Carl Zimmer's Blog, page 14

Missing Microbes

Over the years, as I’ve learned about the microbes that help keep us healthy, some of the most interesting conversations I’ve had about the microbiome have been with Martin Blaser. He’s a microbiologist at the New York School of Medicine, where he and his colleagues have found tantalizing links between the diversity of microbes in people’s bodies and medical conditions ranging from asthma to obesity. While those results are preliminary, they’ve led Blaser to worry about the long-term consequences of our torrid love affair with antibiotics. As we overdose on antibiotics to kill bad germs, we may be driving some good germs extinct.

In the latest issue of Wired, I interview Blaser about his work. And if you want to find out more, his new book, Missing Microbes, has just been published. It’s an excellent look at one of the most intriguing fields of biology today.

From Microbiomes to Neanderthals

I’ll be taking the week off from blogging. Let me leave you with an hour-long interview on public radio in Charlotte, NC, which was recorded on Friday when I was in town to give a lecture for the North Carolina State Science Festival. We ranged over a lot of material, from de-extinctions to science literacy to personalized medicine and more. See you next week!

The Oldest Living Things On Earth

The photographer Rachel Sussman has been traveling the world to take pictures of the oldest living organisms on our planet. She described her journey in this TED talk, and now, at last, she’s created a gorgeous new book, The Oldest Living Things in the World, published by the University of Chicago Press.

Rachel asked if I would write an introduction to the book. After contemplating her photographs and thinking about what these strange Methuselahs mean for us and for science, here’s what I wrote:

HOW LIVES BECOME LONG

It is easy to feel sorry for the gastrotrich. This invertebrate animal, the size of a poppy seed and the shape of a bowling pin, swarms by the millions in rivers and lakes. After it hatches, it takes only three days to develop a complicated body, complete with a mouth, a gut, sensory organs, and a brain. Having reached maturity in just seventy-two hours, the gastrotrich starts laying eggs. And after a few more days, it becomes enfeebled and dies of old age.

To squeeze a whole life into a week seems like one of nature’s more cruel tricks. But that’s only because we are accustomed to measure our lives in decades. If the ancient animals and plants featured in this book could look upon us, they might feel sorry for us as well. We humans marvel at the longest-living human on record, Jean Calment, who lived from 1875 to 1997. But for a 13,000-year-old Palmer’s oak tree, Calment’s 122 years rushed by as quickly as a summer vacation.

Palmer’s oaks, gastrotrichs, and all the species in between are the products of evolution. The head-swimming diversity of life is joined in an evolutionary tree made up of tens of millions of branches. And one of the most spectacular of that diversity’s dimensions is longevity. If natural selection provides Palmer’s oaks with millennia, why does it only spare a gastrotrich a week of existence?

Starting in the 1960s, evolutionary biologists have searched for an overarching explanation to account for all the different ways to grow old. The best-supported ones so far are variants on the old truth that a jack-of-all-trades is a master of none. An organism can collect a finite amount of energy, whether it’s a lion killing gazelles, a tulip capturing sunlight, or a microbe breathing iron at the bottom of the sea. It can use that energy to grow, to produce offspring, to defend itself against pathogens, to repair damaged its damaged molecules. But it has a limited budget. The energy spent on one task is energy that can’t be spent on others.

Molecular repair and pathogen defense are both good ways to live longer. But a long-lived organism that produces few offspring will not pass on many copies of its genes to future generations. The organisms that will succeed are the ones that do a mediocre job of keeping their bodies in order, leaving more energy for making babies.

This balance goes a long way to explaining why some species live long and some short. It may give scientists clues to how we humans might battle the burdens of aging, such as Alzheimer’s disease. But this balance is only part of the answer to why things live as long as they do. The environments in which species live may also be a part of the answer. In some places, life may simply run slower. Some lineages may evolve a way out of the binds that tie most species. They may escape the trade-offs that come with channeling energy in one direction or another, and be free to live longer.

The durable mystery of longevity makes the species in this book all the more precious, and all the more worthy of being preserved. Looking at an organism that has endured for thousands of years is an awesome experience, because it makes us feel like mere gastrotrichs. But it is an even more awesome experience to recognize the bond we share to a 13,000-year-old Palmer’s oak tree, and to wonder how we evolved such different times on this Earth.

Personalized Medicine: Taming the Big Data Ocean

The idea of personalized medicine is very simple. Your doctor peruses your genome to tailor your medical treatment. If you get cancer, she compares the genome of your tumor cells to your ordinary genome.

