Sight The Evolution of the

Eyes are beautifully complex structures, and their evolution was a source of some mystery to Charles Darwin. The idea that the eye could not have arisen from the process of natural selection is a common misconception even today and is rooted in the idea of irreproducible complexity (see Chapter 22), which states that complex structures could not have arisen as a result of a gradual evolutionary process because humans can't imagine how intermediate forms would be advantageous. You often see this argument stated this way: "What good is half an eye?"

Darwin never suggested that natural selection couldn't produce the eye, of course; he just admitted that he didn't know exactly how the process unfolded. He imagined that many intermediate steps had to occur, leading from a very simple light-sensing structure to the structures you're using to read this page; he just didn't know what they were. Fast-forward to today, when scientists know that many of the intermediate stages exist in other animals. From this fact, they can imagine the series of small steps that would lead from the simplest light-sensitive cell to a more complex eye. For example:

i Step 1: Start with the simplest light-sensitive cells. A patch of these cells can determine the presence or absence of light but not much else.

i Step 2: The cells are set slightly into the body in a little pit or cup.

After the cells reside in a depression in the surface of the organism, the light-sensing apparatus becomes capable of determining the direction from which the light is coming.

i Step 3: The edges of the pit grow together so that light enters the pit through a very small opening. This arrangement is the principle behind a pinhole camera. Even though the camera has no lens, restricting light to traveling through a small hole results in a crisper image.


The principle behind the pinhole camera is simple physics, and you can test it yourself. If you have to hold a book at a distance to focus (you young folks wait a few years), poke a tiny hole in a piece of paper and peer through it. You can read the text without having to move the book away (or so far away).

^ Step 4: A lens is added to the opening of the light-sensitive cells. You don't have to imagine the lens evolving all at once as a lens; you can easily imagine that a layer of translucent cells over the opening of the pinhole had a protective function. And we have plenty of examples of see-through cells in the animal kingdom. When that layer was in place, any changes that resulted in a crisper image would be selectively advantageous.

Imagining such intermediate steps goes a long way toward helping you see how a series of small changes can lead to complex structures like the eye.


A common pattern that's repeated across a large number of animals in different locations is the evolution of cave blindness — the evolution of sightlessness in lineages that have come to inhabit caves. Cave blindness is an excellent example of convergent evolution, in which the same trait evolves independently in different organisms (refer to Chapter 9).

The ancestors of most cave-dwelling organisms came from non-cave environments that had light. In fact, you can go to any big cave with its own ecosystem full of cave critters, and you'll find blind cave animals whose closest relatives (in the tree of life) can see.

You can easily see why the selective pressures on organisms existing in darkness would be different from those existing in light: Perhaps the energy required to produce those structures was needed for other functions — it's wasted making eyes in the dark and is better spend it some other way. Perhaps rewiring the sensory system — cave critters often have a good sense of smell, extra-sensitive tactile feelers and antenna, or other stuff that's good to have in the dark — requires minimizing the eyes.

A common theme in evolutionary biology is that things can happen over and over. If something is good once, maybe it's good twice. Cave blindness is an example; over and over, organisms that move into caves lose their sight. Flight (discussed in "Vertebrate Flight," later in this chapter) is another good example; it evolved in insects, mammals, birds, and even the extinct lineage pterosaurs (which you can read about in Chapter 20).

Finally, as discussed in Chapter 5, we always need to be cautious about assuming that an evolutionary change is an adaptation. Once it's dark, mutations that degrade the eye are no longer bad; they just don't matter. So over enough time, genetic drift might be expected to result in the loss of eyes even if the change isn't adaptive — in which case cave blindness is an example of evolution but not adaptation.

Back to the Sea

Eons ago, the first vertebrates crawled out of the ocean and onto land. It seemed like a good idea at the time. But since then, a few species have headed back to sea. Some have gone back completely; others return to the land to reproduce. Sea snakes, penguins, seals, whales, manatees, and sea otters are examples of animals that evolved independently back to sea animals from terrestrial ancestors.

