Carl Zimmer's Blog, page 13

On Smallpox and Killer Robots

I had a fun half hour yesterday evening chatting with the folks on Nerd’s Forum on Huffington Post Live. We reviewed some of the science news of the past week, from the eradication of smallpox to the threat of super-intelligent machines. You can watch the recording here.

Ebola: New or Old?

As viruses go, Ebola has a grim star power. When a new outbreak hits, Ebola kills a high fraction of its victims, causing horrific bleeding along the way. The latest outbreak started in March in Guinea. As of today, the World Health Organization reported 231 cases and 155 deaths.

In order to better treat Ebola, Pardis Sabeti of Harvard and her colleagues have been analyzing the virus’s evolution. It turns out that Ebola is not some freakish new plague, but rather old. If that seems puzzling, a research scientist in Sabeti’s lab, Stephen Gire, has created this animation, which I’ve embedded below, to explain it.

Gire’s video is part of a contest being run by the National Institutes of Health. Check them all out and vote for your favorites. It’s great to see scientists being encouraged to explain what they do in a new medium like this. Wonderful things can evolve from this kind of experiment. A few years ago, for example, Brown University biologist Casey Dunn and his students started toying around with stop-action animation to tell stories of marine biology, and now their “Creature Cast” series is regularly featured on the New York Times web site.

Who knows–perhaps the next Carl Sagan will be a cartoonist?

More Stories! Laser Cowboys, Killer Flu, and the Bloody Fountain of Youth

Allow me to direct your attention to three stories of mine that have come out in the past few days:

1. In Popular Mechanics, I take a look at the convergence of the old and the new. Paleontologists are using the latest laser-scanning technology and 3D-printing devices to visualize and replicate fossils. When you are faced with a graveyard of forty fossil whales, this kind of thing is a really big help.

2. In 1918, a third of people came down with a new kind of flu that killed 50 million people. It was the worst pandemic of the past century by far. What was so awful about it? For my latest “Matter” column for the New York Times I look at a provocative new explanation: maybe it was mostly a matter of bad timing.

3. Is there something in the blood of the young that can reverse aging in the elderly? An eerie new set of experiments adds more evidence in favor of the answer being yes. I have the details in today’s New York Times. Already on Twitter and Facebook, people have offered up references to vampires, Keith Richards, Elizabeth Bathory, Flowers for Algernon,  and Methuselah’s Children. I guess it’s just one of those stories that hits a very big cultural nerve.

Parasite Cuisine: Eating the Eaters

This week I took a trip to the University of Maryland to give a talk about parasites. I waxed poetic about how sophisticated parasites are in their manipulations of their hosts, and how we might do well to learn from their wisdom about how the brain works. At dinner, I sat next to David Inouye, the incoming president of the Ecological Society of America. The waiter set down plates in front of us, loaded with plants, animals and fungi–free-living organisms, in other words. As we looked at the plates, a question came up: is there a parasite you can eat?

Obviously, no one sits down to a piping hot bowl of smallpox soup. But parasites can also take the form of plants, animals and fungi–just like the plants, animals, and fungi we were eating.

Having written a book (and many articles) on parasites, I couldn’t think of a parasite that people eat. But if there’s one thing I’ve learned about parasites, it’s never to make an assumption about them, because the truth will always be weirder than I imagined.

Inouye, on the other hand, immediately thought of one: pea crabs.

Pea crabs get their names from their tiny size. They slip into the shells of mussels and oysters, where they take up residence on the gills of their hosts. They feed on the bits of food in the water that their hosts pump into the shell. Pea crabs are bad for their hosts, gradually eroding their gills that they depend on to take in oxygen. But despite their cruel way of life, they’re tasty. George Washington, Inouye informed me, was the most famous fan of pea crabs, delighting to eat them in oyster stew.

In Mexico, another parasite is a popular delicacy. Called huitlacoche, this parasitic fungus infects corn. As it feeds on an ear of corn, it balloons out into a gruesome grey bulb. But served up in a quesadilla, it’s reportedly delicious.

