attention. A new study appearing in Science, and appearing online at Science Express, describes the work of Ohio State's Jiyan Ma and his colleagues in which they have shown how normal proteins can be converted into prions, the causative agent of spongiform encephalopathies. Prions are abnormally folded proteins which stimulate the formation of other such proteins in the development of the brain disease. However, since the original description of prions in the 1980s it has been unclear how the process operates, with a major drawback being the inability of researchers to employ recombination techniques in the creation of infectious prions. That's exactly what Ma and his associates were able to do. Employing mouse proteins, they determined that it is through an interaction with lipids in the cell membrane that the protein is altered.

They were also able to induce TSE in laboratory mice, which developed TSE symptoms within a few months after recombinant prions were injected into their brains. (On a side note - I'm all for the ethical treatment of animals. I think work like this certainly fits that description). This certainly represents a major step forward in our understanding of prion disease.

Now, for those of you that might have wanted a less dry treatment of mad cow disease - hope this is warped enough for you...

Excuse me? I didn't catch that last part...

Ok, here's the deal. We're gonna stop growing pine trees, see? And we're gonna replace the pine trees with these genetically engineered eucalyptus trees from Australia, see? And we're gonna grow these trees really fast and harvest 'em and use 'em to produce biofuels, see? And we can grow 'em here because they're genetically engineered to not freeze, right? And we're gonna plant these genetically engineered eucalytpus on, I don't know, maybe 10 million acres across the South. And, get this cause it's like the the best part, we know that these trees won't cause any problems because they've also been genetically engineered to produce an enzyme that destroys the reproductive parts of the tree.

Kudzu says "Hi".

tgif...

Looks like Friday is now meeting day. Some time this weekend. Maybe.

A thought. It's not over in Haiti. The news media will back off, because the story's not so dramatic - but a lot of lives hang in the balance. And, chances are, you got just paid. Consider hittin' it one more time.

Some weekend music. Enjoy.

The Red Queen

Why sex? Because, if we stop, they'll catch us. More to come.

Remember...

Thursday's lab day.



But, here's a little something from the Wayback Machine.

"Help me, Doctor! Please!"



Several times, I've taught a class in our Honors Program in which we investigate the influence of Charles Darwin on farflung fields ranging from the sciences to literature to economics. Here's an interesting little tidbit in that arena. Brian Regal, an assistant professor at Kean University in Union, NJ, believes that Charles Darwin has pretty much single-handedly killed off the last remaining werewolves. His idea, presented last summer at meeting in the UK, is that the development of the theory of evolution by natural selection has changed the nature of our boogymen. Throughout human history, the werewolf legend has been a part of our night terrors. Not so much any longer. Regal believes that this is partly due to the evolutionary distance between canines and primates, allowing Darwin to transform the werewolves of our heritage into more evolutionarily suitable analogues like yetis, sasquatches, and skunk apes.

I'm not sure I buy that. I'm not convinced that purveyors of horror spend a lot of time thinking about the genetic similarity of their chimaeras. Remember Jeff Goldblum's 1986 entomological moment? Of course, that was a remake. But what about the recent vampire craze? Most mammalian cladograms wouldn't put the chiropterans any closer to primates than the carnivores.

No, I suspect that Dr. Regal has hit on an interesting idea that doesn't really shed a lot of light on our cultural evolution. I only wish that the general public knew enough about biology to watch a monster movie and say, "Wait a minute.... that doesn't make sense - you know, in an evolutionary context."

A dinosaur of a different color...

If you're at all into documentaries or the Discovery Channel, you've watched scenes like this...



...and probably made the assumption that the depiction is fairly realistic. Truth is, we've learned enough about the skeletal structure of dinosaurs and other prehistoric species that we can render a picture that's accurate in size and shape. Even aspects of how they might have moved is revealed from an analysis of structure. The one area, though, where images like these remain highly speculative is in coloration. Our best guess of the color of a T. rex has been largely that - a guess. ScientificAmerican.com tells us about a new study that will appear in the January 28 issue of Nature that may fill in some of the missing hues. Examining 125 million year old fossils of dinosaur feathers under a scanning electron microscope,researchers have been able to identify organelles responsible for pigment production. Applying what we know about pigments in living birds and reptiles, they are able to make an educated guess about what the fossilized creatures might have looked like.



Among the animals examined was Sinosauropteryx, a turkey-sized, feathered predatory dinosaur. The analysis revealed that the little guy had a tailed marked by "russett, gingery" bands, according to the University of Bristol's Michael Benton.

The dinosaur colorists owe a debt of gratitude to Jakob Vinther, a Ph.D. student in paleontology at Yale. Vinther noticed that fossilized melanosomes in the ancient squid that he was studying looked identical to those in living squid. He speculated that this might be true of melanosomes in other structures, and the work took off from there. Of course, there's still a lot of work to be done, and still a lot of conjecture. Still, we may be headed toward more realistic images of the animals that we've all been fascinated with since elementary school.

This probably shouldn't surprise me....

...but it does. It's better to run barefoot.

Convergence in bats and whales...

Dolphins aren't the only mammals that employ echolocation for navigation and prey detection. It's a trait that's also well developed in bats. It's clearly convergent, as the ancestry of the two groups is quite different. However, new research appearing in Current Biology tells us that echolocation in bats and whales arises through nearly identical genetic changes. A gene known as prestin has evolved along the same lines in both the bats and in the dolphins examined. As a result, if we examined the phylogeny of the groups based on this gene alone, they would appear to be closely related when, in fact, they aren't.

The results suggest that, when a mammal finds itself in an environment where the ability to hear high frequency sounds and utilize them for echolocation, there may be only a very few genetic approaches to solving that problem. Perhaps, only one.