Through phylogenetic analysis (see Chapter 9), scientists can tell that vertebrates have returned to the sea on several occasions; that in each case, the aquatic group is nested within a larger terrestrial group; and that the common ancestor of all the individuals in the group was terrestrial. DNA-sequence evidence has been especially helpful in confirming relationships. The skeletal structures of whales and hippos, for example, provide evidence that they're related, even though they don't look all that similar. Through DNA evidence, scientists also know that the seal group is nested within the carnivores.

Living in the ocean selects for several suites of characters:

1 With the exception of the sea snakes, which live in warm tropical waters, all these groups have made adaptations to keep warm.

Penguins have an insulating layer of blubber, as do all the mammals that live in the ocean, except for sea otters, who have water-resistant coats that trap insulating air layers.

1 All ocean-dwelling species are reasonably streamlined to facilitate faster motion in water. The manatee group is the least streamlined and, not surprisingly, the slowest. But then, manatees are also vegetarians, and plants don't run very fast.

1 Their appendages have become modified for locomotion in water: flippers in the case of many of the mammals; wings that act like flippers and webbed feet in the case of the penguins. Sea snakes have a flattened body, especially in the tail region, allowing them to swim with an eel-like motion.

1 All have characteristics that indicate their descent from land animals.

They all breathe air, for example, which can be very inconvenient when you live in the water, but each has evolved a rather impressive capability for holding its breath. (Sperm whales can routinely hold their breath for an hour!) They also have vestigial structures indicative of terrestrial ancestors. One of the best examples is the hind leg bones of whales. These small bones are completely within the body (whales don't have hind limbs) but correspond to the rear leg bones of terrestrial quadrupeds.

And Back to the Land Again

Current research suggests that the elephant may have an aquatic ancestor.

Keep in mind, though, that the jury's still out on this particular hypothesis.

But I decided to share it with you nonetheless because it's a good story.

Think of it as a trip to the cutting edge of science but remember: There's not a lot of room on the edge, so sometimes we fall off!

The evidence that the elephant evolved from an aquatic ancestor is threefold:

i Elephants' closest living relatives are manatees. The fossil record for the evolutionary transition of the manatee lineage to the aquatic environment is reasonably complete. Fossil manatees with the vestigial legs have been found, and in Jamaica recently, scientists discovered a fossil manatee with functional legs that could support the weight of the animal yet still showed adaptation to an aquatic lifestyle. The aquatic ancestor of elephants would have been similar to such a creature, but the elephant lineage returned to the land rather than transition to a fully aquatic lifestyle, as the manatee lineage did. What we know from the fossil record and the structure of existing manatees and whales is consistent with the hypothesis that the most recent common ancestor of these beasts already had its feet in the water. One branch of the family tree kept going, while the other headed back to shore.

i Elephants are surprisingly good swimmers. Although they can't raise their heads out of the water while swimming, they can use their trunks as snorkels. If you've ever breathed through a snorkel while standing in water (rather than floating on the top of the water), you know that this feat is difficult because of the pressure of the water. Well, snorkeling is even harder for elephants because of the length of their trunks, but they do it relatively easily because they don't have a pleural cavity (a membrane surrounding the lungs that's unique to mammals). The absence of this cavity prevents the pressure difference from damaging the lungs.

i Elephants have traits that are common to mammals that have returned to the ocean. Chief among these traits is internal testes — a characteristic found in no other land mammal but in all aquatic mammals.

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Photosynthetic organisms convert light energy from the sun to chemical energy, which they use to power their bodies. Photosynthesis is responsible for almost all the energy used by organisms on this planet. Either directly, as a result of internal photosynthesis, or indirectly, by eating something that photosynthesizes itself (or that ate something that did), most species run on photosynthetic energy. Because oil is ancient fossilized plant matter, your car is running indirectly on photosynthetic energy, too.

When you think of photosynthesis, plants are probably the first (and likely the only) organisms that come to mind, but they aren't the only organisms that use photosynthesis. Some bacteria do, too. Figuring out the origin and evolution of the various chemical mechanisms by which bacteria photosyn-thesize is a source of active research. As with so many things, biologists are still learning about the evolutionary diversity of photosynthetic mechanisms. In the summer of 2007, a new type of photosynthetic bacteria with different chemical pathways was discovered in a hot spring in Yellowstone National Park.

