Saturday, January 29, 2011

Your Inner Fish – Neil Shubin

If you consider that over 99 percent of all species that ever lived are now extinct, that only a very small fraction are preserved as fossils, and that an even smaller fraction still are ever found, then any attempt to see our past seems doomed from the start.

Fossils are one of the major lines of evidence we use to understand ourselves. (Genes and embryos are others … ). Most people do not know that finding fossils is something we can do with surprising precision and predictability. We work at home to maximise our chances of success in the field. Then we let luck take over.

Our example will show us one of the great transitions in the history of life: the invasion of land by fish. For billions of years, all life lived only in water. Then, as of about 365 million years ago, creatures also inhabited land. Life in these two environments is radically different. Breathing in water requires very different organs than breathing air. The same is true or excretion, feeding, and moving about. A whole new kind of body had to arise. At fist glance, the divide between the two environments appears almost unbridgeable. But everything changes when we look at the evidence; what looks impossible actually happened.

My colleague … and others have uncovered amphibians from rocks in Greenland that are about 365 millions years old. With their necks, ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find fish that look like, well, fish. … Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.

Now the challenge is to find rocks that were formed under conditions capable of preserving fossils.

The best place to look are those where we can walk for miles over the rock to discover areas where bones are “weathering out.” Fossil bones are often harder than the surrounding rock and so erode at a slightly slower rate and present a raised profile on the rock surface. Consequently, we like to walk over bare bedrock, find a smattering of bones on the surface, then dig in.

So here is the trick to designing a fossil expedition: find rocks that are the right age, of the right type (sedimentary), and well exposed, and we are in business. Ideal fossil-hunting sites have little soil cover or vegetation, and have been subject to few human disturbances. Is it any surprise that a significant fraction of discoveries happen in desert areas? In the Gobi Desert. In the Sahara. In Utah. In Artic deserts, such as Greenland.

… the (Canadian Arctic) area perfectly fit our criteria: age, type, and exposure. Even better, it was unknown to vertebrate paleontologists, and therefore unprospected for fossils.

... The next piece of evidence came from Philadelphia a week later. Fred, a magician with his dental tools, uncovered a whole fin in his block. At the right place, just at the end of the forearm bones, the fin had that bone. And that bone attached to four more beyond. We were staring at the origin of a piece of our own bodies inside this 375-million-year-old fish. We had a fish with a wrist.

Just as Darwin’s theory predicted: at the right time, at the right place, we had found intermediates between apparently two different kinds of animals.

Seeing Tiktaalik is seeing our history as fish.

Bend you wrist back and fourth. Open and close your hand, When you do this, you are using joints that first appeared in the fins of fish like Tiktaalik. Earlier, these joints did not exist. Later, we find them in limbs.

…why not take cues from the expert? ... Chuck did not look at every rock, and when he chose to look at one, for the life of me I couldn’t figure out why. Then there was the really embarrassing aspect of all this: Chuck and I would look at the same patch of ground. I saw nothing but rock – barren desert floor. Chuck saw fossil teeth, jaws, and even chunks of skull.

An aerial view would have shown two people walking alone in the middle of a seemingly limitless plain, where the vista of the dusty red and greed sandstone mesas, buttes, and badlands extended for miles. But Chuck and I were only staring at the ground … The fossil we sought were tiny, no more that a few inches long, and ours was a very small world. The intimate environment stood in extreme contrast to the vastness of the desert panorama that surrounded us. I felt as if my walking partner was the only person on the entire planet, and my whole existence was focused on pieces of rubble.

Chuck was extraordinarily patient with me as I pestered him with questions for the better part of each day’s walk. I wanted him to describe exactly how to find bones. Over and over, he told me to look for ‘something different’, something that had the texture of bone, not rock, something that glistened like teeth, something that looked like an arm bone, not a piece of sandstone. Try as I might, I still returned home each day empty-handed. Now it was even more embarrassing, as Chuck, who was looking at the same rocks, came home with bag after bag.

Finally, one day, I saw my first piece of tooth glistening in the desert sun. It was sitting in some sandstone rubble, but there it was, plain as day. The enamel had a sheen that no other rock had; it was like nothing I had seen before. Well, not exactly – I was looking at things like it every day. The difference was this time I finally saw it, saw the distinction between rock and bone. The too glistened, and when I saw it glisten I spotted its cusps. The whole isolated tooth was about the size of a dime, not included the roots that projected from its base. To me, it was as glorious as the biggest dinosaur in the halls of any museum.