We know that there was at least some overlap between modern humans and neanderthals in western Europe around 40,000 years ago, but that the Neanderthals eventually were replaced or assimilated. However, there is strong evidence of the existence of a Neanderthal refuge in in the region of modern-day Spain and Portugal for several thousand years after they had vanished from the rest of Europe. What has been uncertain is exactly how long these populations persisted, and what ultimately became of them. Science Daily reports on new research by Joao Zilhao and his team which indicates that modern humans were established in the region by 37,000 years ago, suggesting that the Neanderthal refuge had declined by that time. This means that the Neanderthals persisted in the region for only about 5,000 years, considerably less than the 15,000 or so that had been previously suggested.

There's another interesting implication of this find. A 30,000 year old fossil find of a chlid in Portugal demonstrates some previous features, and there have been some rather off-the-wall suggestions that this might be evidence of hybridization between a relict Neanderthal population and modern humans. Doesn't look like the new time frame allows for that possibility.

Brains - big and little

Of course, Brett's big brain didn't do him much good. But, in the normal course of events, isn't a big ole brain the way to go? We humans are certainly proud of our large reasoning organs - couldn't be biased, could we? A new paper in the online journal BMC Biology (and referenced at ScientificAmerican.com) takes a look at brain/body sizes over primate history and concludes that evolution hasn't always trended toward the giant economy size.

That conclusion is particularly significant in our interpretation of one little guy - the hobbit. No, not Frodo. And actually, not a guy either. The small female hominid discovered in Indonesia in 2004 and christened Homo floresiensis by her finders and the "hobbit" by the popular media has a brain size about 1/3 that of a modern human. Since the fossils are only about 13,000 years old, the tiny-brained hobbit and her ilk would have had to coexist with their big-brained cousins for almost 200,000 years. A number of ideas have been advanced to explain the find, with some contending that H. floresiensis had adapted toward a smaller size because of their island habitat and others claiming that the specimen simply represents a malformed individual. Still others have suggested that the little lady is the culmination of an ancient lineage that, for whatever reason, had evolved toward smaller brain and body size.

The researchers, led by Cambridge's Stephen Montgomery, examined sizes of bodies and brains of 50 primate species, 35 living and 23 extinct, and concluded that, while there has been an overall trend toward increased brain size, there are certainly exceptions in some lineages. The earliest primate brains were little more than a tenth of a gram. The Cadillac today, of course, is the human brain which averages around 1.3 kg, and over the extent of primate history there has been an average increase in brain size in the neighborhood of 2.5% per million years. However, this is by no means universal, and decreases are the rule along some lines. In fact, the researchers conclude that the decrease in brain size seen in our little hobbit friends are "not unusual in comparison to these other primates."

So, good news for the little lady. Still in the club. Take your little hat off and take a bow.

juicy links.

Professor Baba Shiv at Stanford University may be able to tell you why a night of cramming may make you more likely to eat junk food:
Willpower And The 'Slacker' Brain - NPR

And some new info on the origins of amputation from the Times Online, courtesy of Jordan Blaize:
Evidence of Stone Age amputation forces rethink over history of surgery - Times Online

Deadbeat moms

Thanks go to Kyle for bringing to my attention an interesting story about about the ongoing evolutionary wars out there (the ones between animals - not the ones between people). In this case, the strategy is brood parasitism, in which a parastic species has evolved a life history strategy that allows it to use another species to rear its young. It's a great idea (biologically speaking) if you can get away with it. Here, a brood parasitic catfish that utilizes mouth brooding cichlids in the Great Lakes of the African Rift Valley...

If you're a bird watcher, you're probably struck by the similarities between the strategy employed here and those of the brown-headed cowbird (very abundant locally right now). Cowbirds lay their eggs in the nests of a wide range of other species. The eggs hatch early, the nestlings grow fast, and often wind up pushing other eggs and nestlings out of the nest. Here's some video of a cowbird laying an egg in an cardinal nest.

For your viewing pleasure...

Epibulus insidiator, the slingjaw wrasse.

and on a similar note...

Follow the breakup of Gondwana, if you can get past the awful audio (albeit, with a very pleasant Kiwi narrator)..



The movement of continental plates led to the formation of the great southern continent we call Gondwana about 200 million years ago, and began to split it apart some 30 million years later. Among the products of the breakup were the southern continents of of Antarctica, Australia, South American, and Africa - and the islands that today make up New Zealand. By more recent times, the formerly continuous land mass was a fragmented puzzle separated by vast expanses of the southern ocean. Biogeographic questions abound, including the degree to which the current flora and fauna of these derive from a Gondwanan heritage or a later dispersal to their current locations.

A new paper in the American Journal of Botany provides evidence that,for some plants at least, addresses this issue for certain components of the flora of New Zealand. Researchers led by Gregory Jordan of the University of Tasmania report on two new fossils from the heath family (Family Ericaceae) discovered in New Zealand deposits dated to the Late Oligocene/Early Miocene. That puts them between 15 million and 28 million years old. They seem to be of a different lineage than much older fossil pollen finds from New Zealand which go back to the Late Cretaceous, over 67 million years of age. The analysis of the fossils suggests that the ancient pollens represent ericacid lineages that went extinct, with the living heaths of the islands being descended from a much more recent line.

Score one for the dispersalists.

They may like to move it...

...but the question is, how? Some biogeography news that might shed some light on the whole Madagascar-moving issue.

The island subcontinent, which has had some pretty good PR recently, is the proud owner of one of the most unique faunas on the planet. In fact, the world's fifth-largest island, which lies just 300 miles of the coast of southeast Africa, has more endemic animals than any other location with the exception of the much larger island continent of Australia. The most famous of the island's inhabitants are the high profile, photogenic lemurs, but almost 90% of the other amphibians, reptiles, and mammals are found nowhere else.

The animals of Madagascar had to come from somewhere. The island has been isolated for over 100 million years - vertebrate life has been there for less than 65 million. Historically, two competing ideas have suggested different mechanisms for the intial inoculation of the island's fauna - a land bridge which would allow for overland movement or an overseas "sweepstakes" dispersal explanation which envisions ancestral Madagascarians (my word) rafting their way on floating debris.