Deep-Sea Thermal-Vent Organisms

Photosynthesis may be responsible for most of the energy that organisms use, but a group of organisms that live deep in the ocean use another source of energy. Down at the ocean bottom, in regions of sub-oceanic volcanic activity, are thermal vents that spew out hot, mineral-rich streams of water from within the Earth. These mineral-rich streams of water, which were unknown before the 1970s, can be used to generate energy in much the same way that photosynthesis does.

Specifically, some bacteria can generate energy by oxidizing the hydrogen sulfide (the substance that makes rotten eggs smell rotten) that is present in the hot vent water. So these organisms derive energy not from photosynthesis, but from chemosynthesis. The energy that forms the base of the food chain in these deep thermal vents is not the energy of the sun, but the energy at the core of the Earth.

Just as plants form the basis of an entire community on the surface of the earth, these bacteria form the basis of a whole community on the ocean floor. And what a community it is! Creatures found nowhere else live near these thermal vents. The sulfur-oxidizing bacteria live within large worms that have no digestive systems but derive their energy solely from the bacteria, which in turn get a secure location anchored right near the stream of hydrogen sulfide.

Finally, these deep thermal vents have a very dim glow, so additional photo-synthetic bacteria may be lurking there somewhere. Things are always more complicated than they seem at first!


One of the most amazing evolutionary events is called endosymbiosis. According to this theory, some of the structures in eukaryotic cells — such as mitochondria and chloroplasts — once were free-living bacteria that became engulfed in ancestral eukaryotic cells, and a symbiotic relationship evolved. Somehow, and we don't completely understand how, two ancient critters joined up and eventually became so tightly interdependent that they effectively became a single organism. Remember that we're eukaryotes so that means that we are derived from two different lineages that came together deep in the distant past to make the eukaryotic cell. That's why your mitochondria have their own genome — their distant ancestors used to fly solo.

Here are the details supporting this theory: Mitochondria and chloroplasts bear a strong resemblance to bacteria. When the eukaryotic cells divide, the organelles divide too, and the division process of these organelles is reminiscent of the division of bacteria. Most importantly, these organelles have their own DNA, and analysis of the DNA sequences shows that the organelles are closely related to some free-living species of bacteria.

As you can imagine, this hypothesis was quite controversial initially. Think about it: Descendents of ancient bacteria are living in all your cells. But the DNA evidence seems to be beyond doubt. Your mitochondria have their own genome, albeit much reduced, and it's a lot more similar to a bacteria genome than it is to anything in your nuclear genome. Luckily, we eukaryotes are all living happily ever after, and we've been doing so for at least 2 billion years.

Vertebrate Flight

Flight is another trait that has evolved several times in several lineages. Birds, bats, pterodactyls — all evolved true flight, and a couple of others have rudimentary gliding ability. Flight is a remarkably successful trait. Groups that are capable of flying radiate extensively. Bats account for one quarter of all mammal species, for example. And pterodactyls, though extinct, survived for 150 million years and encompassed many species, including the largest creatures ever to take to the air.

Theories about the evolution of flight can be divided into two groups: up from the ground and down from the trees. The second group is easier to visualize, because species living today, such as flying squirrels (which don't really fly, by the way), have structures that allow them to glide from tree to tree. Current thinking is that bats arose from an arboreal ancestor, so the gliding hypothesis may apply to them, too. Pterodactyls, on the other hand, don't seem to have descended from arboreal ancestors, so maybe both mechanisms are possible.

What scientists do know is that bats, pterodactyls, and birds evolved flight structures in different ways. In bats, the wing is constructed of a membrane stretched between what for humans would be the fingers of the hand. In the case of the pterodactyls, the wing is supported by just one elongated digit. In birds, the wing is comprised of feathers all along the arm. And that list covers just the vertebrates; flight has also evolved in the insect lineage. Bottom line: Several different mutational pathways generated wings.

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