This is a story of about how the parts of a puzzle locked into place 800 million years ago. The puzzle is an ion pump that you can find in any mushroom, mold, or yeast. I’ve reproduced a picture of it here.

Fungus cells, like our own cells, have lots of little pouches inside of them for carrying out special kinds of chemical reactions. In order for those reactions to work, there have to be a lot of positively-charged protons inside the pouches. To get those protons into the pouches, ion pumps like this one force them through membranes.

This pump (which is is offically known as a vacuolar ATPase complex) is a wonderfully complex collection of proteins. They fit together elegantly, and they cooperate to get this vital job done. One particularly cool feature of this pump is the ring lodged in the pouch’s membrane, where it spins around like a wheel. The ring is made up of six proteins–four copies of a protein called Vma3, and a single copy of two other proteins called Vma11 and Vma16–that lock together. If a mushroom can’t make all three types of proteins, ...]]> http://blogs.discovermagazine.com/loom/2012/01/10/resurrecting-evolution-to-solve-an-800-million-year-old-puzzle/feed/ 6 http://blogs.discovermagazine.com/loom/2011/12/19/the-french-disease-the-italian-disease-the-christian-disease-the-new-world-disease/ http://blogs.discovermagazine.com/loom/2011/12/19/the-french-disease-the-italian-disease-the-christian-disease-the-new-world-disease/#comments Mon, 19 Dec 2011 22:35:13 +0000 Carl Zimmer http://blogs.discovermagazine.com/loom/?p=5309

In 1494, King Charles VIII of France invaded Italy. Within months, his army collapsed and fled. It was routed not by the Italian army but by a microbe. A mysterious new disease spread through sex killed many of Charles’s soldiers and left survivors weak and disfigured. French soldiers spread the disease across much of Europe, and then it moved into Africa and Asia. Many called it the French disease. The French called it the Italian disease. Arabs called it the Christian disease. Today, it is called syphilis.

I’ve been intrigued by the murky history of syphilis for a few years now. The text above is from the start of an article I wrote for Science in 2008. At the time, scientists were split between two explanations for sudden appearance of syphilis at the end of the fifteenth century. According to one, it was caused by bacteria that had evolved in the New World and were brought back to Europe by Columbus’s crew. But other researchers found many skeletons with signs of syphilis in Europe, Africa, and Asia that appeared to have been from long before Columbus’s voyage. They argued that it must ...]]> http://blogs.discovermagazine.com/loom/2011/12/19/the-french-disease-the-italian-disease-the-christian-disease-the-new-world-disease/feed/ 17 http://blogs.discovermagazine.com/loom/2011/12/12/a-long-walk-to-land/ http://blogs.discovermagazine.com/loom/2011/12/12/a-long-walk-to-land/#comments Mon, 12 Dec 2011 21:33:52 +0000 Carl Zimmer http://blogs.discovermagazine.com/loom/?p=5284 Long before Darwin published The Origin of Species, there was talk of evolution. The more acquainted naturalists became with the major groups of animals, the gaps between them grew smaller. Once it seemed as if mammals were profoundly different than other vertebrates, for example. And then European explorers encountered the platypus, a mammal that laid eggs. Perhaps the major groups of animals had not been separately created, some naturalists suggested. Perhaps life had changed over time.

In 1837, a profoundly paradoxical creature was shipped from West Africa to London, packed in clay. It was destined for Richard Owen, the greatest British anatomist of his age. He picked away the clay, to reveal a creature that looked like a fish. It has a knife-shaped body, gills, and fins. “If indeed the species had been known only by its skeleton,” Owen wrote, “no one could have hesitated in referring it to the class of Fishes.”

But inside its body, Owen found what he could only call lungs. Its whisker-like fins had a chains of bones that faintly resembled arms. Owen was a fierce opponent of all the transformationists of his day, and ...]]> http://blogs.discovermagazine.com/loom/2011/12/12/a-long-walk-to-land/feed/ 10 http://blogs.discovermagazine.com/loom/2011/11/28/peace-war-and-evolution-my-profile-of-steven-pinker-in-tomorrows-new-york-times/ http://blogs.discovermagazine.com/loom/2011/11/28/peace-war-and-evolution-my-profile-of-steven-pinker-in-tomorrows-new-york-times/#comments Mon, 28 Nov 2011 18:49:41 +0000 Carl Zimmer http://blogs.discovermagazine.com/loom/?p=5211 The New York Times has launched a series called Profiles in Science. When I was invited to join the undertaking, I proposed writing about the Harvard psychologist Steven Pinker. I had run into Pinker at the World Science Festival in June, and he had told me about his next book, The Better Angels of Our Nature, which was due out in the fall. In the 800+ page tome, Pinker argues that rates of human violence have been crashing for millennia, and he offers psychological explanations for the fall.