Each of the ideas has its problems. There's no geological evidence of a land bridge connection between Madagascar and the African continent, and our knowledge of plate tectonics doesn't allow for a drifting continent connection. Furthermore, a land bridge connection would allow for a fairly nonselective introduction of species to the island - large animals like lions and hippos and giraffes in addition to the smaller ones that form the bulk of Madagascar's fauna. On the other hand, the rafting hypothesis is complicated by the fact that existing ocean currents flow in the wrong direction to faciliate an easy drift across the Mozambique Channel.

In a new paper in Nature, Purdue's Matthew Huber and Jason Ali of the University of Hong Kong report the results of computer simulations indicating that ancient ocean currents would have made the rafting possibility much more likely. Huber's simulations, performed on a supercomputer at Purdue and employing information about climate patterns 20 million to 60 million years ago, indicate that currents at the time likely flowed east - toward Madagascar from Africa. Furthermore, they would have likely been strong, fast currents, enabling a small reptile or mammal swept to sea on a raft of floating vegetation to make the shores of Madagascar without starving or dying of thirst.

In biogeography, distribution explanations employing this type of sweepstakes dispersal are sometimes met with skepticism. They are, after all, sort of a wild card. Can't explain a distribution pattern any other way? Then they must have floated there. Modeling techniques such as these may make it easier for us to provide some supporting evidence.

Most remote...

Twelve humans have walked on the surface of the moon. Two have been to the Challenger Deep of the Marianas trench. Fifty years ago. But, marine biologists are focusing once again on this deepest point in the world ocean to learn how life can cope with one of most extreme environments imaginable.

Try this

Mud-ring feeding by bottlenose dolphins...

Brothers in arms...

Malaria is one of the most deadly infectious diseases that mankind has ever had to confront, rivaled only by the bubonic plague which swept through Eurasia in the 14th Century and the smallpox epidemic donated by westerners to the New World. Roughly a half billion people fight the disease annually, with some two million losing the battle. Most of the fatalities are young children in sub-Saharan Africa.

Malaria is caused by a group of protozoans in the genus Plasmodium, the most deadly of which, P. falciparum, is the agent of almost all lethal infections. The parasite is carried from host to host by the bite of the female Anopholes mosquito. Within the human host, the parasites reproduce within red blood cells. The infected experience fever, pain, and weakness. The most unfortunate - coma and death.

A new study led by researchers in France and Gabon has identified another host for P. falciparum - gorillas. The research also provides additional evidence that this deadliest form of the parasite had its origins in another Plasmodium species found in chimpanzees. These conclusions are drawn from fecal samples taken from 125 chimpanzees and 84 gorillas in Cameroon. In the gorillas, the researchers found two new Plasmodium species - and P. falciparum.

The bad news here is that increased contact between the apes and humans resulting from deforestation could lead to increased malarial transmission rates. Another cross to bear, as well, for already dwindling gorilla populations. The "good news", at least on the human side of the equation, is that this adds to our knowledge about the parasite and also about the potential for interspecific transmission of infectious diseases.

And again...

If the last couple of weeks have taught us nothing else, it's that there are far too many causes out there in need of assistance from good people. I won't pretend that the Floreana mockingbird is more deserving than the Haitian people. But the day may come when you have a few extra dollars and there's not a human disaster staring at you nightly from your TV screen. If that happens, the birds that actually influenced Darwin more than those finches deserve a look. Without help, they're probably on the way out.

Nocturnal reading...

A while back, a friend gave me a copy of Pavlov's Trout, by Paul Quinnett. Autographed, actually - Thanks, K. Quinnett's a psychologist, and he writes about the psychology of fishing. It goes a little beyond that, though. One quote in particularly stuck with me...

"Not getting answers to 'Why' leads kids to stop asking, and contributes to the death of their curiosity and hope, perhaps even condemning them to a life of boredom and watching daytime television. Fishermen who keep coming up with one more why question become fish biologists, or ichthyologists, or ecologists..."

True that. Looking for the why.

Creation

You probably haven't heard about Creation, the new biographical movie that deals with the turmoil Charles Darwin endured as he moved toward publication of On the Origin of Species. Here, you can hear ScientificAmerican.com's John Pavlus interview the film's director, Jon Amiel, along with Randal Keynes. Keynes is Darwin's great-great-grandson and the author of Annie's Box: Darwin, His Daughter, and Human Evolution, the book on which the film is based. Although Creation focuses largely on the very human side of Darwin as he faces a literally life-changing decision, the director feels that enough of the content deals with the actual science behind the theory that a movie-going biologist will not feel cheated.

Creation opens in 1858 as Darwin struggles to complete Origins. It's 22 years since he returned from his circumglobal expedition on the HMS Beagle that forever changed his thinking about the natural world, and 20 years after a reading of Mathus' Essay on the Principle of Population provided the thunderbolt of inspiration that would lead to the theory of evolution by natural selection. More significantly for the movie's storyline, it's also seven years after the death of his daughter Annie, an event that, perhaps, influenced Darwin the man as much as the Galapagos Islands influenced Darwin the scientist. Annie plays a prominent role in the film, appearing in Charles' imagination to offer support and encouragement. Charles' wife Emma, played by Jennifer Connelly, also figures heavily in the plot. Emma was deeply religious, and feared that her husband's work would undermine the Church and, perhaps more significantly, the life that they had built. (On a side note, if Emma did, in fact, look like Jennifer Connelly it would certainly provide a bit of salve for any degree of emotional turmoil.)

So, why has this film flown under the radar? Well, only recently has it found a U.S. distributor, with most companies fearing the "controversy" that would be generated by a film about Darwin's life. The source of controversy, of course, is not the film itself, but rather the vocal mob with flaming torches that hounds anything that threatens their eroding world view. Check out the IMDB page for Creation, and read a few of the comments. We're fighting an an uphill battle.

Here's the trailer...




Chances are it won't play in a theater anywhere close to our part of the world. Netflix again.

Nothing but a hound dog...