But in between idea and practice are rough waters yet to be crossed. That’s because the genome doesn’t speak for itself. Instead, we will probably need the help of computers with a human-like power to learn.

For my new “Matter” column in the New York Times, I take a look at this challenge, on the occasion of a new study being launched on brain cancer patients. Helping out the oncologists will be the most famous supercomputer on Earth, Watson, the machine that beat humans on Jeopardy. Check it out.

Darwin in the City: My Talk About Humans Driving Evolution

Yesterday I delivered the Director’s Lecture at Harvard’s Arnold Arboretum. Speaking as I was at a lovely green island in a venerable city, I decided to talk about how life evolves in our human-dominated world. My talk ranged from New York City mice to HIV to GM-crop-feasting insects to climate-driven extinctions.

I’ve embedded the video below the fold. The lighting on my is fairly dim, but the slides show up fine and the sound is clear. Below the video, I’ve also embedded the slides for easy viewing.

The video:

The slides:

I hope you enjoy it.

Flying Through Inner Space

It’s hard to truly see the brain. I don’t mean to simply see a three-pound hunk of tissue. I mean to see it in a way that offers a deep feel for how it works. That’s not surprising, given that the human brain is made up of over 80 billion neurons, each branching out to form thousands of connections to other neurons. A drawing of those connections may just look like a tangle of yarn.

As I wrote in the February issue of National Geographic, a number of neuroscientists are charting the brain now in ways that were impossible just a few years ago. And out of these surveys, an interesting new way to look at the brain is emerging. Call it the brain fly-through. The brain fly-through only became feasible once scientists started making large-scale maps of actual neurons in actual brains. Once they had those co-ordinates in three-dimensional space, they could program a computer to glide through it. The results are strangely hypnotic.

Here are three examples, from the small to the big. (Click on the cog-wheel icon if you can to make sure you’re watching them at high resolution.)

First is a video from a project called Eyewire. Volunteers play a game to map the structure of individual neurons. Here are a handful of neurons from the retina of a mouse. (More details about the video can be found here.)

The second video is a flight through the entire brain of a mouse, made possible by a new method called CLARITY. This method involves first adding chemicals to the brain to wash out the lipids and other chemicals that give it color. The brain is rendered transparent, even though its neurons remain intact.

Next, scientists douse the brain with compounds that only latch onto certain types of neurons, lighting them up. The researchers can then take pictures of the brain from different angles and combine them into a three-dimensional representation of the brain in which you can distinguish individual neurons. In this video, from the lab of Karl Deisseroth at Stanford University, a very common type of neuron is colored. Flying through the brain, we can start to get a feel for the large-scale connections that stretch across it.

And finally, we come to the newest method–one that didn’t even exist when I was working on my article. Adam Gazzaley of the University of California at San Francisco and his colleagues have made it possible to fly through a representation of a thinking human brain–as it thinks.

Here’s how they built this fly-through, which they call the Glass Brain. First, they gave volunteers a high-resolution MRI scan to get a very detailed picture of the overall shape of their brain. MRI doesn’t let you see individual neurons, but it does mark out the major structures of the brain in fine detail.

Next, they added in more anatomy with a method called diffusion tensor imaging. To use this method (known as DTI for short), scientists reprogram MRI scanners to measure the jostling of water molecules inside of neurons. Many of the neurons in the brain are located in the outer layers of the brain, and they extend long fibers across the inner regions and link up to the outer layers at a distant spot. Many of these fibers are organized together in pathways. The water molecules in the fibers jostle back and forth along that pathway, and so scientists can use their movement to reconstruct their shape.

The combination of MRI and DTI gave Gazzaley and his colleagues both the structures of the brain and the pathways connecting them, all lined up in the same three-dimensional space.

Now came the third ingredient: recordings of the brain’s activity. Gazzaley used EEG, a method that involves putting a cap of electrodes on someone’s head and measuring the electrical activity that reaches from the brain up through the skull to the scalp.

EEG is very fast, measuring changes in brain activity at a resolution of a tenth of a second or less. The drawback to EEG is that it’s like trying to eavesdrop on people in the next room over. A lot of detail gets blurred away as the signals travel from their source. To reconstruct the brain’s inner conversations, Gazzaley and his colleagues programmed a computer to solve mathematical equations that allow it to use the scalp recordings to infer where in the brain signals are coming from. Their program also measured how synchronized signals in different regions were with each other. Combining this information with their map of the brain’s pathways, the scientists could reconstruct how signals moved across the brain.