Later in the week, Inouye decided to present our question to an email list of ecologists. It turned out there were a lot more parasitic dishes.

Take lampreys. Lampreys belong to an ancient lineage of vertebrates, branching off on their own before the evolution of jaws. Instead, these creatures have a disk-shaped mouth ringed with rasp-like teeth. Many species of lampreys are parasites. They use their suckers to grab onto other fish. Riding along, they dig into the flesh of their host, and feed on its blood and flesh.

Despite being rather loathsome parasites, lampreys are a delicacy. Henry I, the king of England, reportedly died from eating too many lampreys. Queen Elizabeth was served a lamprey pie on her coronation day. (The Internet being the Internet, there is a whole page dedicated to the 1000-year history of the lamprey pie.)

I could imagine eating a lamprey pie (if it was diced into very small pieces), but some forms of parasite cuisine are beyond my comfort zone. The zoologist Tim Flannery describes watching someone in New Guinea gut a marsupial, remove any tapeworms from its intestines, and put the still-squirming parasites in his mouth. In 1955, a biologist doing field work in Alaska reported that Inuits liked to eat the warble fly maggots that develop in the hide of the reindeer.

And in his 2003 presidential address to the American Society of Parasitologists, Robin Overstreet discussed another delicacy of the Inuits:

These people, however, obtain an even larger parasite snack by eating Pennella balaenopterae, a poorly understood [crustacean] species that can grow to monstrous proportions. Specimens up to 30 cm long routinely embed deeply into the blubber of baleen whales, with the posterior of their bodies trailing free from the host. The plump and juicy body extremity is plucked from the host and eaten raw, and the “sweet” contents of the blood-filled neck are sucked out.

Overstreet’s whole speech was about ingesting parasites. Apparently, you cannot impeach a president for such an act. If you’re so inclined, you can read the speech here. It’s fascinating, but the quality of the photographs that accompany it is far too good for my peace of mind.

Finally, people eat parasites as medicine. Dodder is a parasite, growing on other plants and drawing out their nutrients. In the Philippines, people take dodder as a traditional treatments for aches and other ailments. Another fungus, called Cordyceps, turns ants into zombies. To keep the insides of their ant homes clean of germs, they make antibiotics. The popularity of the fungus in Chinese medicine has led to a Cordyceps boom in Tibet, the subject of this fascinating National Geographic story.

The list of parasites as food turns out to be encyclopedic. And so, when your local artisanal hipster eatery runs out of ideas, don’t be surprised if they reopen under a new name: Cafe Liver Fluke.

Where Genes Come From

In today’s New York Times, I’ve written a story about a simple but important question: where do new genes come from?

Some four billion years ago, when cellular life emerged, a typical primordial microbe likely had only a small set of genes. Today, however, genes abound. We, for example, have 20,000 genes that encode proteins. Dogs have their own set, and so do starfish and fireflies and willow trees and every other species on Earth.

Somehow, in all that time, evolution produced a lot of new genes. As I explain in my story, one way to make a new gene is to copy an old one. The two duplicates can then evolve in different directions. Duplicate each of them, and now one gene has become four. There’s plenty of evidence that gene duplication drives the origin of a lot of new genes.

But there are other ways. In my story, I focus on one example. In animals and plants and related species (known collectively as eukaryotes), protein-coding genes are nestled in vast stretches of DNA that don’t code for proteins. It takes only a modest mutation to non-coding DNA to get a cell to read some non-coding DNA and treat it like a gene. The protein the cell makes may be a complete mess, or it may be harmless. As I write in my story, there’s a growing body of evidence that this process generates new protein-coding genes at a steady clip. In fact, so many new genes have arisen that scientists are trying to figure out why species don’t have many more genes than they do. (The answer seems to be that sometimes the new genes get accidentally deleted as DNA gets copied.)