...but that's a lot. Dogs on my mind this morning.

In my circle of canine friends and family, there's a German Shorthair Pointer, a Chihuahua, a Labrador Retriever, a pit bull, a Chinese Crested, and an assortment of other mutts. All very different, all loved. We're used to the diversity, of course, but it's still remarkable. In fact, the degree to which we've artificially shaped Canis familiaris over a fairly brief time period is usually part of my introduction to the power of selection. A new study in American Naturalist (referenced here at Science Daily but, for the life of me, I can't find in on the journal's home page) looks at the degree of diversity in domestic dogs by comparing skulls shapes with those of other members of the Order Carnivora. Not surprisingly, the authors found as much diversity within the dogs as they did within the rest of the Order as a whole. Not only that, but they found that the extremes of skull shape within dogs was greater than the extremes found between all other carnivores. A greater difference between a small pugnosed breed and a large, long-nosed variety, for example, than between cats and pinnipeds. The differences, of course, go far beyond skull shape. When we consider build, coat color and length, ear size and shape, etc., the degree of diversification within domestic dogs is pretty astonishing.

Think about that. Dogs are a fairly recent arrival on the evolutionary scene. There's debate about when they were first domesticated, although many experts put an estimate at around 15,000 years ago. However, most of the more than 300 currently recognized breeds have been developed over the last few hundred years. The diversity that we see today has been brought about within a few thousand generations by the application of a fairly strict regime of artificial selection - picking the traits that we like in a particular breed and avoiding the ones that we don't like. Nature may be a bit more sloppy - the big dog doesn't necessarily get to leave more offspring than the runt in a natural population - but it's had a lot more time to operate. Selection is a very, very powerful mechanism. Don't understimate it.

While I'm on the subject of dogs, best wishes to my favorite dobie. Feel better, big girl.

TriBeta...

Very successful meeting last night with our biology honor society group here on the campus of our little university. Twenty-four students, and four professors. Discussed undergraduate research projects, with an eager bunch of five or six that are ready to get out in the streams and start looking at darter microhabitats. As soon as winter turns loose of us - it's starting to feel that way.

There are a lot of times when this job is very frustrating. There are occasional moments when it's worth it. Last night was a worth-it.

Get my island ready...

Despairing this morning about a world in which people like James Inhofe and Ray Comfort can convince supposedly educated people that there is merit in the drivel they spew. I'm afraid the world is, in fact, going to hell in a handbasket. But probably not the same way that they and their friends believe. I'm old enough that I probably won't feel the full, ballpeen blow of the world that they are trying so hard and so deviously to deliver. My daughters, on the other hand...

Please, for the sake of your children and your children's children.... educate yourself.

Thumbs up...

Since we start the zoology class off with a treatment of evolution by natural selection, I always show my guys a documentary dealing with Darwin, the Beagle, and the theory in an early lab session. I've used a variety over the years, including the opening episode of the PBS Evolution series. This year, I'm showing them a relatively new (2008) National Geographic production called Darwin's Secret Notebooks. In it, evolutionary biologist Armand Leroi traces some of the steps Darwin took on the voyage and comments on the implications of what he saw on the development of the theory. Incomplete, of course. But well-produced, entertaining, and absolutely gorgeous. Recommend it highly. Netflix it.

An interesting fish story brought to us by the good folks at Science Daily. It's the tale of red grouper (Epinephelus morio) in the Gulf of Mexico off Florida. They're apparently in the construction business, and have a lot to say about what shares the community with them. Researchers at Florida State University, reporting in the online Open Fish Science Journal, tell us that the fish dig out and maintain complicated three-dimensional structures that are significant not only to the grouper themselves, but to a wide range of marine life. They show this behavior throughout their lives, with juvenile grouper excavating in inshore habitats and larger individuals working at greater depths.

Young red grouper in Florida Bay were observed removing sediment that had accumulated in solution holes, craters in the substrate that were formed during times of lower sea level as fresh water dissolved away the limestone. The result is to transform what would be a flat, structure-free habitat into one that is complex and three-dimensional. This pockmarked substrate is attractive to a variety of marine life, including spiny lobsters looking for a place to hide. In other words, the red grouper is functioning as something of a keystone species in much the same fashion as gopher tortoises in pine communities.

There is concern that increased fishing pressure on the red grouper could have a cascading effect on the other species that are dependent on it.

Wanna go...

Soon. Ecuador's Yasuni National Park. Almost 600 documented bird species. More species of frogs and toads than the U.S. and Canada combined. More tree species in a single hectare than are native to the U.S. and Canada. Over 100,000 species of insects per hectare. And it sits on top of a rich pool of oil. This can't possibly go badly. Right?

Check out the paper at PLoS One.

Tunes...

You've probably noticed that I like to share some music in here. Usually just trying to be cute. You can count on Octopus' Garden on my first cephalopod opportunity - coming soon, by the way. Sometimes, though, I'll just offer up something that I think you need to see/hear. Like this... Bruce Springsteen, live in 1978 when the world was young. Why Springsteen? Well, a former student - a good one - who will rename nameless other than to say that his name is Marshall - asked me not too long ago about my musical interests. I told him that, at the time, I was listening to a lot of Springsteen. He laughed, and made some reference to my age. Hurt my feelings. I am, after all, a sensitive guy.

So check this out, Marshall. If it doesn't do anything for you, so be it. Or, maybe you should go back and read the opening post.

I give you The Boss. Science of Life content? Pretty much none. Science of Living content? You tell me.

Fish eyes...

It's been an unusually busy few days. Finally taking a few minutes to call attention to a few interesting things that have appeared recently. A paper that appeared in the December 21 edition of the Public Library of Science's open access biology journal, PLoS Biology, examines the manner in which gene coding sequence and gene expression interact to help produce the tremendous diversity seen in the rapidly evolving cichlids in the East African lakes. The work of Karen Carleton and her colleagues compares cichlids found in the clear waters of Lake Malawi to those found in more turbid Lake Victoria.

