Blogs / The Loom

Measles looks to be 1000 years old. It jumped from cattle. And you can read more about it here.

Today the Enlightenment and Thomas Jefferson were disappeared from Texas.

Here’s a live blog from this morning’s hearings at the Texas State Board of Education. (Emphasis mine.)

9:30 – Board member Cynthia Dunbar wants to change a standard having students study the impact of Enlightenment ideas on political revolutions from 1750 to the present. She wants to drop the reference to Enlightenment ideas (replacing with “the writings of”) and to Thomas Jefferson. She adds Thomas Aquinas and others. Jefferson’s ideas, she argues, were based on other political philosophers listed in the standards. We don’t buy her argument at all. Board member Bob Craig of Lubbock points out that the curriculum writers clearly wanted to students to study Enlightenment ideas and Jefferson. Could Dunbar’s problem be that Jefferson was a Deist? The board approves the amendment, taking Thomas Jefferson OUT of the world history standards.

9:40 – We’re just picking ourselves up off the floor. The board’s far-right faction has spent months now proclaiming the importance of emphasizing America’s exceptionalism in social studies classrooms. But today they voted to remove one of the greatest of America’s Founders, Thomas Jefferson, from a standard about the influence of great political philosophers on political revolutions from 1750 to today.

9:45 – Here’s the amendment Dunbar changed: “explain the impact of Enlightenment ideas from John Locke, Thomas Hobbes, Voltaire, Charles de Montesquieu, Jean Jacques Rousseau, and Thomas Jefferson on political revolutions from 1750 to the present.” Here’s Dunbar’s replacement standard, which passed: “explain the impact of the writings of John Locke, Thomas Hobbes, Voltaire, Charles de Montesquieu, Jean Jacques Rousseau,  Thomas Aquinas, John Calvin and Sir William Blackstone.” Not only does Dunbar’s amendment completely change the thrust of the standard. It also appalling drops one of the most influential political philosophers in American history — Thomas Jefferson.

Incidentally, Thomas Jefferson was arguably America’s first paleontologist. Which certainly didn’t help his case in Texas.

I’ve just been checking out one of the oldest pieces of sculpture made by humans. The Smithsonian Institution has set up a major web site on human evolution. There’s lots of stuff worth exploring on the site, although there are still some bugs and some of the stuff is unnecessarily obscure for a site intended for us non-paleoanthropologists. I’m particularly fond at the moment of the 3-D scans of ancient artifacts that you can rotate around on your computer. Check out the lion-man, for starters.

[Image: Wikipedia]

Check out the latest Carnival of Evolution (with two items from the Loom) over at Mauka to Makai!

My post on birds and dinosaurs yesterday led to a little debate on Facebook, including this, from paleontologist Thomas Holtz:

All living birds share a common ancestor that would also be considered a bird, so they are a monophyletic group. Nevertheless, that group is deeply nested among euornithine ornithothoracine pygostylian avialian eumaniraptoran paravian metornithine maniraptoran maniraptoriform tyrannoraptoran coelurosaurian avetheropodan tetanurine averostran neotheropod theropod saurischian dinosaurs.

…and breathe.

A few questions came up during the webinar this afternoon that we didn’t have a chance to get to.

1. I talked about a poll of Texans about evolution. Someone asked for the source of the chart I showed. Here it is. I used this poll mainly to illustrate the fact that being a journalist who writes about evolution in the United States is an inherently interesting job. (You get really interesting comments, for example.) But I don’t think that Texas warrants singling out, judging by nationwide polls.

I also get annoyed when pollsters ask questions that demonstrate that they don’t understand evolution very well. Walk into a museum with a good dinosaur exhibit, and you’ll discover that birds are dinosaurs. And so, if someone changed that statement to “Humans and dinosaurs live at the same time,” and asked me if I agreed with it, I’d say, “You betcha!”

2. Another person asked how much space in The Tangled Bank I spend on the mechanisms of evolution, such as epistasis, fitness landscapes, evolvability, modularity, and genotype-phenotype maps. The answer is that I lay out some of the fundamental mechanisms, such as selection and drift, and try to delve into mechanisms that have been investigated more recently–without turning the book into a textbook for biology majors, instead of the non-majors book that it is. So, rather than deriving theorems, I tend to use illustrations, metaphors, and specific biological examples to get the concepts across.

