Monday, September 10, 2012

So Long, and Thanks for All the Inner Fish

Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body, a book with a rather curious title, traces our shared lineage with other organisms going back hundreds of years to our aquatic ancestors. Its author, Neil Shubin was a member of the team that, in 2006, discovered the purported missing link between fish and terrestrial tetrapods. It was a paleontological breakthrough that fascinated academics and laypersons alike (links: Nature and New York Times). The 375 million year old fossilized animal, excavated from the Canadian Arctic exposures, was named Tiktaalik, or "large freshwater fish" in the Inuktitut language. As a paleontologist who taught anatomy to university students, Shubin has written this wonderful book which helps us understand anatomy in light of our shared descent with the rest of the animal kingdom. According to him:
The best road maps to human bodies lie in the bodies of other animals. The simplest way to teach students the nerves in the human head is to show them the state of affairs in sharks. The easiest road map to their limbs lies in fish. Reptiles are a real help with the structure of the brain. The reason is that the bodies of these creatures are often simpler versions of ours. 
Book review: Your Inner Fish by Neil Shubin

As a paleontologist, Shubin was a part of several intense expeditions. The first chapter of the book is a rare glimpse into such adventures that are the heart and soul of a career in paleontology. Shubin talks about his summer in the Canadian Arctic, "spent in snow and sleet, cracking rocks on cliffs." There was a time they spotted a white speck that "looked like a polar bear about a quarter mile away." Shubin says, "our bear was a white Arctic hare two hundred feet away. With no trees or houses by which to judge distance, you lose perspective in the Arctic." Prior to the Arctic expedition, Shubin and his team were searching for fossil evidence for the origin of animal limbs in the Catskill Formation in Pennsylvania. There they stumbled upon a shoulder bone belonging to a Devonian tetrapod named Hynerpeton. But the rest of the skeleton was never found. It was after toiling for many summers in the Arctic that they struck gold in form of several Tiktaalik fossils. Like early terrestrial tetrapods, it had a flat head (like that of a crocodile), a neck, and limbs with shoulder, elbow, and wrist joints. Like fish, it had scales on its back and fins with fin webbing. Tiktaalik was that was long-sought-after, missing puzzle piece.


Shubin elaborates how our anatomies are linked to fish, reptiles, amphibians, worms, even prehistoric creatures (which blur the lines between these modern categories), and beyond. He relies on both fossil and genetic evidence to establish these anatomical connections. His starting point is the forelimbs, a major subject of his own paleontological exploits. It was Charles Darwin who first attributed commonalities between fins, hands, wings, and flippers to common ancestry. Yet these organs may have different structures and function. While humans and many other species have a clear bone pattern (upper arm, forearm, digits, and shoulder, elbow, and wrist joints), fish have  fin webbing and many bones at the base. Lungfish are living fossils that bridge part of this gap as they have a single bone at the base of the appendage. Shubin pinpoints how fossilized creatures have helped bridge the remaining gap (Eusthenopteron, which bones analogous to our upper arm and forearm bones, Tiktaalik, which had shoulders, elbows, wrists composed of the same corresponding bones in humans ("it was capable of doing push-ups"), and Acanthostega, another paleontological steal, uncovered by Jennifer Clack, which, in addition to an anthropomorphic pattern of arm bones has fully formed digits - true finger and toes).

The quest for missing links is not restricted to dig sites. It continues in full force within the confines of biology labs where scientists seek the same anatomical connections by looking at the genome of extant species. How exactly are fins, hands, wings, and flippers similar and how are they different? Shubin focuses on one specific commonality between many species - the disparity between the thumb (digit one) and the little finger (digit five) sides of our hands. He talks about the first tissue studies which helped identify a specific patch of tissue called the zone of polarizing activity (ZPA), which when transplanted to the thumb side in chicken embryos gave rise to a full duplicate set of digits in the wing with a mirror image pattern. Once genomics picked pace, the source of this asymmetry was attributed to the Sonic hedgehog gene,which was first found in flies. Interestingly, this gene was traced across species, including chickens and even sharks. By manipulating this gene, scientists could generate the same mirror-image duplication trait in all the species. Quoting the author:
All appendages, whether they are fins or limbs, are built by similar kinds of genes. What does this mean for the problem we looked at in the first two chapters of the transition of fish fins into limbs? It means that this great evolutionary transformation did not involve the origin of new DNA: much of the shift likely involved using ancient genes, such as those involved in shark fin development, in new ways to make limbs with fingers and toes.
In the subsequent chapters, Shubin goes on to trace evidence of these ancient genes elsewhere in the body.