I’ve followed Pinker’s work since I first came across his 1994 book, The Language Instinct. In the wake of the book’s success, he quickly became a leading exponent of evolutionary psychology, coming out swinging against its critics such as Stephen Jay Gould. When Pinker described his book to me, I was intrigued. I wondered how someone who argued that human nature was shaped long ago by natural selection would end up arguing that human nature–or at least human experience–is now changing rapidly for the better. But there were other things I was wondering–how, for example, does a writer of massive books about human nature live inside the ...]]> http://blogs.discovermagazine.com/loom/2011/11/28/peace-war-and-evolution-my-profile-of-steven-pinker-in-tomorrows-new-york-times/feed/ 9 http://blogs.discovermagazine.com/loom/2011/11/22/are-we-the-teachable-species/ http://blogs.discovermagazine.com/loom/2011/11/22/are-we-the-teachable-species/#comments Tue, 22 Nov 2011 15:14:07 +0000 Carl Zimmer http://blogs.discovermagazine.com/loom/?p=5169 We know that our species is unique, but it can be surprisingly hard to pinpoint what exactly makes us so. The fact that we have DNA is not much of a mark of distinction. Several million other species have it too. Hair sets us apart from plants and mushrooms and reptiles, but several thousand other mammals are hairy, too. Walking upright is certainly unusual, but it doesn’t sever us from the animal kingdom. Birds can walk on two legs, after all, and their dinosaur ancestors were walking bipedally 200 million years ago. Our own bipedalism–like much of the rest of our biology–has deep roots. Chimpanzees, whose ancestors diverged from our own some seven million years ago, can walk upright, at least for short distances.

If looking for human uniqueness on the outside is difficult, is it any easier to look on the inside–in particular, at our mental lives? There’s no doubt that our minds allow us to do things that even our great ape relatives cannot. For one thing, we can represent the world symbolically in our heads, and we can use words to communicate that symbolic thought to one another. ...]]> http://blogs.discovermagazine.com/loom/2011/11/22/are-we-the-teachable-species/feed/ 23 http://blogs.discovermagazine.com/loom/2011/11/14/neanderthal-neuroscience/ http://blogs.discovermagazine.com/loom/2011/11/14/neanderthal-neuroscience/#comments Mon, 14 Nov 2011 21:18:28 +0000 Carl Zimmer http://blogs.discovermagazine.com/loom/?p=5140 When the Society for Neuroscience gets together for their annual meeting each year, a city of scientists suddenly forms for a week. This year’s meeting has drawn 31,000 people to the Washington DC Convention Center. The subjects of their presentations range from brain scans of memories to the molecular details of disorders such as Parkinson’s and autism. This morning, a scientist named Svante Paabo delivered a talk. Its subject might make you think that he had stumbled into the wrong conference altogether. He delivered a lecture about Neanderthals.

Yet Paabo did not speak to an empty room. He stood before thousands of researchers in the main hall. His face was projected onto a dozen giant screens, as if he were opening for the Rolling Stones. When Paabo was done, the audience released a surging crest of applause. One neuroscientist I know, who was sitting somewhere in that huge room, sent me a one-word email as Paabo finished: “Amazing.”

You may well know about Paabo’s work. In August, Elizabeth Kolbert published a long profile in the New Yorker. But he’s been in the news for over fifteen years. Like many other ...]]> http://blogs.discovermagazine.com/loom/2011/11/14/neanderthal-neuroscience/feed/ 65 http://blogs.discovermagazine.com/loom/2011/10/24/dinosaurs-in-flight-the-movie/ http://blogs.discovermagazine.com/loom/2011/10/24/dinosaurs-in-flight-the-movie/#comments Mon, 24 Oct 2011 20:15:39 +0000 Carl Zimmer http://blogs.discovermagazine.com/loom/?p=5094 Earlier this year in National Geographic, I wrote about how feathers evolved long before flight. This timing naturally raises the question, how did feathered dinosaurs take to the air?  My article was accompanied by a picture from the University of Montana lab of Ken Dial, who argues that before dinosaurs flew, they flapped their wings to help them travel up and down inclines. While not all experts accept Dial’s hypothesis, it has the undeniable strength that he can gather evidence for it in living birds, rather than just inferring behavior from fossils alone.

This video shows some of the astonishing climbs birds can make with the help of some wing flapping. It’s a mix of lab climbs and footage from the wild, with an evolutionary tree of birds.

This is a skill that takes time for birds to develop, as shown in this video below. Dinosaurs might have gradually acquired the skill as well, as their arms evolved into more bird-like wings.

Dial argues that this flapping would also help on the way down, too. Here’s a young bird leaping to the ground, and flapping its wings to control its fall.