3. A third person mentioned that she does research on the teaching and learning of evolution, and wondered if I would consider writing a book specifically for teachers to help them teach evolution. I’m no expert on pedagogy (which is why I had a board of advisers for The Tangled Bank made up of scientists who not only do important research on evolution but also teach non-majors). Fortunately, there are already lots of resources out there intended specifically for teachers, such as Understanding Evolution. (Full disclosure: I wrote the history sections on the site, and my chapter on evolutionary medicine can be downloaded for free there.)

Thanks again to AIBS, Chris Mooney, and all the people who joined us. It was my first webinar experience, and it was not only painless, but downright enjoyable. And congratulations to the people who won copies of our books!

Update: 8:15 pm. Jamie Vernon left a comment worth replying to at length:

Hi Carl,
I truly respect what you have done for science communication, however I must take exception to your implication that humans walk with dinosaurs. Dinosaurs? Really? “Terrible lizards?” You see, I live and teach in Texas so I see on a regular basis the problems of improper science education. Now, I can appreciate the humor in that statement and the provocative nature of it, but for those who clearly don’t understand evolution, it can be confusing and misleading. I assume when you agree that “humans walk with dinosaurs” meaning birds, you intend to provoke the question, “Really? How? Where?” Unfortunately, not everyone is as inquisitive as you might think. This leaves us, teachers, to clean up the mess. The statement isn’t anymore true than someone who says, “humans descended from chimpanzees.” So, the least you could do is clarify by stating that “humans walk with the descendants of dinosaurs.” Eh?

No, humans walk with dinosaurs.

It would not be true to say that humans walk with other species of dinosaurs, such as Tyrannosaurus rex or Velociraptor. But birds are dinosaurs, too. That is, they belong to the group of species defined as dinosaurs by paleontologists, based on their shared common ancestry. The statement “humans walk with dinosaurs” is not analogous to “humans descended from chimpanzees.” That would be like saying “birds descended from Tyrannosaurus rex.” Birds are dinosaurs in the same way humans are mammals.

This statement is not misleading, nor is it intended merely to provoke. It’s just an accurate depiction of the state of the science today. It problably comes as a surprise to many students, but that makes it–as they say–a teachable moment. The link to the American Museum of Natural History web site I provided above offers some good information to help students understand this statement. It’s also something I discuss in The Tangled Bank. Here’s an evolutionary tree I put together with the help of paleontologists to get this across…

Many animals have evolved camouflage, but nobody quite pulls it off as beautifully as the octopus and its tentacled cousin the cuttlefish. These invertebrates, which belong to a group called cephalopods, are covered in microscopic pigment organs that they can squeeze and stretch to take on the patterns around them. They can curl their tentacles to assume different shapes, and they can even change the texture of their skin to bumpy or smooth, as necessity demands.

Nobody knows the tricks of cephalopods better than Roger Hanlon, a biologist at the Marine Biological Laboratory in Woods Hole, Massachusetts. As I wrote in this New York Times profile of Hanlon, he has documented their powers of disguise both in the wild and in his lab. You can see some of the cephalopods in action in this Times video I narrated, as well as in these videos at Hanlon’s web site. Hanlon has carefully documented how cephalopods can melt away into their backgrounds; he’s also shown that male cuttlefishes can disguise themselves as females to sneak past bigger males to get a chance to mate. There’s still a lot Hanlon has yet to study about cephalopod camouflage, though; many of the most spectacular displays of shape-shifting are one-offs that Hanlon or a wildlife videographer happened to catch on a few seconds of video.

The video shown here is the latest addition to the repertoire of cepahlopod camouflage. As Hanlon and his colleagues write in a paper to be published in Biological Bulletin, the Atlantic longarm octopus (Macrotritopus defilippi) does an uncanny impression of a flounder.

Hanlon first saw this trick before he actually knew what it was. In the early 1980s, he captured a young Atlantic longarm octopus and reared it in a tank at Texas A&M University. It was the first time anyone had ever paid close attention to the biology of this obscure creature, which lives on sandy expanses of the Caribbean sea floor. While observing the octopus, Hanlon noticed that sometimes it would flatten out its tentacles and swim close to the bottom of the tank. At the time he didn’t know what to make of it.