While a whopping 3% of our genome is devotes to odor detection, an alarming 300 of these 1000 or so genes are rendered non-functional by mutations. Shubin writes:
Why have so many odor genes if so many of them are entirely useless? We humans are part of a lineage that has traded smell for sight.
It turns out most of this olfactory investment is a vestige of our descent:
If you compare the odor genes of a mammal with the handful of odor genes in a jawless fish, the extra genes in mammals are all variations on a theme: they look like copies, albeit modified ones, of the genes in jawless fish. This means that our large number of odor genes arose by many rounds of duplication of the small number of genes present in primitive species. 


There are interesting theories in the book pertaining to color vision:
Of our three receptor-making genes, two are remarkably like one of those in other mammals. This seems to imply that our color vision began when one of the genes in other mammals duplicated and the copies specialized over time for different light sources. ...
Our kind of color vision arose about 55 million years ago. At this time we find fossil evidence of changes in the composition of ancient forests. Before this time, the forests were rich in figs and palms, which are tasty but all of the same general color. Later forests had more of a diversity of plants, likely with different colors. The switch to color vision correlates with a switch from a monochromatic forest to one with a richer palette of colors in food.
As before, Shubin discusses fossil and genetic data that helped us understand our vision apparatus better. He talks about polychaete worms as missing links, with two kinds of "eyes," one set similar to modern invertebrates and one set similar to humans and other vertebrates. My favorite part was his description of the experiments by Walter Gehring, who first grew  eyes in the antenna of flies by manipulating the Pax 6 or "eyeless" gene in those cells, and later put mouse Pax 6 in flies and showed that it gave rise to fly eyes and not mouse eyes!


Our legacy as descendants of ancient animals propagates to our auditory apparatus as well. Our middle ears consist of three small bones the malleus, incus, and stapes. Shubin illustrates how malleus and incus are related to the reptile jaw and how the stapes originated from the hyomandibula in fish (a jaw support bone which connects the upper jaw to the braincase). A series of mammal-like reptile fossils discovered in South Africa and Russia helped explain the transition from jaw bones to the malleus and incus, while the progressive reduction in the size of the hyomandibula from sharks to creatures like Tiktaalik to amphibians helped trace the origin of the stapes.
Why would mammals need a three-boned middle ear? This little linkage forms a lever system that allows mammals to hear higher-frequency sounds than animals with a single middle ear bone.
In a similar tone, parts of our inner ear which helps us maintain balance are closely related to the neuromast, a jelly-filled sac that helps fishes discern direction of water flow. Formation of the inner ear is dependent on a gene called Pax 2, which is "active in the head and, lo and behold, in the neuromasts."

To summarize in Shubin's own words:
Looking back through billions of years of change, everything innovative or apparently unique in the history of life is really just old stuff that has been recycled, recombined, repurposed, or otherwise modified for new uses. This is the story of every part of us, from our sense organs to our heads, indeed our entire body plan.
And, to conclude this post, here is one more quote from the book I really liked: 
Carl Sagan once famously said that looking at the stars is like looking back in time. The stars' light began the journey to our eyes eons ago, long before our world was formed. I would like to think that looking at humans in much like peering at the stars. If you know how to look, our body becomes a time capsule that, when opened, tells of critical moments in the history of our planet and of a distant past in ancient oceans, streams, and forests.

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