Inside each of us is a miniature version of ourselves. The Canadian neurologist Wilder Penfield discovered this little person in the 1930s, when he opened up the skulls of his patients to perform brain surgery. He would sometimes apply a little electric jolt to different spots on the surface of the brain and ask his patients–still conscious–to tell him if they felt anything. Sometimes their tongues tingled. Other times their hand twitched. Penfield drew a map of these responses. He ended up with a surreal portrait of the human body stretched out across the surface of the brain. In a 1950 book, he offered a map of this so-called homunculus.

For brain surgeons, Penfield’s map was a practical boon, helping them plan out their surgeries. But for scientists interested in more basic questions about the brain, it was downright fascinating. It revealed that the brain organized the sensory information coming from the skin into a body-like form.

There were differences between the homunculus and the human body, of course. It was as if the face had been removed from the head and moved just out of reach. The area that each body part took up in the brain wasn’t proportional to its actual size. The lips and index finger were gigantic, for instance, while the forearm took up less space than the tongue.

That difference in our brains is reflected in our nerve endings. Our fingertips are far more sensitive than our backs. That’s because we  don’t need to make fine discriminations with our backs, while we use our hands for all sorts of things–like picking up objects or using tools–that demand sensory power.

The shape of our sensory map reflects our evolution, as bipedal tool-users. When scientists have turned to other species, they’ve found homunculi of different shapes, the results of their different evolutionary paths. This picture, taken from my book The Tangled Bank, shows three subterranean mammals: a mole, a naked mole rat, and a star-nosed mole.

The top row shows their actual body shape, and the bottom row shows the relative amount of space on the sensory map devoted to each part. The expanded parts reflect the kinds of sensory information they gather. Moles dig with their hands, for example, to search for worms and other prey. They can’t rely on their sight in the dark; instead, they use their sense of smell, their whiskers, and the sensitive skin on their nose. Naked mole rats, on the other hand, use their teeth instead of their hands to dig. Star-nosed moles, finally, have evolved a bizarre hand-like structure on their noses, which they use to quickly probe the soft mud that they dig through.

Dennis O’Leary, a biologist at Salk Institute for Biological Studies, and his colleagues have spent the past few years investigating how the sensory map takes shape. They have studied mice, which have a sensory map finely tuned to their own way of life as nocturnal rodents that search for food aboveground. The mice depend on their whiskers to let them know about their surroundings. Each whisker is surrounded by a dense cluster of nerve endings, all of which feed information into the brain.

Here’s a drawing of the mouse in its actual proportions, with the whiskers and other regions of its body highlighted.

And here is a picture of the mouse’s sensory map–what O’Leary and his colleagues have nicknamed the mouseunculus:

Reflecting their dependence on their whiskers, the sensory map is dominated by clusters of neurons that process whisker signals. Each of those clusters, called a barrel, is bigger than the cluster of neurons dedicated to the mouse’s entire foot.

The mouseunculus–or any other mammal sensory map–does not instantly take shape in the embryonic brain. It requires experience to grow. Before birth and afterwards, the neurons in the skin deliver signals into the brain. Those signals stimulate the growth of new neurons, as well as the emergence of connections between the cells. If the brain can’t get signals from part of its body–perhaps due to a birth defect that leads to the loss of a limb, say, or due to nerve damage–the sensory map will develop abnormally.

Does that mean that our sensory maps depend on their existence simply on the signals they receive from the skin? O’Leary and his colleagues have found that the answer to this question is no, as they report in the new issue of Nature Neuroscience. A mammal’s genes also help guide the cartographer’s pen.

The new study builds on O’Leary’s earlier discovery that mutations to certain genes alter the structure of the cortex, the thin outer layers of the brain where its most sophisticated information processing takes place. O’Leary and his colleagues decided to look at how one of those genes, called Pax6, influenced the development of the sensory map in particular.

To find out, they developed an intricate technique to shut down Pax6 only in the sensory map and nowhere else in the brain of mouse embryos. The mice were born healthy, and were able to feed their sensory maps with their typical diet of information.

A week after the mice were born, the scientists followed in Penfield’s steps and mapped the mouseunculus. And here’s what they saw:

The map nicely shows that without Pax6, many of the barrels only grew to a small portion of their normal size, in some cases ending up 80% smaller than in mice with Pax6 switched on in the sensory map. A few barrels never developed at all.