In 2000 wildlife photographers took pictures of Atlantic shortarm octopuses in their natural habitat and suggested that they took on the strange shape to mimic flounders. Four years later, Hanlon took another picture that showed the octopus not just flat against the sea floor, but assuming the pattern of the surrounding sand–a trick that flounder use as well. The next year Hanlon and his colleagues spent 51 hours diving of the coast of the island of Saba searching for the octopuses on the sand plains. They managed to film one animal apparently pretending to be a flounder. And since then, professional photographers have supplied Hanlon with still more videos.

Hanlon and his colleagues have compared the footage of the octopus to footage of the peacock flounder, which lives in the same waters. The similarities are uncanny. Flounders hug the sandy bottom as they swim, even following the sand’s ripples. So do octopuses. The octopuses swim in the same short bouts as the flounder, and at about the same speed. They form their tentacles into a sheet-like mass with the same body outline as the flounder. The big difference between the octopus and the flounder is the way they blend into the background. The flounder are relatively slow at matching their surroundings, while the octopuses can change their skin quickly and with great precision. If there are white rocks scattered around on the sandy plain, Hanlon has noticed, a stationary octopus will produce a white spot on its body as well.

The Atlantic longarm octopus is not the only octopus to pretend to be a flounder. On the other side of the world, off the coast of Indonesia, Hanlon and his colleagues have documented two other species that pull off the same trick. (Here’s a video of one of the Indonesian species.) Pretending to be a flounder is such a useful strategy that three distantly related species of octopus have independently evolved it.

With flounder-mimicking octopuses now firmly established in the Atlantic Ocean as well as the Pacific, it’s high time to ask what is so great about flounders? Sandy plains are dangerous places for soft-bodied octopuses. Predators can spot them as they move across the open expanses. It’s possible that octopuses are not mimicking flounders per se, but are just taking advantage of the same kind of camouflage. But it’s also possible that small fish that do spot the octopus may leave it alone because it looks like a flounder. While a small fish could easily take a bite out of a soft, fleshy octopus tentacle, a tough, scaly flounder would pose a threat.

Paleontologists can make spectacular discoveries in remote badlands and deserts. But there are also things waiting to be found–or at least recognized–in the back rooms of museums. Things like giant filter-feeding fish.

The giant filter-feeding fish in this painting was discovered by Matt Friedman, a paleontologist at the University of Oxford. Friedman knows a thing or two about the treasures lurking in museum drawers. As I wrote in 2008, he showed that previously neglected fossils were actually transitional forms that track the evolution of the bizarre bodies of flatfish. Recently Friedman took a trip to the Rocky Mountain Dinosaur Resource Center in Colorado to check out some other fish fossils. While he was there, the center paleontologists asked him to take a look at a massive slab of rock they had just brought in. They knew it contained a fish that dated back to some time between 89 and 66 million years ago, but they couldn’t tell quite what sort of fish.

Clearly, the fish was big. The bony shells that encased its eyes were the size of grapefruits. The slab contained huge scimitar fins. On closer inspection, Friedman recognized that the fish belonged to an extinct lineage of fish called pachycormids. Pachycormids branched off early from other ray-finned fish and evolved into tuna-like predators. As Friedman examined the fossil, though, he found something very strange. Its jaws were toothless. Instead, Friedman found a loose set of rods, each measuring over four feet long. The fish, which Friedman dubbed Bonnerichthys, did not bite its prey. Instead, it opened its mouth wide and trapped tiny animals in bony filters in its mouth.

Today, a number of big filter feeders swim in the oceans. Among sharks and their relatives, filter feeding has evolved a few times, in forms such as manta rays and whale sharks. Baleen whales evolved filter feeding as well, and have evolved into the biggest animals ever–perhaps the biggest animals possible.

Filter-feeding sharks and whales are relative new on the scene, only appearing after the end of the Mesozoic Era 65 million years ago. During the 150-million-year Mesozoic, the oceans were home to many giant marine reptiles. Yet none of them appear to have evolved into filter feeders. Scientists have puzzled why none of them evolved to take advantage of that particular niche. Perhaps there was some constraint that blocked them from that way of life.

Bonnerichthys hinted at a different explanation. Paleontologists had previously found a few filter-feeding pachycormid dating back to a narrow time range around 160 million years. They generally dismissed these fish as a fleeting evolutionary experiment. But Bonnerichthys was another filter-feeding pachycormid living 100 million years later. Friedman began to scour museum collections for similar fish. As Friedman and his colleagues report today in Science, they  found a number of new species spanning those 100 million years, which had gone unnoticed before. Instead of a dead-end experiment, the filter feeders enjoyed a 100-million year dynasty.

