Seeking symmetry on a sunday morning (updated)

I spent last Sunday hiking with friends in the Shawangunk Ridge, in New York state. The Gunks, as it is locally known, is a ridge of bedrock that extends from the northernmost tip of New Jersey to the Catskill Mountains in New York. It was an incredibly foggy day, so we didn’t get to see any of the scenic vistas. But we did get to enjoy the weirdly diverse vegetation, all of which was covered in dew. The highlights were hiking through a beautiful ice cave, and having lunch on a ledge overlooking a 180 feet (54.6 m) tall waterfall. That’s a few feet higher than the vertical drop of Niagara falls. Check out some of my pictures below (fullscreen for full effect).

In the last image, you can use the people as a scale to get a sense of the size of this waterfall. The vertical cliff face that you see was once the site of a geological fault, where a crack formed in the bedrock and broke the symmetry. Rock on one side of the fault then slipped under, as rock on the other side got pushed above. Erosion has since gotten rid of the topsoil at this fault line, exposing the layers of bedrock beneath. It’s a striking testament to the power of geological forces.

The layers of rock that you see have been dated to about 430 million years ago. This was an interesting time in our history. It is when our ocean-dwelling fish ancestors started incorporating a new invention into their bodies – bone. It was also the time when these ancestors (who would later give rise to amphibians, reptiles, birds and mammals) parted ways with the ancestors of some rather interesting characters. These were the Coelacanth and the Lungfish, the so-called ‘living fossils’ of the ocean.

Meet the Coelacanth. One of our more interesting relatives

Of course, there’s really no such thing as a living fossil, as Darwin was well aware when he coined this phrase. Every species alive today has been evolving for just as long as we have (and usually much longer, because evolution is measured in generations and not years). But the Coelacanth, and to a lesser extent the Lungfish, are the few cases where this phrase is appropriate. Fossil records and genetic comparisons bear out that Coelacanths have indeed not changed a whole lot for hundreds of millions of years. Our ancestors from this time may, at least superficially, have looked something like this.

Continue reading Seeking symmetry on a sunday morning (updated)

Why have sex? To fight parasites, of course!

This post was chosen as an Editor's Selection for ResearchBlogging.orgThis post was selected by Vincent Racaniello as an editor’s selection on The (revised) title of this post was suggested by Lucas Brouwers. Check out his excellent blog on evolution, Thoughtomics.

New Zealand mud snails, before and after infection by parasites. These tiny creatures may move slowly, but peering beneath the surface reveals an incredible race for survival.

Why do we have sex? If this question keeps you up at night, you either have really loud neighbors, or you have the makings of an evolutionary biologist. Some of the most brilliant minds in the field – William Hamilton, John Maynard Smith and George Williams – have spent much of their careers wondering about the value of sex. This is not a reflection on the quality of their sex lives. Rather, it has more to do with their creative insight and ability to look at the world with fresh eyes.

A billion years ago, our ancestors inhabited a world without sex. This was the era of the clones. In this strange world, all organisms reproduced by creating identical genetic copies of themselves, somewhat similar to how modern-day bacteria reproduce [1]. But this clonal strategy has a problem. Populations made up of identical twins are more vulnerable to infection. When a disease comes along, it doesn’t just wipe out a few individuals. It can take out the whole lot.

When sex arrived, it introduced a new pace to life. Organisms were mixing and matching genes in combinations never seen before. Imagine a world where you had to dress well to survive. In such a world, the invention of sex is like going from wearing uniforms to having your own wardrobe. You could pick a gene from here, another from there, and put together a novel offspring. And if a particular outfit were deemed ‘unfit’, it’s not a huge tragedy as there are plenty of alternatives.

In this way, sex helps us by innovating new evolutionary solutions and by protecting us from disease. But sex is not without its discontents. For one thing, sexual reproduction implies that you only pass down half your genes to your offspring. The other half come from the other parent, and they combine to make an offspring with a full set of genes. On the other hand, in asexual reproduction, the mother passes on a full set of genes to her offspring. So by adopting sex, your genes are travelling half as far. In evolutionary terms, this is a huge cost, and sex had better have a lot to offer for it.

John Maynard Smith described "the two-fold cost of sex" - Asexual populations (b) grow twice as fast as sexual populations (a).

Do the benefits outweigh the costs? We would certainly like to think so. But when evolutionary biologists did the math, they worked out that the answer is usually no. Your genes typically have more to gain if you reproduced asexually.

So what gives? Why, then, do so many species adopt a sexual lifestyle? Well, here’s a brilliant solution offered by Hamilton and others: if you are under constant attack by rapidly evolving parasites, then sex is a better strategy than cloning yourself. This idea came to be known as the Red Queen hypothesis and can be summarized in one line: it’s harder to hit a moving target.

"Now, here, you see, it takes all the running you can do, to keep in the same place."

Continue reading Why have sex? To fight parasites, of course!

Why moths lost their spots, and cats don’t like milk. Tales of evolution in our time.