All of a sudden, the desert exploded with bone; where once I had seen only rock, now I was seeing bits and pieces of fossil everywhere, as if I were wearing a special new pair of glasses and a spotlight was shining on all the different pieces of bone. Next to the tooth were small fragments of other bones, then more teeth. I started to return home with my own little bags each night.

Now that I could finally see bones for myself, what once seemed a haphazard group effort started to look decidedly ordered. People weren’t just scattering randomly across the desert; there were real though unspoken rules. Rule number one: go to the most productive-looking rocks, judging by whatever search image or visual cues you’ve gained from previous experience. Rule number two: don’t follow in anybody’s footsteps; cover new ground (Chuck had graciously let me break this one). Rule three: if your plum area already has somebody on it, find a new plum, or search a less promising site. First come, first served.

In seeing embryos, I was seeing a common architecture. The species ended up looking different, but they started from a generally similar place. Looking at embryos, it almost seems that the differences among mammals, birds, amphibians, and fish simply pale in comparison with their other fundamental similarities.

If we were to cut ourselves in half (an early development of embryonic development)… we would find a tube within a tube. The outer tube would be our body wall, the inner tube our eventual digestive tract. A space, the future body cavity, separates the two tubes. This tube-within-a-tube structure stays with us our entire lives. The gut tube gets more complicated, with a big sac for a stomach and long intestinal twists and turns. The outer tube is complicated by hair, skin, ribs, and limbs that push out. But the basic plan persists. We may be more complicated that we were at twenty-one days after conception, but we are still a tube within a tube…

Here’s a humbling thought for all of us worms, fish, and humans: most of life’s history is the story of single-celled creatures. Virtually everything we have talked about thus far – animals with hands, heads, sense organs, even body plans – has been around for only a small fraction of the earth’s history. Those of us who teach paleontology often use the analogy of the ‘earth year’ to illustrate how tiny that fraction is. Take the entire 4.5-billion-year history of the earth and scale it down to a single year, with January 1 being the origin of earth and midnight December 31 being the present. Until June, the only organisms were single-celled microbes, such as algae, bacteria, and amoebae. The first animal with a head did not appear until October. The first human appears on December 31.

… Rocks older than 600 million years are generally devoid of animals or plants. In them we only find single-celled creatures or colonies of algae.

… more exciting would be some tangible experimental evidence that shows how predation could bring about bodies. That is essentially what Martin Boraas and his colleagues provided. They took an algae that is normally single-celled and let it live in the lab for over a thousand generations. Then they introduced a predator: a single-celled creature with a flagellum that engulfs other microbes to ingest them. In less than two hundred generations, the algae responded by becoming a clump of hundreds of cells; over time, the number of cells dropped until there were only eight in each clump. Eight turned out to be optimum because it made clumps large enough to avoid being eaten but small enough so that each cell could pick up light to survive. The most surprising thing happened when the predator was removed: the algae continued to reproduce and form individuals with eight cells. In short, a simple version of a multicellular form had arisen from a no-body.

There are obvious advantages of becoming a creature with a large body: besides avoiding predators, animals with bodies can eat other, smaller creatures and actively move long distances. Both of these abilities allow the animals to have more control over their environment. But both consume a lot of energy. Bodies require even more energy as they get larger, particularly if they incorporate collagen. Collagen requires a relatively large amount of oxygen for its synthesis and would have greatly increased our ancestor’s need for this important metabolic element.

But the problem was this: levels of oxygen on the ancient earth were very low. For billions of years oxygen levels in the atmosphere did not come close to what we have today. Then, roughly a billion years ago, the amount of oxygen increased dramatically

… A cause for the origin of bodies was (also) in place: by a billion years ago, microbes had learned to eat each other. There was a reason to build bodies, and the tools to do so where already there.

Something was missing. That something was enough oxygen on the earth to support bodies. When the earth’s oxygen increased, bodies appeared everywhere. Life would never be the same.