In other words, the filter-feeding niche wasn’t empty through the Mesozoic. It was occupied by bizarre fishes that no one had noticed before, even as their bones sat for decades in museum drawers. At the end of the Mesozoic, the pachycormids died off in the same pulse of extinctions that wiped out the big dinosaurs on land. And only then did other animals–sharks and whales–take over the filter-feeding way of life. Friedman won’t speculate further about these remarkable animals for now. He’s going to hunt through some museum collections instead.

[Update 7 pm: Deep apologies for leaving off the painting credit! Image courtesy of Robert Nicholls, www.paleocreations.com]

In my new brain column for Discover, I take a look at recent research on fear. As dread turns to terror, our brains look an awful lot like the brain of a mouse as it realizes the feline end is nigh. Check it out.

It’s been nearly ten years since President Bill Clinton stood on the White House lawn with a team of scientists to announce the completion of the first survey of the human genome. “Today, we celebrate the revelation of the first draft of the human book of life,” he said. It’s a pleasing metaphor, but it’s deeply flawed. There is not a single Human Book of Life. If there were, after all, Clinton and the scientists and all the rest of us would all be identical clones.

There is a vast amount of genetic variation from person to person, and from one continent to another. The survey that Clinton was announcing was a cobbling-together of DNA from several individuals. Since then, researchers have produced much higher-quality reads of the genomes of actual people. They’ve learned a lot from those studies, but, in the scope of human genetic diversity, these studies have been timid ventures. If you compare someone from South Korea to someone of northern European descent, you’re only capturing a small sliver of the variation in our species. If you really want to get into the thick of it, there’s really one place to go: Africa.

This chart helps to illustrate why. If you trace the origins of the genetic material in our species, you end up in Africa. One reason we know this is that human populations outside of Africa share some genetic markers that Africans lack. That’s consistent with the hypothesis that Homo sapiens evolved in Africa, and then a small group of Africans migrated off the continent and gave rise to all the other populations of humans alive today. Another clue is in the genetic diversity of Africans themselves. Looking at relatively small collections of DNA, scientists have found much more genetic diversity in Africa than elsewhere. That would make sense if African populations have existed longer than populations elsewhere, giving them more time to accrue new mutations.

Africa is, of course, a huge continent, with a billion people and 2000 distinct ethno-linguistic groups. Some of those groups, including some of the most populous ones, are relatively young. In some cases, they expanded over large areas as they developed agriculture. Some smaller ethnic groups are only distantly related to other Africans, since their ancestors split off a long time ago. Those groups are crucial to a full-spectrum picture not just of African diversity, but the diversity of all humanity.

So it’s heartening to find that today scientists are publishing a genome of a man from one of those deeply diverging groups–the Khoisan of southern Africa, also known as the Bushmen of the Kalahari.

The Khoisan are not a single group of Africans, but a large number of small groups. They originally probably spanned much of southern Africa, making a living by hunting and foraging for food. Bantu farmers moved into southern Africa much later, taking up a lot of the arable land. Most Khoisan live now in Botswana and Namibia, eking out a precarious existence.

A team of scientists from the United States, Australia, and Africa sequenced the complete genome of a Khoisan named !Gubi (far left in the top photos). They also sequenced portions of the genomes of three other Khoisans from Namibia to gauge the diversity within the group. And, for comparison, they also sequenced the genome of a Bantu from South Africa. Not just any Bantu, mind you, but none other than Archbishop Desmond Tutu.

The survey confirmed the conclusion of earlier studies: Khoisans have a lot of genetic diversity. On average, each pair of the Khoisans differed at 1.2 out of every 1000 nucleotides (the “letters” of DNA). On average, a European and an Asian differ at 1 out of every 1000.

Khoisans lack some key adaptations that arose in Africans who have taken up agriculture. For example, they lack a mutation that allows adults to digest milk. They also lack a common mutation that provides resistance to malaria–a disease that took off when parasite-carrying mosquitoes could lay eggs in farm fields and bite farmers sleeping in nearby huts. But these absences don’t mean that Khoisans are primitive cavemen, or that their genomes are a time capsule from antiquity. Most of the distinctive features of their genomes arose only after their ancestors split off from the ancestors of other humans. A number of those new mutations show some indications of being adaptations for life in the desert, such as controlling levels of salt in the blood.