In the children’s game of hide-and-seek, it doesn’t matter much whether you win or lose. In the animal kingdom, however, the stakes are significantly higher. If you’re found, you’re food.

And death is not just the end of the individual, it’s the end of a lineage. Organisms that die before they can reproduce deny their genes a road to the next generation. In this simple fact lies the engine of change. For example, genes that make a prey more camouflaged will end up increasing their reproductive success, whereas genes that make them more noticeable are not going to get very far. In this way, natural selection is driving prey to become better hiders, and predators to become better seekers.

Nowhere is this evolutionary race more evident than in the case of the peppered moth. This is a species of moth that is found all across England and Ireland. When people first studied them in the early 1800s, almost all the moths looked something like this:

As you can see (if you’re looking closely), the white and black speckles are effective camouflage. For ages, these moths have hidden on light colored trees and lichens. Over time, they have evolved this distinctive pattern to help them evade the notice of the birds that prey on them.

But just fifty years later, things were beginning to change. By the 1850s, moths of the same species had stumbled upon a new color. These new moths were called carbonaria after their carbon-black color, to distinguish them from their salt-and-pepper colored relatives with the dull name typica.

By the end of the nineteenth century, the change was drastic. In 1895, a study in Manchester showed that 95% of the peppered moths were now of the black type. So what was going here? What could cause such an incredible change in appearance in just a hundred years?

Continue reading Why moths lost their spots, and cats don’t like milk. Tales of evolution in our time.

Destroying the disposers of death: will India rescue its few remaining vultures?

Indians today can hardly recall the last time that they saw a vulture. In the 1990s, these majestic birds were a common sight in the subcontinent, and would show up wherever there was exposed carrion. As a child, I remember marveling at vultures circling at impressive heights, probably looking back down at me with their incredible eyesight, their wings outstretched as they effortlessly hovered on columns of warm air.

But since the nineties, their numbers have been falling dramatically in India, Pakistan and Nepal. The scale is astonishing – for every thousand white-rumped vultures in 1990, only one is alive today. A similarly sad story holds for the Indian vulture and the slender-billed vulture. Together, all three Asian vultures are now listed as being critically endangered.

The White rumped vulture, Gyps bengalensis

So what’s going on? It’s not that they are being hunted. For one thing, the killing of all wild animals in banned in India. But also, vultures have always provided a much valued ecological service. Most villagers dispose of dead animals by dumping the carrion. And they rely on the vultures to clean up.

Vultures have an undeservedly bad reputation. Because we associate carrion with disease, people believed that vultures spread diseases. But in fact, we now know that the opposite is true. Their powerfully corrosive stomach acids allow them to safely digest carrion that would be lethal to other scavengers, wiping out bacteria that can cause diseases like botulism and anthrax. They are the purgers of death and disease.

In their absence, populations of feral dogs have exploded, bringing with them the threat of rabies and human attacks. And if rats follow suit, India would face a new public health nightmare as it tries to control the spread of rodent-borne diseases like bubonic plague [1].

Continue reading Destroying the disposers of death: will India rescue its few remaining vultures?

When nice guys finish first: a lesson from tiny robots

Meet Alice. She is 4 centimeters tall and moves about on wheels. Her goal in life is to look for food. Remarkably,the foraging behavior of this tiny robot has not been programmed by humans. Instead, her creators gave Alice a brain, and let evolution do the job of programming it. And Alice is going to show us why it is that individuals often make sacrifices for each other.

Animals often behave in seemingly selfless ways. The most regimented examples come from the social insects – the ants, termites, wasps and bees. Here selflessness is built in to the fabric of their society, as there are sterile castes of workers who tend to the eggs of the queen. Worker bees will often make the ultimate sacrifice and die protecting the hive from invaders. These are all altruistic acts, as they harm the individual while benefitting someone else.

A sweet deal? That's not a drop of honey, but in fact it's the engorged abdomen of the honeypot ant. These ants are used by the rest of the nest as living storage pots.

Take a moment to think about this behavior from the point of view of evolution. If everyone’s competing to get ahead, why take an unnecessary risk or suffer to help someone else? You really couldn’t do much worse than adopt a sterile lifestyle – it’s an evolutionary dead end.

People used to talk about such altruistic behavior as  being ‘for the good of the species’. But this explanation does not work. Natural selection does not operate at the level of species, it is solely concerned with the reproductive success of the individual. Any gene that inclines an individual to be more concerned with the welfare of the species than with their own welfare is not going to get very far.

This type of evolutionary logic paints a picture of a world red in tooth and claw, one where you need to constantly be watching your back. But if everyone is looking out for their own selfish interests, where does selflessness come from? The solution to this puzzle was put forward by J. B. S. Haldane in the 1930s, and made precise by William Hamilton in 1963. Hamilton had the remarkable insight to think of this as an economics problem, and rephrase it in terms of costs and benefits.

Continue reading When nice guys finish first: a lesson from tiny robots

Blind fish in dark caves shed light on the evolution of sleep

An eyeless Mexican cavefish. If you think it looks sleepy, read on.