Cichlids have several genes that code for different opsins (light-sensitive protein receptors found in cone cells of eye) that can give them sensitivity to light ranging from ultraviolet to the red end of the spectrum. The genes are expressed to differing degrees in different species, resulting in an array of different visual systems. In the relatively clear waters of Lake Malawi, a wide range of opsins were expressed. This may result in closely related species using a dramatically different range of wavelengths. The difference is related to feeding behavior, with cichlids feeding largely on zooplankton relying more heavily on ultraviolet wavelengths. This apparently enables them to more easily detect their small, transparent prey. Those fish feeding on larger prey were more likely to use light of longer wavelengths. In the murkier waters of Lake Victoria, on the other hand, cichlids are more likely to use longer wavelengths of light, independent of feeding habits. This is likely due to the fact that the longer wavelengths is transmitted more readily through the turbid waters.

Another of those amazing "just-so stories" reminding us that the ways in which biodiversity can evolve is as diverse as the organisms themselves. Another interesting paper, by the way, in the same issue of PLoS Biology, which we'll look at it more detail later. Tristan Long and colleagues at UC-Santa Barbara have looked at a potential cost of male mate choice to highly fecund females. Since we'll be talking about mate selection later, we'll probably revisit this one.

Gator breath...

The little red feathered dinosaur pictured here, and all its feathered relations, have respiratory systems structured very differently from yours and mine. Their lungs are small, but are supplemented by a group of internal air sacs - 7 or 9 of them, depending on the bird. The air sacs are significant for a couple of reasons - they allow a more or less constant supply of air to the lungs, and they also result in the flow of air through the lungs being unidirectional. The lungs of birds don't have alveoli like ours. Instead, they contain large numbers of tiny,highly vascularized tubules known as parabronchi. The unidirectional flow of air through the parabronchi minimizes the mixing of oxygen-rich and oxygen poor air and allows birds to extract oxygen more efficientlly. It has long been thought that this respiratory anatomy was associated with the development of birds and thier aerial lifestyle. New information suggests that it may not be that simple. This new insight comes from those close relatives of birds - alligators.

Nothing startling there. We've long known that alligators are more closely related to birds than they are to the animals in the traditional Class Reptilia. That similarity, indicated by a number of anatomical characteristics such as skull structure and backed up by DNA evidence, has led to the recognition that the Class Reptilia is not a good, monophyletic taxonomic division. Unless birds are included. Tables of contents of zoology text books are about to change.

Still, a study just published in the journal Science provides interesting new insight. Turns out that the american alligator (Alligator mississippiensis) also has a unidirectional flow of blood through its lungs. Of course, alligators are notoriously poor fliers. The fact that this unique respiratory anatomy is shared between alligators and birds pushes the development of it further into the past. Back into the Triassic, some 250 million years ago, prior to the split of the lineage leading to birds and crocodilians. The authors speculate that this remarkable adaptation, rather than being associated with the development of flight, may have given the ancestors of both birds and alligators a competitive advantage in the dryer, less oxygen-rich environment at the time. It's likely that other relatives of birds and alligators breathed in much the same way. That would be the dinosauars.

It's possible that you've run across this rather horrific image recently. It's been showing up in blogs or inboxes for a couple of months now. Most of the times that I've seen it, the suggestion has been that the jig is up for the duck. Teachable moment here. The large bird is a shoebill (Balaeniceps rex), a large, pelican-like bird that lives in the swamps of tropical east Africa. Adults may stand 5 feet tall with a wingspan approaching 10 feet. The common name refers to the distinctive shape of the bird's beak, better seen in an image without an obstructing duck. The beak is well-suited for scooping up prey in aquatic habitats. Like so many of the world's more interesting animals, the shoebill is in trouble. Estimates put the number of surviving shoebills at less than 10,000, and it is considered vulnerable to extinction. As with most threatened species, habitat destruction poses the greatest danger.

Turns out that the story has a happy ending. The photo was actually shot by Mark Kay at the San Diego Zoo. The shoebill was apparently simply moving the duck out of its path. Other photographs taken by Dr. Kay illustrate the outcome.

While perhaps not as exciting, the actual feeding habits of shoebills are fairly interesting. They wade in the east African swamps in search of fish, frogs, small crocodiles, and, yes, sometimes even small waterfowl. One of their preferred items, though, is the African lungfish. Follow the link for some remarkable footage of a shoebill catching and eating a lungfish.

There's absolutely nothing cooler than big fish. Of course, being of the ichthyological persuasion, I might be biased. But I think a lot of people would agree with me. And there's something particularly magical about big FRESHWATER fish. Sure, bluefin tuna, blue marlin, and great white sharks can be huge. But they're way out THERE. A 12 foot fish in your local river is something else entirely.

That's one reason the news reported yesterday at ScientificAmerican.com is especially sad. Two of the world's largest freshwater fish are in danger of extinction. Shocker, right? The Kootenai River population of white sturgeon (Acipenser transmontanus), reported to reach lengths of 18 feet and weigh a half ton, has dwindled from an estimated population of 10,000 in the 1970s to some 500 today. You probably wouldn't be that surprised by the cause of this decline either. Freshwater river living in rivers, declining in numbers in the last century? You can generally bet "dam", and you won't be wrong very often. Libby Dam, built in 1975, impounds the Kootenai and creates Lake Koocanusa, which extends some 90 miles up the river basin behind the dam. The impoundment prevents the periodic flooding, which served as a spawning signal for the river's sturgeon. As a result, the Kootenai white sturgeon have not spawned in the wild for 35 years.
Wildlife biologists are not giving up, and are spearheading a drive to save the sturgeon by opening the floodgates to increase river flow at key times. The Fish and Wildlife Service reports that, thus far, these efforts have been unsuccessful.