I didn’t have the space to discuss the other ways new genes evolve. Sometimes mutations will change the point where a cell starts to read a gene, for example, shifting down the length of DNA. The result may be a new protein with a new structure. A microbe may pass a gene to another species, and the gene in each species may then evolve in different directions.

What’s fascinating to me about the evolution of new genes is that it changes the way I think of evolution as a whole. I sometimes think of the genes in an organism as the musicians in an orchestra. As each gene evolves, I imagine each musician playing a new melody. But evolution can invite new musicians to pull up a chair and add their music to the song.

 

Springtime Yammerings

I’ll be giving some talks in the next few months, and I wanted to let you know the when’s and where’s…

This Saturday at 1 pm, I’ll be at the USA Science & Engineering Festival in Washington DC. I’ll be moderating a panel discussion on personalized medicine. The panelists will include Francis Collins, the director of the National Institutes of Health. Details here. 

On Wednesday, April 30, I’ll be delivering the University of Maryland’s fourth annual Lee Hellman Lecture. My talk is called, “Possessed: The Biology of Parasite Manipulation.” The talk, which is free and open to the public, is at 4:30 pm in CHM 1407 (Map).  Details here.

On May 7, I’ll be taking part in Story Collider’s Fourth Anniversary celebration. My fellow story-tellers include the great Jon Ronson, so it’ll definitely be worth sitting through my spot. Details here.

On May 21, I’ll be taking a stroll to my fine local library, the Guilford Free Library in Guilford, Connecticut, to give a talk called “Can Your Genome Save Your Life?” Details here.

On June 26, I’ll be in New Haven, Connecticut, to participate in the annual International Arts & Ideas Festival. My talk will be entitled, “How To Make A Human Being.” Details here.

And finally (for now), on September 11, I’ll be at the Fall for the Book Festival in McLean, Virginia, in a conversation with the delightful author of The Disappearing Spoon and the Violinist’s Thumb, Sam Kean. Details here

Stretching the Seasons

Across much of the Northern Hemisphere, the land is now greening up. The first signs of spring are arriving earlier with each passing decade, thanks to the changes we’ve already made to the world’s climate. But, as I write in my “Matter” column this week in the New York Times, our alteration of the seasons is proving to be more extensive and complex than previously thought. It’s important to figure out how we’re changing the seasons today, because we will likely be wreaking far more dramatic changes in decades to come. Check it out.

The Wisdom of (Little) Crowds

In 1785, a French mathematician named Marie Jean Antoine Nicolas de Caritat (known as Marquis de Condorcet) used statistics to champion democracy.

Democracies are based on the collective decisions of large groups of people. But citizens aren’t experts on every topic, and so they may be prone to errors in the choices they make. And yet, Condorcet argued, it’s possible for a group of error-prone decision-makers to be surprisingly good at picking the best choice.

Condorcet’s logic was simple. Assume you have a group of people each independently making a choice about a question. Assume that they have a chance of making the wrong choice–but that their choices are better than random. If the decision they’re trying to make is either thumbs up or thumbs down, for example, their chance of picking the right answer only needs to be greater than 50 percent. The odds that a majority of them will pick the right answer is greater than the odds that any one of them will pick it on their own. What’s more, Condorcet argued that the group’s performance gets even better as its size goes up.

Condorcet’s argument is the foundation of what’s now commonly called the “wisdom of crowds.” Individuals who have imperfect understanding of a situation can band together to become good at collective decision-making.

There are some famous stories that illustrate the wisdom of crowds. Just over a century ago, Sir Francis Galton asked 787 people to guess the weight of an ox. None of them got the right answer, but, pooled together, their collective guess was almost perfect. In his book, The Wisdom of the Crowds, James Surowiecki writes about the game show “Who Wants to Be a Millionaire?” Contestants could get help answering questions either from an individual friend whom they considered an expert, or from a poll of the audience. The majority of the audience picked the right answer 91 percent of the time, while individual friends only did so 65 percent of the time.