This post has been submitted to the NESCent Evolution Blogging Contest

Out of the approximately 3 billion letters of DNA that make up your genome, there are about a 100 letters that neither of your parents possess. These are your own personal mutations. The machinery that copies DNA into new cells is very reliable, but it is not perfect. It makes errors at a rate equivalent to making a single typo for every 100 books filled with text. The sperm and egg cells that fused to form you carried a few such mutations, and therefore so do you.

Every child who grew up watching cartoons like X-men or the ninja turtles associates mutations with superpowers. But the sad reality is that, somewhat like a double edged sword, mutations are more likely to hurt you than do any good. Imagine if you were to change a few letters at random in a book. Chances are, you are not improving the story. A typo doesn’t usually do much. It’s easy to overlook and doesn’t change the essential meaning of a sentence. This is the idea of the neutral theory of evolution, that most mutations have little or no effect on the organism. While this may be the case, the rare events pack quite a punch. Beneficial mutations are rare, but they are the only road through which organisms become better adapted to their environments.*

Changes to DNA are more likely to be disruptive than beneficial, simply because it is easier for changes to mess things up than to improve them. This mutational burden is something that all life forms have to bear. In the long run, individuals that carry harmful mutations will, on average, produce fewer offspring than their peers. Over many generations, this means that the mutation will dwindle in frequency. This is how natural selection is constantly ‘weeding out’ disruptive mutations from our genomes.

There is a flip side to this argument, and it is the story of the blind cave fish. If a mutation disrupts a gene that is not being used, natural selection will have no restoring effect. This is why fish that adapt to a lifestyle of darkness in a cave tend to lose their eyes. There is no longer any advantage to having eyes, and so the deleterious mutations that creep in are no longer being weeded out. Think of it as the ‘use it or lose it’ school of evolution.**

Continue reading Blind fish in dark caves shed light on the evolution of sleep

Sylvia’s super awesome maker show

I just bought an Arduino, which is a cheap open-source electronics board. You can program it from your computer and build all sort of interesting devices that can respond to their surroundings. It can take as inputs pretty much any kind of electronic sensor you can get your hands on (light, temperature, pressure, sound, force sensors, and countless others) and can use them to drive motors, switch things on and off, make music, run a web server, play pong, and so on. I just started tinkering around with it and it’s incredibly liberating to be able to get a computer to do something physical.

While looking around for interesting Arduino projects, I came across this incredible video via Make magazine. It’s an episode from a show hosted by Sylvia, a 9 year-old tinkerer and Arduino hacker.

When it hurts so bad, why does my brain light up?

If you’ve ever been rejected by a loved one, you knows that it hurts. Think of the language that we use to describe the feeling – hurt, pain, broken hearts, heartache, and so on. Across cultures, many of the same words are used to describe social rejection and bodily pain. Is this all just metaphor, or are people who have been dumped genuinely feeling physical pain? A recent study by Ethan Kross and colleagues set out to address this question by putting volunteers who had recently experienced such intense rejection into brain imaging machines.

The principle behind brain imaging is straightforward. As you start taxing your brain, different neural circuits are called into action. These brain regions need to consume more oxygen, which is provided through the blood supply. Oxygen travels in your blood by binding to the iron that is present. This changes its magnetic properties in a way that an MRI machine can detect. The machine tracks where all the oxygen-carrying blood is going, and the places that ‘light up’ with oxygen are the brain regions being used the most.

The researchers recruited people who felt intensely rejected as a result of being dumped (an “unwanted romantic relationship break-up”) sometime in the last 6 months. The subjects were asked to perform two sets of tasks while in the brain scanner.

Continue reading When it hurts so bad, why does my brain light up?

Hollaback to the male humpback whale

There’s something irresistible about pop music. Every few months, a song is born that transcends cultural differences and plants itself into our minds. Many of us manage to resist the allure of pop through indifference or stubborn determination. Among the humpback whales, however, keeping up with the latest musical fads is a matter of survival.

Humpback whales use their immense bodies as resonating cavities to produce a truly impressive vocal range. A single male has a range wider than any human choir. They can sing from two octaves lower than a bass singer, to three octaves higher than a soprano. This whale choir broadcasts across the ocean, their songs travelling along for thousands of kilometers. Only the males sing, and they do so only during breeding seasons, suggesting that it plays an important role in attracting a mate.

And just like the songs that we listen to, the songs of the humpback have a precise musical structure. They can be broken into separate themes, each of which contain a number of phrases. Each phrase in turn contains a series of notes, ranging from chirps, bleeps and squeaks that sounds like something from a science fiction movie, to more gravelly grunts and a kind of deep, majestic roar. (Audio samples below)
Continue reading Hollaback to the male humpback whale

Perfumes, smells and quantum wells

Luca Turin is one of the authors of the paper mentioned in the previous post. He’s quite a colorful character, and his TED talk from 2005 is definitely worth checking out.

And, via Sean Carroll, I came across an interesting talk by Seth Lloyd on ‘Quantum Life’. He describes ways in which living things take advantage of quantum mechanics – an idea that would have got you laughed out of the room a few years ago.