And here’s a video of what they ended up with. In this case, the volunteer was simply asked to open and shut her eyes and open and close her hand.

As gorgeous as this is simply as a video, there’s more to it. It didn’t take Gazzaley’s computer weeks to crunch all the data from the experiment, calculate the sources of the EEG signals and map them onto the brain. The system can create this movie in real time.

Imagine, if you will, putting on an EEG cap and looking at a screen showing you what’s happening in your brain at the moment you’re looking at it. That’s what this system promises.

I called Gazzaley to get the details of this new view of the brain. It took him and his team a year to build and to validate it–that is, to make sure that the patterns in the video have the same features that well-studied imaging technologies have found in the brain. Now Gazzaley hopes to start using it to record data during experiments and to test some prominent ideas about how the brain processes information.

And this imaging may be useful outside the lab. Gazzaley and his colleagues recently designed a video game that improved the cognition of older people. It may be possible to incorporate their new brain display into a game, allowing people to try to alter their brain activity through a kind of neuro-feedback.

Just recently, Gazzaley got another idea. He put an EEG cap on a colleague and then pushed the output to a set of Oculus Rift virtual reality goggles. Gazzaley put the goggles on and then used an Xbox joystick to fly through his colleague’s brain, which he could look at all around him in three dimensions.

“I had never seen a brain inside out before,” Gazzaley told me. “After that I couldn’t get back to work. I had to lay on the grass for a while.”

Tomorrow I will be speaking about brain mapping in Rochester, New York, in their Arts & Lectures series. You can get information about tickets here.

The Mystery of the Sea Unicorn

In 1577, the English explorer Martin Frobisher led an expedition of 150 men to the northern reaches of Canada, in search of a passage to India and a fortune in gold. As they surveyed the islands near the coast, they came across something Frobisher could never have anticipated: a unicorn fish.

“Upon another small island here,” Frobisher wrote in his journal, “was also found a great dead fish, which, as it would seem, had been embayed with ice, and was in proportion round like to a porpoise, being about twelve foot long, and in bigness answerable, having a horn of two yards long growing out of the snout or nostrils. This horn is wreathed and straight, like in fashion to a taper made of wax, and may truly thought to be the sea-unicorn.”

When Frobisher returned to England, he presented the horn to Queen Elizabeth, who commanded that it be kept with the crown jewels.

Unicorn horns–or at least what traders claimed were unicorn horns–had circulated around Europe for centuries before Frobisher’s voyage. They were worth many times their weight in gold; Elizabeth was said to have paid 10,000 pounds for a unicorn horn, the price of a castle. Unicorn horn was in the cups that monarchs drank from, the scepters that they wielded.

The myth of the unicorn reaches back to the classical world, but the business of unicorn horn trade was sustained through the Middle Ages and the Renaissance by Vikings who killed the so-called sea unicorns in the North Atlantic, cut off their horns, and sold them at astronomical prices–never revealing their origin.

As Europeans naturalists became more familiar with the world’s animals, the myth of the unicorn faded, and it became clear that Frobisher’s sea-unicorn was actually a whale–what is known today as the narwhal. But while the source of the horn has become clear, the horn itself still inspires confusion and debate among scientists.

Narwhals outside Pond Inlet in Tremblay Sound, Canada. Photo: Glenn Williams

The horn is not a horn at all, but a tooth. The relatives of narwhals include species like beluga whales, orcas, and dolphins. They all have sets of simple, peg-like teeth in their mouths they use to catch prey. In the mouth of male narwhals, one tooth has grown to monstrous proportions, its counterpart usually growing to a much shorter length. The narwhal’s tooth is comparable to the tusks of elephants or warthogs, but doesn’t have a hint of a curve to it.

But why should a whale grow a tusk? Or, more precisely, how did such a freakish tooth evolve in this one species after its ancestors branched off from whales with ordinary teeth?

The ideas scientists have put forward over the years have been legion. The list includes–but is not limited to–an acoustic probe, a means for dumping extra heat, a rudder, an ice-picker, and a spear for battling predators or perhaps other narwhals. Most of those ideas emerged not from close observation but speculation. The narwhals live in remote Arctic fjords and the ice-strewn ocean. They do not make it easy for scientists to see them use their tusk for anything at all.