We humans are part of a lineage that has traded smell for sight. We now rely on vision more than smell, and this is reflected in our genome. In this trade-off, our sense of smell was desensitized, and many of our olfactory genes became functionless.

… Like photocopies that lose their fidelity as they are repeatedly copied, our olfactory genes get more dissimilar as we compare ourselves to successively more primitive creatures. … That baggage is a silent witness to our past; insides our noses is a veritable tree of life.

Hurt your knee and you almost certainly injure one or more of three structures: the medial meniscus, the medial collateral ligament, or the anterior cruciate ligament. So regular are the injuries to these three parts of your knee that these structures are known among doctors as the “Unhappy Triad”. They are clear evidence of the pitfalls of having an inner fish. Fish do not walk on two legs.

Our humanity comes at a cost. For the exceptional combination of things we do – talk, think, grasp, and walk on two legs – we pay a price. This is an inevitable result of the tree of life inside of us.

… In many ways, we humans are the fish equivalent of a hot-rod Beetle. Take the body plan of a fish, dress it up to be a mammal, then tweak and twist that mammal until it walks on two legs, talks, thinks, and has superfine control of its fingers. We can dress up a fish only so much without paying a price. In a perfectly designed world – one with no history – we would not have to suffer everything from haemorrhoids to cancer.

Nowhere is this history more visible that in the detours, twists and turns of our arteries, nerves and veins. Follow some nerves and you’ll find that they make strange loops around other organs, apparently going in one direction only to twist and turn and end up in an unexpected place. The detours are fascinating products of our past that … often create problems for us – hiccups and hernias, for example. And this is only one way our past comes back to haunt us.

Our deep history was spent, at different times, in ancient oceans, small streams, and savannahs, not office buildings, ski slopes, and tennis courts. We were not designed to live past the age of eighty, sit on our keisters for ten hours a day, and eat Hostess Twinkies, not were we designed to play football. This disconnect between our past and our human present means that our bodies fall apart in certain predictable ways.

… we were not designed rationally, but are the products of a convoluted history.

During our history as fish we were active predators in ancient oceans and streams. During our more recent past as amphibians reptiles, and mammals, we were active creatures preying on everything from reptiles to insects. Even more recently, as primates, we were active tree-living animals, feeding on fruits and leaves. Early humans were active hunter-gatherers and, ultimately, agriculturalists. Did you notice a theme here? That common thread is the word “active.”

The bad news is that most of us spend a large portion of our days being anything but active. … Our history from fish to early human in no way prepared us for this new regimen. This collision between past and present had its signature in many of the aliments of modern life.

… Neel suggested that our human ancestors were adapted for a boom-bust existence. … periods of plenty would be punctuated by times of scarcity, when our ancestors had considerably less to eat.

… in this context fat storage becomes very useful. … but it fails miserably in an environment where rich foods are available 24/7. Obesity and its associated maladies – age-related diabetes, high blood pressure, and heart disease – become the natural state of affairs. The thrifty genotype hypothesis also might explain why we love fatty foods.

Our sedentary lifestyle affects us in other ways, because our circulatory system originally appeared in more active animals.

… Because arteries are closer to the pump, the blood pressure in them is much higher than in veins. This can be a particular problem for the blood that needs to return to our heart from our feet. Blood from the feet needs to go uphill, so to speak, up the veins of our legs to our chest. If the blood is under low pressure, it may not climb all the way. Consequently, we have two features that help the blood move up. The first are little valves that permit the blood to move up but stop it from going down. The other feature is our leg muscles. When we walk we contract them, and this contraction serves to pump the blood up our leg veins.

… This system works superbly in an active animal, which uses its legs to walk, run, and jump. It does not work well in a more sedentary creature. If the legs are not used much, the muscles will not pump the blood up the veins. Problems can develop if blood pools in the veins, because that pooling can cause the valves to fail. This is exactly what happens with varicose veins.

Talking comes at a steep price: choking and sleep apnea are high on the list of problems we have to live with in order to be able to sleep. … we use the same passage to swallow, breathe, and talk. These functions can be at odds, for example when a piece of food gets lodged in the trachea.

The parallels between our hiccups and gill breathing in tadpoles are so extensive that many have proposed that the two phenomena are one and the same. Gill breathing in tadpoles can be blocked by carbon dioxide, just like our hiccups.

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