Clearly, O’Leary’s research shows, genes play a big part in building an accurate sensory map. But they do more. Their effects ripple downwards, to earlier steps in the information pathway through the brain.

This diagram shows some stops along that pathway. The signals from the body travel to the back of the brain, and then forward to a structure deep in the brain called the thalamus, before finally reaching the sensory map. At each step, the neurons that process the signals are also organized in maps that correspond to the mouse’s body. They have distinct clumps of neurons for each neuron, called barreloids or barrelettes depend on which part of the brain they’re found.

O’Leary and his colleagues found that when they shut down Pax6 in the sensory map, it wasn’t just the sensory map that changed shape. The thalamus changed too. As with the sensory map, the thalamus’s barreloids shrank or disappeared. O’Leary and his colleagues’ research indicates that the thalamus depends on signals from the sensory map to develop normally. Without those signals, some of the developing neurons in the thalamus die.

The sensory map and the neurons that feed it data turn out to be entangled in an intimate conversation. Signals rising from the skin shape the map, while the genes in the map’s neurons influence it as well–and their influence extends downward into the pathway. This dialogue may be crucial for fine-tuning the entire nervous system, so that we develop sensory maps and sensory neurons that match each other tightly.

Like Penfield’s original map, O’Leary’s research illuminates some of the fundamental questions about how the sensory map works, and it may likewise turn out to offer some practical benefits. Â Mutations to genes like Pax6 may alter the sensory map, and their disruption may extend downstream to the thalamus. Those mutations may play a role in brain disorders like autism.

As O’Leary and his colleagues point out in their new paper, previous studies on people with autism have revealed some differences in the activity of genes in the brain. In particular, the genes involved in marking off different areas of the cortex have different patterns of activity.

This change to the brain-shaping genes may explain the fact that some scientists have found changes to the structure of the cortex. While the overall size of the cortex is the same in autistic brains and normal brains, the front portion of the cortex is enlarged in people with autism.

This shift may also mean that the region of the cortex further towards the back of the brain gets smaller. And it just so happens that our homunculus lurks back there. It’s possible, in other words, that in people with autism, the disruption of the cortex leaves them with a smaller sensory map.

If the sensory map is indeed smaller in people with autism, the effects might radiate outward to the thalamus. AÂ recent study on the brains of 17 autistic people revealed that they did indeed have a smaller thalamus on average.

If this hypothesis is correct–and it’s important to note that it’s still based on the study of relatively few people–it could explain why people with autism often have trouble with processing the information of their senses. And it might even point towards new ways to treat autism, by nurturing the inner homunculus.

[Update 3 pm: This post was updated to O’Leary’s correct institution–the Salk Institute, not Scripps Institute. Two great institutes very close both in space and in my mind.]

[Update 11 pm: The post initially stated moles are rodents. My bad.]

In my column this week for the New York Times, I write about the discovery of record-breaking viruses called pandoraviruses. They’re 1000 times bigger than a flu virus and have almost 200 times as many genes–over 2500. That’s twice as many genes as the previous giant-virus record holder, which I blogged about in 2011.

These giant viruses are important to our understanding of what the difference is–if any–between viruses and the rest of life. But they’re also part of a bigger story, one that inspired the title of my recent book A Planet of Viruses. Viruses are the most common life form on Earth, they are by far the most genetically diverse, and we have barely started to explore the viral frontier.

That frontier includes giant viruses–and tiny ones, too. Just last week, for example, Jessica Labonte and Curtis Suttle of the University of British Columbia published a survey of another group of viruses called single-stranded DNA viruses. Their ranks include parvoviruses, which cause an infection sometimes known as the Fifth Disease. If you’ve gotten it, like I did a few years ago, you know that feeling it provides you that someone has been using your body as a punching bag for hours.

The ranks of single stranded DNA viruses include many other pathogens of plants and animals, plus others that infect bacteria. They are exquisitely small, with as few as three genes.

Labonte and Suttle searched through sequenced of DNA that have been trawled up from sea water at a few sites around the world. They found a lot of single-stranded DNA virus genes, which they compared to the seven known families of the viruses. They realized they have probably discovered 129 new families.

Just another week on the viral frontier…

For a couple years now I’ve been fascinated by some recent ideas about how complexity evolves. Darwin’s great insight was recognizing how natural selection could create complex traits. All that was needed was a series of intermediates that raised the reproductive success of organisms. But recently some researchers have developed ideas in which natural selection doesn’t play such a central role.