Martin Nweeia, a Connecticut dentist and a clinical instructor at the Harvard School of Dental Medicine, has been traveling to the Arctic for fourteen years to study narwhals, and, in particular, their tusks. He’s given some scientific talks about his research over the years and published some details in book chapters. But now he and a team of colleagues from Harvard, the Smithsonian, the University of Minnesota, Fisheries and Oceans Canada, and elsewhere have published a detailed account of their studies on the narwhal tusk in the Anatomical Record. They conclude that the tusk is a sense organ that lets male narwhals perceive the ocean, possibly helping them find mates or food.

Part of their argument is based on the anatomy of the tusk. Rather than being a solid hunk of bone, it’s shot through with nerves. And it appears specially adapted to bring those nerves nearly in contact with sea water. In us and in other mammals, teeth are armored in sheets of enamel. Narwals don’t have enamel on their tusks. Instead, the surface of the tusk is covered in fine channels that can bring water down into the tusk’s interior, close to the nerve endings there. And some of those nerve endings have the structure you find in nerves sensitive to pain.

To see if the narwhals used this intricate anatomy to sense their surroundings, Nweeia and his colleagues captured live narwhals off of Baffin Island and slipped a conical jacket over their tusks. The scientists then pumped water into the jacket, either with a high or a low level of salt. Electrodes that Nweeia’s team put on the skin of the narwhals measured their heart rate through the experiment, which only lasted less than half an hour per animal.

When the scientists put salt water into the tusk jacket, they recorded an average heartbeat of 60.42 beats per minute. But when they poured in fresh water, the heart beat more slowly, at 52.56 beats per minute. The difference was statistically significant, and the scientists took it to mean that the narwhals could sense the difference between salt and fresh water with their tusk alone. It’s possible that when the narwhals swim into salty water, they feel a pain akin to a toothache. It’s also possible that other nerve endings in the tusk sense other things, such as temperature or pressure.

Here is a figure that elegantly sums up the anatomy they found:

Neeiwa et al, Anatomical Record. Click to enlarge

If the narwhal tusk is indeed a sensory organ, it’s only benefiting the males. Nweeia and his colleagues suggest that the males may use it to sense things that can help them win mates. They may be able to track down female narwhals by sampling the chemicals in the water, searching for the ones found where the females feed. They might even be able to sense whether females are receptive for mating from the chemicals they release. Some males might be able to use their tusk to find food for newborn calves. Males with more sensitive tusks would have better luck at reproducing than others, and that difference would drive the evolution of the wildly elongated tusk.

I got in touch with some other experts on whale anatomy to see what they thought of all this. In general, they were pretty dazzled by the data Nweeia and his colleagues have brought together.

“They have done a great job collating several hundred years of hypotheses about narwhal tusk function, and then throwing nearly every existing line of evidence at the problem,” Nick Pyenson, the curator of marine mammals of the Smithsonian Institution told me.

Joy Reidenberg, the Icahn School of Medicine anatomist whom I wrote about last year, summed up her reaction as, “WOW.” Each line of evidence they compiled could have been a separate paper, and she gave Nweeia and his colleagues high praise for combining them all into one coherent account. “It is so refreshing to see a paper where the focus is not on the least publishable unit, but rather, on a comprehensive understanding of form, function, and evolution.”

Inuit boy with narwhal tusk. Maynard Owen Williams/National Geographic Creative

But some researchers were not persuaded by the conclusions that Nweeia and his colleagues drew from all that data. Their biggest critic was Kristin Laidre of the University of Washington. For starters, she notes that having sensitive teeth is not unique to narwhals. “When you eat ice cream, your teeth hurt, and the nerves in your teeth tell your brain you’re eating something cold,” she told me.

That’s good information to have, but it wouldn’t make sense to say that our teeth are sense organs. They evolved to let us bite and grind food.

Nweeia and his colleagues acknowledge that teeth can sense things in other species, but they argue that the narwhal tusk is doing something beyond what ordinary teeth are capable of. Laidre doesn’t think that the heartbeat readings let them reach that conclusion. “Heart rate collected 30 minutes after an animal has been put through an invasive net capture event and beached in shallow water tells you the animal is stressed, not how it reacts to various saline solutions on its tooth,” she told me.

Laidre also disputes the scenarios Nweeia and his colleagues present for how males might use their tusks for sensing. Studies on the stomach contents of narwhals have revealed that males and females feed on the same kind of prey, in the same parts of the ocean, at the same times of year. And it’s females that care for young narwhals, without any evidence that males provide any help. Females are so important for the survival of young narwhals, in fact, that Laidre has a hard time imagining males having such a sensitive organ and the females lacking it.