The Neotropics have (had?) their own, equally impressive giant, the Amazonian arapaima (Arapaima gigas). The arapaima, also known locally as the piraracu, is the world's largest scaled fish, reaching lengths of over 8 feet (it should be noted that a single, unverified report indicates a maximum size of over 12 feet). Recent museum studies suggest that the arapaima is not a single species, but actually four unique types of fish. This has led to the fear that one or more species may already be gone. The problem for the arapaima is not river impoundment, but overfishing. It is a prized food fish in South America, and its air-breathing habits make it particularly vulnerable to a variety of fishing techniques.
Wanna see the arapaima in action? Sure you do...

He's a semi-aquatic, egg-laying mammal of action....



...and he's got a secret weapon that James Bond would be proud of.

There's no question that the platypus (Ornithorhynchus anatinus) is one of the cooler animals on the planet. It's one of only five surviving species of egg-laying mammals (along with four species of echidnas), it has a tail like a beaver, and a beak like a duck (reflected in both its genus and species names). It is unique enough, and symbolic enough of its homeland, that it's featured on the Australian twenty cent piece. What is less well known about the platypus is that it is also one of very few venomous mammals. Most of the others are shrews, or shrew-like solenodons, which produce venom in modified salivary glands and deliver it through their bite in the same way that venomous snakes do. The platypus is different, in that it has an ankle spur on its hind limb connected to crural gland which produces a pretty impressive witch's brew of proteins. The venom is capable of killing small animals - it's not lethal to humans but, by all accounts, will produce an experience not soon forgotten. The excruciating pain can persist as hyperalgesia that may last for weeks. Both males and females have spurs, but only males produce the venom - that makes it even more interesting from an evolutionary perspective. Throw in the fact that venom production increases in during the mating season and it seems likely that we're looking at an adaptation associated with a dominance heirarchy associated with reproduction.

In a study just published by the American Chemical Society, Misaki Kita and colleagues describe their analyses of the venom of the platypus. Employing a bioassay using nerve cells, they identified eleven novel peptides, with one called heptapeptide-1 playing a particularly significant role. Their studies suggested that the venom might act by affecting the influx of calcium ions in nerve cells. The venom is described as being "like hundreds of hornet stings." So, while he may look cute, step lightly. He's packin'.

It's going to be a long road back for the Haitian people. If you'd like to help out, I'm sure there will be lots of opportunities. Here's one.

Thoughts go out to the good people of Haiti. Enough problems to deal with without this. I know there are many, many causes out there deserving of your charitable dollar. This will certainly be one.

Three species of iguanas in the genus Brachylophus are restricted to the remote Pacific islands of Fiji and Tonga, and represent the most geographically isolated iguanas in the world. For years, they were believed to be the descendants of South American iguanas that had rafted to the islands some 13 million years ago. The prospect of a pregnant iguana, or a boa constrictor for that matter, taking refuge on a mass of floating vegetation and drifting for thousands of miles across the Pacific until it ultimately makes landfall on a desert isle has long been biogeography's ace in the hole. Typically referred to as a "sweepstake" route, this type of somewhat random, long-distance dispersal can certainly be used to explain unusual distribution patterns. Got a group of organisms that are distributed on a continental mainland and on some, but not all, nearby (or not so nearby) islands? Then we can postulate that it rafted from the mainland to those islands where it's found, and not the one's where it's missing. Without question, this is undoubtedly the correct answer to some biogeographical puzzles. However, as with any ace in the hole, you have to be careful how you use it. The probability of such an event, although real, is astronomical. If we have to pull out the sweepstakes dispersal argument too often, it begins to lose its power.

The Fijian iguanas are among the most problematical of such cases - it's a long, long way from South American to Fiji. Even with drifting continents, it's been a long way for a long time. The working hypothesis had the ancestors of the islanders drifting perhaps as much as 5,000 miles. New evidence suggests that it might not have been that difficult - maybe they just walked. Brian Noonan of the University of Mississippi (that's Ole Miss for you SEC fans) and Jack Sites from Brigham Young have published work in The American Naturalist in which they use new molecular data to produce a new estimate regarding the divergence of the island iguanas from their continental relatives. Their analysis suggests a much more ancient divergence of the two lines than had previously been believed. Noonan and Site's data suggests that the Fijian iguanas diverged from their South American cousins over 50 million years ago. This changes the playing field. Literally.

In the Eocene epoch, the position of the continents was dramatically different. There was likely a land bridge (or, at least, an "island-hopping") connection between South America and Antarctica, and between Antarctica and Australia. Throw in the considerably warmer and more homogeneous climate patterns of the Eocene, and we have a much more workable hypothesis to get our iguanas to the isolated islands.

But wait... If we can explain the presence of iguanas on Fiji and Tonga as the result of a widespread distribution across the Southern Hemisphere dating back to the Eocene, then why aren't they found on many other islands in the South Pacific? Noonan and Site have a plausible explanation for that as well. Fossil evidence suggests that iguanas did, in fact, inhabit other South Sea islands, but disappeared. In most cases, that disappearance seems to coincide with the arrival of humans on the islands. And yes, the islanders apparently had a sweet tooth for iguana flesh.

So why haven't the species found on Fiji and Tonga disappeared yet? Well, simply because humans haven't been on those islands as long as an most islands in the region. But give us time...

The last year, of course, has been a big one for evolutionary biologists. We marked Charles Darwin's 200th birthday on February 12 of last year, and on November 24th celebrated the 150th anniversary of the publication of Origin of Species. As a result, we've seen a tremendous outpouring of words regarding the influence of Darwin's work. Still a long way to go, though, to reach the level of awareness that's needed.

We now require a course in evolutionary biology for all of our biology majors. The student reaction varies greatly, typically depending on their field of interest. The field biology types love it, and can't get enough examples and ideas as they try to understand the adaptations they see in their favorite plants and animals. Future educators are a little apprehensive but, for the most part, understand why they need to have some background as they prepare to go out and teach reluctant high schoolers. The toughest group are the premeds. It's not that they're necessarily any more resistant to evolutionary thought than other students; in fact, as a group they are might be a bit more well-read and open-minded than others. It's just that your typical premed is very focused, very driven, and very goal-oriented. A cliche, of course, but not an inaccurate one. At the curriculum level, this translates to, "Don't put me in any class that's not going to help me get into med school." It's sometimes hard for to convince them to how a course dealing with Darwin and speciation and natural selection is beneficial to them.