One idea, laid out in the book Biology’s First Law, holds that life has a built-in propensity to get more complex–even in the absence of natural selection. According to another idea, called constructive neutral evolution, mutations can change simple structures into more complex ones even if those mutations don’t provide an advantage. The scientists who are championing these ideas don’t see them as refuting natural selection, but, rather, complementing it, and enriching our understanding of how evolution works.

I’ve tried for a while to write a story about these ideas, but it’s been pretty tough. It takes some time for me to wrap my head around the arguments. They require a fair amount of space to explore, and–while I find them intriguing–they don’t have a simple news peg. At one point, in fact, I actually had an assignment from a magazine and got well into the research and writing. But I could see my story just wouldn’t end up right for them, and I withdrew it.

It was around this time that I talked with Thomas Lin, the managing editor of Simonsfoundation.org. The Simons Foundation was getting into supporting science journalism in a big way, especially stuff that might not easily find a home elsewhere. I told him about my obsession with complexity, and soon we were off to the races. I was happy to find that the editing was rigorous, and the fact-checking brutal.

Meanwhile, Lin has been very busy at Simons. Yesterday he launched a full-fledged magazine there, called Quanta. Lin described the project here. I’m thrilled that my story on complexity is their first offering in this new format. You can read it here.

The Simons Foundation is following in the tradition of Pro Publica–not just as a foundation supporting journalism in tricky times, but also finding lots of ways to get journalism in front of as many readers as possible. Thus they’re collaborating with a number of existing publications. So you can also find my story over at Scientific American.

These are uncertain but exciting times for science journalism. I really appreciate that places like Simons are ready to go out on a limb.

 

The remora is so ridiculous that no one would try to make it up. The top of its head is a giant, flat suction cup. It uses the cup to lock onto the bodies of bigger animals, such as sharks, sea turtles, and whales. As the big animal swims for miles in search of a meal, the remora hangs on for the ride. When its host finds a victim, the remora detaches and feasts on the remains. It sometimes cleans its host’s body and mouth of parasites, and then clamps its head back on for another ride.

The remora’s ridiculousness makes it a fascinating evolutionary puzzle just waiting for the solving. Other species clamp themselves onto other animals–whale barnacles, for example, grow prongs from their shells that anchor them to whale skin–but among fish, remoras are exceptional. Their closest relatives include Mahi-Mahi and amberjacks, neither of which has anything on their head that even faintly resembles the remora’s sucker. Only after the ancestors of remoras and these ordinary fish split apart some 50 million years ago, the remoras evolved a remarkably new piece of anatomy.

When you look closely at the remora’s suction disk, its remarkableness only grows. It looks like a spiked Venetian blind. Pairs of slat-like bones called lamellae form a series of rows running down the length of its head, and muscles running from the remora’s skull to those bones pivot them, creating spaces between the rows.

That negative pressure pulls the remora towards its host’s body. Each lamella also has a comb-like set of pins that help make its clamp even more secure. The whole structure is surrounding by a loose fleshy lip, ensuring that no water slips in, keeping the seal tight.

As a result, remoras can create a vacuum that’s not just strong enough to attach them to an animal, but to stay attached as water rushes past them. They can even hold tight as their hosts try to scrape them off on rocks. But a remora can instantly release itself when it’s time to eat, with just a flick of its muscles.

As impressive as the remora’s suction disk may be, however, it’s not actually all that new. As is so often the case in nature, it’s actually just evolutionary tinkering with old parts.

Scientists have gotten some clues to the remora’s origins by looking at how they grow up. When remoras hatch, they don’t yet have a suction disk. Last year Ralf Britz of the Natural History Museum in London and David Johnson of the Smithsonian made a careful study of young remoras to document their development.  They found that the bones and muscles of the remora’s sucker start out much like the bones and muscles in a fin found on the back of other fish, known as the dorsal fin. They develop in the same location and have the same structure. But later, the bones and muscles move forward to the head.

They also change shape along the way. The fin spines spread out into lamellae that sprout a comb of spikes. In ordinary fish, the fin spine sits atop a small round bone. In remoras, that small bone widens out into another set of lamellae.

While the development of embryos doesn’t recapitulate evolution, it can offer some hints about how new things evolved from old ones. Britz and Johnson’s research indicates that the remora suction disk started out, improbably enough, as a dorsal fin. The fin stretched out into a complex vacuum device and moved up to the head. The underlying similarity between sucking disks and fins only becomes clear when you see how they both develop along the same path at first before diverging.