Many scientists have used Condorcet’s idea (known as the jury theorem) as a launching pad for exploring collective decision-making. They’ve expanded the basic theory to include more features of crowds–such as the way information can move through them. They’ve tested out versions of the jury theorem on real groups of humans and animals. And their research has shown that crowds really can be wise. People can indeed make better decisions in groups than on their own. And while animals may not be able to pick presidents, they can also make good decisions in groups. It may be hard for an individual fish to recognize a predator in a murky ocean and escape in time. But a school of fish can pool its uncertain information to avoid enemies.

In fact, animals can make some remarkably sound choices among remarkably complicated options. In this feature I wrote for Smithsonian, I described the decisions that honeybee swarms make. Thomas Seeley, a Cornell biologist, has shown that a swarm of honeybees can choose among several possible locations to build a new hive. And they’re able to choose the best spot in terms of size, temperature, and other factors.

But now a leading expert on crowd decisions is starting to question some of the basic rules of the wisdom of crowds. In a new study, Iain Couzin of Princeton and his graduate student Albert Kao argue that, in most case, small groups are wiser than big ones.

This result came as a surprise to Couzin. For over a decade he’s been studying collective decision-making, combining mathematical models with sophisticated experiments on fish, insects, and other animals. (For more on Couzin’s work, check out fellow Phenom Ed Yong’s 2013 Wired feature and my 2007 profile in the New York Times.)

To develop their models for how animal swarms make decisions, Couzin and his colleagues have made certain assumptions. That’s how science always works–rather than try to replicate every facet of reality, you assume that some of them are irrelevant to the phenomenon you want to understand. But in recent years, Couzin and Kao started to question two of the most basic assumptions about collective decision-making.

The first assumption goes all the way back to Condorcet. It’s the idea that all the votes cast by a group are truly independent of one another. Each voter, in other words, makes a decision based on his or her own imperfect information about the subject. To do so, each voter has to gather information on a question on his or her own. In these conditions, the casting of each vote is like rolling a separate set of dice.

That might well be true in some cases, but Couzin and Kao could imagine many cases where it wouldn’t be. If people all gather information about a presidential candidate from different news sources, their votes will be based on independent sources of information. But if they all get their information only by watching the same show on MSNBC, their information isn’t independent. Instead, it’s what scientists describe as correlated.

A similar situation holds true for animals. If two fish are swimming on opposite sides of a school, they may have two entirely different fields of view of their surroundings. The information that one fish gets on one side is uncorrelated with the information that the other fish gets. And that means that the decisions they make based on cues in their environment are also uncorrelated. Their uncorrelated information gives them a collective wisdom that a single fish, with its limited amount of information, can’t gather.

By contrast, two fish swimming side by side see almost entirely the same scene. Their information is correlated. And that means their decisions are correlated, too. If one fish gets misled by a mirage, the other one is likely to be misled as well.

Couzin also became concerned by how wisdom-of-the-crowd experiments are set up. Scientists typically present a group of animals (or people) with a single cue they can use to make a decision. They might offer a school of fish a visual cue and see if they decide it’s a predator they have to escape.

But in the natural world, animals are swamped with information from lots of sources. Individuals on the lookout for predators may use not only their eyes, but also their ears and their noses.

This feature of real decision-making may have huge effects on how crowds perform. It’s not simply that each fish is keeping track of more than one cue. It’s also the fact that some cues may be very reliable and others may be unreliable. Some cues may be correlated, and others uncorrelated. And animals may learn to pay more attention to some cues and disregard others.

Couzin and Kao wondered how these factors could affect the wisdom of crowds. They put together a series of mathematical models that included correlation and several cues. In one model, for example, a group of animals had to choose between two options–think of two places to find food. But the cues for each choice were not equally reliable, nor were they equally correlated.

The scientists found that in these models, a group was more likely to choose the superior option than an individual. Even in these more realistic conditions, the wisdom of crowds survives.