Wll, our task is getting easier. In a recent paper appearing in the Proceedings of the National Academy of Sciences (available here for free download), Randolph Nesse and his colleagues make a strong argument that evolutionary biology should be considered a basic science for future physicians. Nesse has been a pioneer in this arena - his 1994 book, coauthored with G. C. Williams, Why We Get Sick: The New Science of Darwinian Medicine, is perhaps the best popular exposition of the ideas underlying the new discipline. In the PNAS paper, the authors highlight the key elements making an understanding of evolutionary processes critical for physicians. Doctors must learn to view the human body, not as a machine beset by potential malfunctions, but as a complex system shaped by evolutionary process. Nesse et al. suggest that premedical students should complete evolution courses that emphasize medically pertinent aspects of the field. They go on to recommend that medical schools should teach evolutionary biology as a basic medical science.

We agree, and will try to do our part.

By the way, the American Museum of Natural History maintains an extensive website dealing with Darwin's life and work. It provides the opportunity to view some of the remaining manuscript leaves from Origin of Species. Pretty cool. Check it our here.

As good an opportunity as I can find, I guess, to post this....

The woman who thinks like a cow is Temple Grandin. Dr. Grandin is a professor of animal science at Colorado State University and a leading researcher in the area of animal behavior. She's also the world's most famous autistic person. Autism is a developmental neural disorder, typically manifesting itself before the age of three and usually resulting in an impairment of communciative abilities and social interactions. Autistic individuals often demonstrate restricted and repeated behaviors. Dr. Grandin has shown remarkable insight into animal behavior, and believes that her autism enables her to more fully understand the neural processes of the animals with which she works.

Autism seems to have a genetic basis, although the inheritance of the disorder is not well understood. You've probably heard a little about the controversy surrounding autism and things like pesticides and vaccines. Thus far, though, there is little scientific evidence to suggest a link between autism and environmental agents. There has been some progress, however, in getting at the real causes of the disorder. A new study published in Nature Neuroscience has uncovered evidence that faulty neural connections in the region of the brain functioning in social cognition may lead to autism. The activation of a molecular pathway known as mTOR seems to be involved. This suggests a possible treatment, since drugs inhibiting mTOR are already FDA approved. Keep an eye on this.

By the way, if you think that Temple Grandin sounds like an interesting character, you might be interested in the upcoming movie based on her life. It's set to premiere on HBO on February 6th, with Claire Danes playing Dr. Grandin. Long way from "My So-Called Life."

The most significant driving force behind evolution, of course, is natural selection. But what is it that's being selected? Seems simple enough on the surface. An individual organism - a whitetail deer, an oak tree, a bacterium - has a trait that results in an increased likelihood of survival or reproduction. As a result, it leaves a few more offspring than its neighbors. But it runs deeper than that. Since those beneficial traits are the results of the organism's genetic makeup, it's at the level of the gene that selection typically acts. Certain organisms are fortunate enough to carry, in their genome, copies of genes that produce traits that are, in a relative sense, "better" than the traits displayed by other members of the population.

We know that, over the course of human evolution, a host of mutations have accumulated in our current genome. Until recently, however, it's been difficult to actually put our finger on particular beneficial genes. Our ability to do so has been complicated by the fact that, when a gene is selected and becomes more abundant in the genome, a lot of "junk", neighboring genetic material which is selectively neutral, is carried along. An interesting story at ScientificAmerican.com discusses recent work published by a group led by Pardis Sabeti, an assistant professor in Harvard's Department of Organismal and Evolutionary Biology. Sabeti's research team has used a battery of statistical techniques to identify the particular beneficial gene in blocks of genetic information. Among the strategies employed are an examination of the ancestry of particular genomes. Comparing groups that developed under different environmental pressures helps shed light on the whether genetic variation is a beneficial mutation, or just background noise.

The technique resulted in a hundredfold increase in the ability of the researchers to localize a selected gene, and allowed them to identify a number of beneficial variants. These included a gene affecting pigmentation, one related to sensory perception, and a gene called "large" that may be associated with resistance of some African populations the virus that causes Lassa fever.

As advances in techniques allow us to rapidly accumulate massive amounts of genetic information, our ability to extract some meaning from it becomes critical. Techniques such as those developed by Dr. Sabeti and her team may provide the key.

Oh, and one more thing...



What's the significance of the music video? Well, take a look at the lead singer.

That's Pardis Sabeti - Rhodes scholar, Harvard geneticist, architect of groundbreaking research in human genetics... and lead singer of the alternative rock band Thousand Days.

So, what did you do today?

Well, classes start Monday and we'll get busy here. I'll be using this venue as a supplement for the classes I teach. Another, slightly less formal way to share information with students. Maybe spark some interest that might otherwise lie dormant. It's something that I think is important, and I'm more than willing to try some unorthodox approaches. A little music, some movie clips... Who knows - maybe I'll sing.

That said, the content will shift a little as I focus on particular subject areas. This semester, that means Zoology (of the general and vertebrate varieties) and Evolutionary Biology. (Hi guys. Come on in. I hope you find something you like.) Might also slip some Biogeography in here, for some of my online clients. If you're saying, "Man, that seems like a lot of classes", you'd be right. Maybe too many. But, truthfully, I manage to stay on top of them pretty well. By working pretty hard. Not that that makes me anything special here. A lot of my colleagues work very long hours. For very low pay. You might be interested in taking a look at a comparison of salaries for faculty at the various state institutions. You'll note some huge disparities between the big research universities and the smaller schools. Including (especially?) mine. Of course, there's a lot of pressure at the big schools to turn out research and generate grant dollars. The pressure on my colleagues and me is take high school students (who've spent the last few years cheering, playing baseball, sending text messages, and filling out the occasional worksheet while their teacher reads the newspaper) and turn them into biologists. Just sayin'.