By the time dinosaurs had evolved the ability to use feathers ...]]> http://blogs.discovermagazine.com/loom/2011/10/24/dinosaurs-in-flight-the-movie/feed/ 8 http://blogs.discovermagazine.com/loom/2011/10/17/the-language-gene-turns-ten/ http://blogs.discovermagazine.com/loom/2011/10/17/the-language-gene-turns-ten/#comments Mon, 17 Oct 2011 19:18:07 +0000 Carl Zimmer http://blogs.discovermagazine.com/loom/?p=5088 Ten years ago this month, a team of University of Oxford scientists published a description of a family who struggled with words. By comparing their DNA, the scientists zeroed in for the first time on a gene associated with language, dubbed FOXP2. In my newest column in Discover, I look back at what scientists have learned over the past decade about how FOXP2 works, and what it tells us–or leaves us wondering–about how language evolved. Check it out.

Here’s my story, on the cover of tomorrow’s Science Times. I look at how they solve the evolutionary puzzles of altruism, build highway systems, and turn out to be some of the oldest life forms on land.

(And for more on the ever-expanding worldwide diversity of slime mold, check out the Eumycetezoan Project.]

[Image: myriorama/Flickr via Creative Commons]

The man is Lee Berger, a paleoanthropologist at the University of Witwatersrand in South Africa. He’s holding the skull of Australopithecus sediba, a 1.98 million year old relative of humans, otherwise known as a hominin. In April 2010 Berger and his colleagues first unveiled the fossil in the journal Science. As I wrote in Slate, Berger argued that A. sediba was the closest known cousin to our genus Homo. Hominins branched off from other apes about 7 million years ago, but aside from becoming bipedal, they were remarkably like other apes for about five million years. Among other things, they were short, had long arms, and had small brains. Berger and his colleagues saw in A. sediba what biologists often find in transitional forms–a mix of ancestral and newer traits. It has Homo-like hands, a projecting nose, and relatively long legs. It was intermediate in heigh between earlier hominins and the tall Homo. And it still had a small brain and long arms. (In August, Josh Fishman wrote a feature for National Geographic on A. sediba, complete with excellent ...]]> http://blogs.discovermagazine.com/loom/2011/09/08/the-verge-of-human/feed/ 14 http://blogs.discovermagazine.com/loom/2011/08/29/climate-relicts-my-new-story-for-yale-environment-360/ http://blogs.discovermagazine.com/loom/2011/08/29/climate-relicts-my-new-story-for-yale-environment-360/#comments Mon, 29 Aug 2011 13:54:57 +0000 Carl Zimmer http://blogs.discovermagazine.com/loom/?p=4957 I’m among the 800,000 people in Connecticut without power thanks to Irene, so I won’t be blogging much for the foreseeable future. But before I get to other matters like dragging branches around, let me point you to my latest piece for Yale Enivronment 360. I take a look at a new concept called the climate relict. Around the world, there are pockets of plants and animals living hundreds of miles away from their main species ranges. They were left behind in refuges at the end of the last Ice Age, as others moved towards the poles in response to the warming climate. As the climate now warms even more, climate relicts have a lot to teach us about how to manage biodiversity. Check it out.

[Update: bad link to Yale e360 fixed]

Steve will be posting the second part of the talk soon.

Coulter takes this opportunity to remind us that she dedicated a third of her 2006 book Godless to demolishing evolutionary biology. Apparently the scientists who have published over 59,000 papers on the topic of evolution since she published her book didn’t get the memo.

To rectify that situation, Coulter now informs us that “it is a mathematical impossibility, for example, that all 30 to 40 parts of the cell’s flagellum — forget the 200 parts of the cilium! — could all arise at once by random mutation.”

Of course, nobody is saying they evolved all at once by random mutation. Nobody except for Ann Coulter. To see what scientists are actually saying, you can start by reading this review that presents a detailed hypothesis about the incremental evolution of the flagellum and the cilium, based on actual experiments. In a ...]]> http://blogs.discovermagazine.com/loom/2011/08/25/ann-coulter-nostalgia-behold-for-i-am-the-giant-flatulent-raccoon/feed/ 48 http://blogs.discovermagazine.com/loom/2011/08/23/zooming-in-on-the-cholera-tree-of-life-and-death/ http://blogs.discovermagazine.com/loom/2011/08/23/zooming-in-on-the-cholera-tree-of-life-and-death/#comments Tue, 23 Aug 2011 17:10:05 +0000 Carl Zimmer http://blogs.discovermagazine.com/loom/?p=4918 In the wake of last year’s earthquake in Haiti, cholera arrived on the island for the first time in 60 years. According to the World Health Organization, 419, 511 Haitians got sick with cholera as of July 31, of which 5,968 died. The infection rate is dropping right now, but the arrival of Hurricane Irene could change that.