If all this were true, you might be able to test it by looking at the fossils of early relatives of remoras. Perhaps they captured the early stages of the transition.

That is precisely what Matt Friedman at the University of Oxford and his colleagues have done, as they report today in the Proceedings of the Royal Society.

Frieman is an expert on the larger group of fish to which the remora belongs, known as spiny rayed fishes. The group has evolved into some spectacularly weird forms, including sea horses and flatfishes. In 2008, I blogged about how Friedman found an intermediate flatfish, with one eye moving towards the other side. Remoras, with their own brand of weirdness, seemed to Friedman another spiny rayed fish worth spending some time on.

The only problem was that most of the fossils of remoras belonged to living lineages. Their suction disks were pretty much like what you’d find on a remora today. At least, that’s what most paleontologists who study remoras have thought.

Friedman decided to take a closer look at one of those remora fossils, called Opisthomyzon. The 30-million-year-old specimen was the first remora fossil ever found, in 1886, and it has sat in a museum in Switzerland ever since.

The specimen was in bad shape, Friedman found. It had a suction disk, for example, but it wasn’t clear if the whole disk had been pushed away from its original location. Friedman wondered if there might be other Opisthomyzon fossils hidden in other museums. Sometimes paleontologists can’t quite figure out what they’ve found, and they file away fossils without describing them.

At the National History Museum of London, Friedman found not one hidden Opisthomyzon fossil, but two. Mark Graham, a preparator at the museum, painstakingly chipped away at the underside of one of the new fossils, until all that was left was a paper-thin slab of rock. Friedman and his colleagues then compared the anatomy of Opisthomyzon to living remoras, as well as to extinct and living relatives, such as Mahi-Mahi.

Opisthomyzon proved to be exactly what Friedman was looking for: an extinct species that branched off before the origin of the living lineages of remoras. And when he and his colleagues examined its anatomy, they found exactly the kind of fish you’d expect to see from developing remoras: a fish with a suction disk still evolving from a fin.

This figure below sums up the story. The top fish is a conventional relative of remoras, with its dorsal fin bones shown to the right. In the middle is Opisthomyzon, with its corresponding suction bones. And at the bottom is a living remora.

You can see that the suction disk on Opisthomyzon is smaller than that of living remoras and does not sit over its whole head as it does today. The lamellae themselves bear more of a resemblance to the spines of dorsal fins. Opisthomyzon’s lamellae lacked a comb of spikes, for example, still retaining a single spine at the center.

Friedman’s research now gives us a richer hypothesis for how the remora got its sucker. Some of the remora’s closest living relatives, like cobia, tag along with bigger fish to scavenge on their scraps. The ancestors of remoras may have lived a similar life.

It’s not rare for spiny rayed fishes to grow extra dorsal fin spines. In the ancestors of remoras, such an anatomical fluke may have allowed them to latch their dorsal fin into the skin of a host fish, if only briefly. Even if they could spend a little time hitch-hiking this way, they would save energy that they’d otherwise have to spend on swimming for themselves.

Gradually, the remora’s dorsal fin became better adapted to latching onto other animals. As it moved towards the remora’s head, for example, it reduced drag. And as the fin bones spread outward, they attached the remora more strongly.

Sometimes, when we look at an adaptation in living animals, it seems to exquisitely well-suited to the animal’s life that we can’t imagine how a more primitive version of it could have provided any benefit. What good is half a wing, for example? What good is half a sucker? Fossils can give our limited powers of imagination a boost, by showing us that these intermediate forms did indeed exist. Opisthomyzon probably could ride on other animals, although it may have been more prone to get peeled off along the way. Remoras are so good at clamping onto their hosts that they’ve lost some of the traits that other fishes have. Their tails are weak, and they need a strong current of water passing over them in order to breathe through their gills. It’s probably no coincidence that Opisthomyzon had a much stronger tail than living remoras. It was only part-way down the road to ridiculousness.

For 10,000 years, we’ve created a new evolutionary arena where a new kind of plant has evolved: the weed. In today’s New York Times, I talk to evolutionary biologists who are studying how weeds first arose, and the marvelously devious strategies they’ve evolved to thrive on farms. You may have be seeing headlines these days about how GMO crops are creating “superweeds.” The new generation of resistant weeds is definitely a serious problem, but it’s not some new Frankensteinian phenomenon. Weeds are just doing what weeds have done so well before. Understanding their evolution may help farmers fight them more effectively and safely. Check it out.