So anyway....


If you see me coming, better step aside. Especially if it's Thursday - that's lab day.

You'll often hear those in the anti-evolution crowd express the viewpoint that evolution by natural selection can't operate to increase genetic diversity, only to decrease it. That's a clue to their fundamental misunderstanding of how the process works. It's driven by mutations, changes in the genome. Those changes create the variation on which selection can operate. No changes, no variation, no evolution.

So, it goes without saying that the faster the rate at which mutations accumulate, the greater the amount of variation in the genome. True, a lot of that variation will be selectively neutral, or even detrimental. But if we assume a more or less constant chance of a favorable mutation, then the rate at which evolution proceeds must be tied in some fashion to the mutation rate.

So, what is that mutation rate? A study just published in the new issue of the journal Science examines mutation rates in Arabidopsis, a small flowering plant in the mustard family which has become a significant model organism for geneticists and for which the entire genome has been sequenced. The researchers followed five lines of Arabidopsis thaliana for 30 generations, and identified in each line the the changes occurring between the original ancestor and the final generation.

They found, in each line, some 20 base pair changes. Taking into consideration the 120 million base pair size of the Arabidopsis genome, this indicates that the probability that any given base changes in a given generation is about one in 140 million, or that each seedling likely contains one mutated base in each of the two copies of the genome in its diploid state.

To some, this may seem like a vanishly small number, and suggest that evolution must proceed slowly. However, when you consider a large population of Arabidopsis, each producing vast numbers of seeds in each generation, it becomes clear that the raw material is there to allow selection to go to work to produce relatively rapid changes.

I'm walking...



Big news in the vertebrate water-to-land arena. In the new issue of the journal Nature, researchers report the discovery of a Devonian trackway in a mountainous region in southern Poland. The tracks are those of a relatively large animal, with the 10" wide tracks indicating a body length of some 7-8 feet. There is no indication 0f "body drag", indicating an animal using it's forelimbs and hindlimbs to lift its body clear of the substrate. The find is very significant in our understanding of the transition of vertebrate life from strictly aquatic environments to a terrestrial existence. These fossil tracks, well preserved and securely dated, are from rocks 395 million years old, almost 20 million years earlier than the oldest known tetrapod fossils and are some 10 million years older than fossils of tetrapod-like fish such as the famous Tiktaalik. The tracks seem to have been made by an organism with front and hind limbs of similar size, walking in much the way that a modern salamander might. Also of interest is that the deposits indicate a marine environment, rather than fresh water. This runs counter of most current thought regarding tetrapod origins.

Nature provides a fascinating video, in which one of the researchers, Per Ahlberg of Uppsala University in Sweden, describes the find and discusses its significance. Ahlberg is one of leading researchers in the area of early tetrapod evolution, and calls the Nature paper the most important one that he has worked on. The take home message is that the find changes our perception of the type of animal that might have been making its way across a prehistoric mudflat almost 400 million years ago - instead of a fish using its lobed fins to drag its body along, we've got a walker.

The tragic story of a mother and daughter killed by an elephant while on a walk in a Kenyan forest brings to mind a number of recent stories about lethal encounters between people and wildlife. The combination of recovering numbers of certain large species and the expansion of humans into their habitats can only serve to increase encounter rates, and a certain percentage of those encounters will go badly. That's just the nature of the beast. So to speak.

We don't have to worry about elephants in our part of the world, of course, but look for an increasing number of horror stories about the American alligator. Alligator numbers are on the rise across the lower tier of states, after reaching critical lows in the 1960s. When the first list of endangered species was developed in 1967 (under the Endangered Species Preservation Act of 1966, which preceded the Endangered Species Act of 1973), the American alligator was on it. With protection, they recovered rapidly, and were removed from the list in 1987. Now, estimates place Florida's alligator population at well over one million.

In addition to increasing numbers, we're seeing gators gradually extending their range into regions in which they were formerly found. Just in the last few years, alligators have been seen in reaches of the Tombigbee River where they had not been seen in decades.

Meanwhile, people have taken to the water in increasing numbers. The summer months see thousand of anglers, swimmers, water skiiers, and other aquatic enthusiasts taking advantage of recreational opportunities in our lakes and rivers. The result in predictable. In the 1970s, there were three fatal alligator attacks in the United States. In the last decade, there have been at least 13. Expect that number to go up, and expect the occasional horrific story to cross your television screen. You might exercise a little common sense when you go to the river, too.

Here it comes....

You may have heard about the invasive Australian spotted jellyfish, Phyllorhiza punctata, that have become abundant in the Gulf of Mexico in the last decade. The jellyfish are apparently taking advantage of dead zones in the Gulf and other environmental factors. The impact on the Gulf shrimping industry has already been significant, and promises to grow.

The problem is not limited to the Gulf. Recently, outbreaks of the nomura jellyfish, Nemopilema nomurai, in Japanese waters have become more frequent and more significant. The nomura is a much larger animal, reaching weights of over 400 pounds. It has also earned the honor of being the first jellyfish to sink a ship.

What's hot in biology right now? Well, an educated guess by even a casual observer would probably be pretty accurate. All you have to do is read the paper or watch the news. But, why guess? Check out Sciencewatch, a site hosted by Thomson Reuters which tracks trends in the sciences. They estimate the impact of a research paper by looking at the number of times it's cited in someone else's work. Take a look at the hot papers for 2009, and you'll see that they're dominated by stem cell work, human genome investigations, and AIDS research. The Scientist, an online life sciences magazine, tells us that the most cited paper in biology over the last couple of years was the work of Kazutoshi Takahashi and his colleagues, most of them in the Department of Stem Cell Biology at Kyoto University in Japan. It showed the pluripotent stem cells could be produced from adult human fibroblasts, and was cited over 500 times in 2009. If you're into stem cell research, check it our here.