Understanding the genome of Khoisans is not just interesting in itself, but important to the well-being of all people on Earth. To figure out the effects of genes on our health, scientists scan DNA from lots of people, looking for variations that are strongly linked to certain diseases. As I wrote last year in Newsweek, it’s been a struggle. One reason is that the list of genetic variations we’ve been using has, until now, been too short. In the new study, the scientists found 1.3 million differences between Khosians and the reference human genome against which all human DNA is compared. Just as intriguing are some of the variants that Khoisans have that are found in other populations. Some of these familiar variants have been linked to serious diseases. Yet all the Khoisans who were tested in the new study were around 80 years old and in excellent physical shape. The effect of these variants may actually depend on variations in other genes. To figure out what any one human genome means for a person’s health, scientists need to look at a full spectrum of human genomes. The Book of Life is not enough. We need to read the Library of Life.

[Images: Schuster et al, "Complete Khoisan and Bantu genomes from Southern Africa," Nature, doi: 10.1038/nature08795, Campell and Tishkoff]

I was stunned to learn that National Geographic has never published a story on carnivorous plants. So I wrote one. It’s now out in March issue, as well as on the NG web site. It should come as no surprise that the article is accompanied by dazzling photos that will probably make most readers forget that there’s a story lurking in the shadows, too. You can look at the pictures in the NG slideshow, and see some extra outtakes on the web site of the photographer, Helene Schmitz.

Last March a new kind of flu came on the scene–the 2009 H1N1 flu, a k a swine flu. Hatched from an eldritch mingling of viruses infecting humans, birds, and pigs, it swept across the world. Here in the United States, the CDC estimates that between 41 and 84 million people came down with swine flu between April and January. Of those infected, between 8,330 and 17,160 are estimated to have died. For more details on the evolution of this new flu strain, here’s a video of a lecture I gave in November.

This flu strain has been nothing if not surprising. It was lurking around in humans for several months, undetected, before becoming a planetary infection. And before that, the ancestor of the virus was circulating among pigs for a decade, again unknown. And while the new swine flu has killed some 10,000 people in the United States alone and many more abroad, it has proven to be relatively low key–as flu goes. Some 30,000 people die in the United States every year from seasonal flu, the cocktail of flu strains that show up year in and year out.

Now the swine flu is surprising us once more. It has dwindled away to very low levels and stayed there. Meanwhile, the seasonal flu, which was expected to kick in at some point as well this flu season, is a virtual no-show. The San Francisco Chronicle has the story. In this CDC chart of total reports of flu-like symptoms, you can see that we’re in a deep trough. At this point in previous years, we were fast approaching the peak of the flu. This season, the peak came months ago, at the height of the fall swine flu outbreak.

When swine flu started to crash, some observers expected it to bounce back soon, as other flu strains have in the past. Ian York, at his blog Mystery Rays from Outer Space, offers some interesting ideas about why this hasn’t happened. He suggests that the virus has been stymied by pre-existing immunity in a lot of old people, new immunity from vaccinated children, and the protection that infected survivors now have. In other words, the virus just doesn’t have enough hosts now to sustain a new outbreak.

It’s possible that the swine flu’s raging success in the fall may have also led to the weird situation we’re in right now, with no seasonal flu at exactly the time you’d expect it. One possibility is that getting sick with swine flu provides some cross-immunity to seasonal flu. Another is ecological: the swine flu outcompeted seasonal flu so effectively at the start of flu season that the seasonal flu hasn’t been able to get a toehold since.

That, of course, could change. Seasonal flu has been known to peak as late as March. And while flu may be in a lull in the United States, it’s doing just fine in other parts of the world. For example, a nasty kind of flu called influenza B is raging around China right now according to the Chronicle. In normal years B makes up a pretty small fraction of US flu. But this is no normal year.

Scientists did a better job tracking the 2009 H1N1 outbreak than they have with previous emergent strains. They’ve got new machines to sequence virus genes, online databases to pool information from around the globe, and powerful computers to help figure out where the viruses came from. And yet, with just ten genes, the flu still continues to move enigmatically ahead of our understanding.