Couzin and Kao expected that the bigger the group got, the wiser it would become. But they were surprised to find something very different. Small groups did better than individuals. But bigger groups did not do better than small groups. In fact, they did worse.  A group of 5 to 20 individuals made better decisions than an infinitely large crowd.

The problem with big groups is this: a faction of the group will follow correlated cues–in other words, the cues that look the same to many individuals. If a correlated cue is misleading, it may cause the whole faction to cast the wrong vote. Couzin and Kao found that this faction can drown out the diversity of information coming from the uncorrelated cue. And this problem only gets worse as the group gets bigger.

Small groups, Kao and Couzin found, can escape this trap. That’s because probability works differently in small groups as opposed to large ones. It’s not unheard of, for example, to roll the same number a few times in a row. But it’s really weird to do so a thousand times in a row. Likewise, in a small decision-making group, a lot of individuals may end up using uncorrelated cues–the ones that give wisdom to crowds.

Couzin and Kao’s analysis, which has just been published in the Proceedings of the Royal Society, doesn’t prove that the wisdom of big crowds is a fatally flawed idea. But it does serve as a warning that even simple factors can have a big impact on how groups make decisions. And it may help to explain how real animals form groups.

When scientists first came to appreciate how groups can make decisions, a question naturally arose: why don’t all animals live in gigantic groups? Some researchers argued that big groups had drawbacks that balanced the advantage they offered in making good decisions.

But Couzin and Kao wonder if such drawbacks don’t, in fact, exist. Perhaps animals live in smaller groups because smaller groups are better at making decisions.

Even the animals that do live in big groups may not actually be solving problems en masse. Only a small fraction of the group may actually be casting votes, while the rest follow their lead.

Couzin and Kao’s work also raises some questions about how we humans make decisions. If people are basing their decisions on the same information, they may be more prone to bad decisions in big groups. All things being equal, smaller groups might do better. And big groups might improve their choices if people avoided relying on the same sources of information.

In a sense, Couzin and Kao’s new study is an idea whose time has come. Only now is it becoming possible to study the perceptions and decisions of hundreds of animals as they respond to several cues at once. In years to come, Couzin, Kao, and their colleagues may be able to experiment on this model. And, in the process, they may finally be able to put Condorcet’s elegant idea to a natural test.

Weekend Reading: The Long Road to Ancient DNA, and Gene-Stealing Ferns

I’ve been traveling again this week, which makes blogging a challenge. But I still can still offer a couple pieces of reading for your weekend diversion.

–Over the years, I’ve written many articles about the amazing work of Svante Paabo, who has pioneered methods for salvaging ancient DNA from fossils. (Here’s my most recent piece, on the entire genome of a Neanderthal extracted from a toe bone.)

The New York Times Book Review asked me to read Paabo’s new memoir, Neanderthal Man. Here’s my review. As I note in the piece, memoirs by scientists are a tricky genre. Very often, scientists want to delve into fine detail about their research, while tossing off frustratingly fragmented bits about their personal lives. As I was reading Neanderthal Man and getting a bit frustrated by fleeting references to a secret father and such, I asked people on Twitter about their favorite memoir by a scientist. I Storified the ensuing conversation here.

–From time to time, genes jump from one species of plant to another. For my “Matter” column this week in the New York Times, I look at how a jumping gene helped ferns thrive in the shady forests of the Mesozoic–and today. I think these cases of horizontal gene transfer are important not just for what it tells us about how life got to be the way it is today, but also for what it can tell us about our artificial transfer of genes from species to species. It’s simply not true that genes moving between species is “unnatural,” and therefore automatically evil. Is such an engineered organism dangerous? That’s a question that we have to tackle case by case, without mismatched notions of nature getting in the way.

Your Inner Mosh Pit

I am an unreconstructed fan of biology visualizers, the da Vincis of the twenty-first century. So I was particularly pleased to learn of a gorgeous new video that conveys the squiggly complexity inside a cell. That video–and the aesthetic decisions behind it–are the topic my newest column for The New York Times. Check it out.