The notion of the tusk being a critical sensory organ, says Laidre, “remains a toothless theory with no supporting data.”

Instead, Laidre suspects male narwhals use their tusks to compete for mates. Scientists can’t watch them use their tusks as easily as they can watch elk lock antlers or fiddler crabs flip each other over with their giant claws. But they have seen male narwhals “tusking”–that is, crossing their tusks at the surface of the water. And they’ve seen females nearby when this happens, where they may be developing a preference for a particular male.

The last person I consulted about the narwhal study was not a whale expert at all, but a biologist who studies beetles. Douglas Emlen of the University of Montana studies the absurdly giant horns of rhinoceros beetles and other species. He’s taught me a lot about animal weapons in general as we’ve co-authored a textbook on evolution. (On a related note, you can pre-order his fabulous book on weapons, that’s coming out in November).

When I asked him what he thought about the debate over narwhal tusks, he pointed me to a fascinating study published by his student Erin McCullough last year with Robert Zinna of Washington State University. They took a close look at the horn of the Giant Rhinoceros Beetle from Japan. Its surface turns out to be covered with touch-sensitive hairs. Some parts of the horn are densely covered in hair, while others are sparser.

Photo by Seongbin Im http://flic.kr/p/7dYo5v

And McCullough and Zinna found a pattern to the hairs. When two male beetles prepare for battle on a tree branch, they approach each other and tap their horns together. If one is much smaller than the other, it will then back away. If they’re equally matched, they then take the conflict to the next level, and try to toss each other off the branch. It turns out that the densest patches of sensory hairs are precisely where the beetle horns make contact with the horns of their enemies.

Perhaps narwhals are the beetles of the whale world. Choosing between a sensory organ and a weapon may be a false choice. Perhaps male narwhals do go into battle, but they size up their opponents first.

Even if someone were to run with that idea, it would probably be a long time before they confirmed it–if they ever did. It’s been 437 years since Frobisher laid eyes on a dead narwhal, and it’s not that much easier today for scientists to see much more of this strange but elusive species.

[Related: "Narwhal's Trademark Tusk Acts Like a Sensor, Scientist Says."]

[Reference: Sensory Ability in the Narwhal Tooth Organ System, Nweeia et al, Anatomical Record 2013, in press]

A Moss From King Arthur’s Court and the New Science of Resurrection Ecology

Over the past year, I’ve been writing a lot about scientists bringing back life from the distant past–including viruses, water fleas, and–theoretically–mammoths. For my “Matter” column this week in the New York Times, I report on another revival: moss that has started growing after spending 1500 years in a bank of  permafrost. As more species return from the past, some scientists think it’s time to establish a new scientific field which they call “resurrection ecology.” In my column, I consider some of the things that resurrection ecologists can learn about the past and the future. Check it out.

The Birds And the Bees and the Pollinator Syndrome [Science Ink Sunday]

Tattoo by Dave Kotinsley, Gainesville, FL

Jacob Landis writes, “I’m a graduate student at the University of Florida studying flower evolutionary development with a focus on plant/pollinator interactions. My ink represents the concept that I have been working on for almost 6 years now. This piece shows three species in the Phlox family. The red and white flowers are both part of the genus Ipomopsis and the blue/purple flower is in the closely related Polemonium. The pollinator of each flower is shown interacting with the flower. These interactions represent the concept of pollinator syndromes: certain features of the flower will attract certain pollinators. The long red tubular flowers attract hummingbirds, the white tubular flowers attract hawk moths, and the more open blue/purple flowers often attract bees.”

You can see the rest of the Science Tattoo Emporium here or in my book, Science Ink: Tattoos of the Science Obsessed. (The paperback edition comes out in May; you can pre-order here.)

Sponges: Planetary Engineers?

Life changes its surroundings. Beavers build dams that alter the course of rivers. Forests can feed thunderstorms with their moisture. And those changes can, in turn, create new habitats that allow for the evolution of new kinds of life. For my new “Matter” column in the New York Times, I discuss a hypothesis about a truly global act of bio-engineering that may have happened 700 million years ago. Sponges may have transformed the oceans, flushing them with oxygen. And thanks to that change, more complex animals were able to evolve. We may have sponges to thank for being here, in other words. You can read the whole thing here.