Notes to: "Your Inner Fish"

Material covered: 
"Your Inner Fish: A Journey into the 3.5 Billion Year History of the Human Body," by Neil Shuman (ch. 1-3, 5-6, 11)

YIF Chapter one: Finding Your Inner Fish

• "Ancient fish bones can be a path to knowledge about who we are and how we got that way. We learn about our own bodies in seemingly bizarre places, ranging from the fossils of worms and fish recovered from rocks from around the world to the DNA in virtually every animal alive today." 
• "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." 
• "Most people do not know that finding fossils is something we can often do with surprising precision and predictability. We work at home to maximize our chances of success in the field. Then we let luck take over." 
• Dwight E. Eisenhower: "In preparing for battle, I have found that planning is essential, but plans are useless." 
• "In many ways, field paleontologists have a significantly easier time finding new sites today than we ever did before. We know more about the geology of local areas, thanks to the geological exploration undertaken by local governments and oil and gas companies. The Internet gives us rapid access to maps, survey information, and aerial photos. I can even scan your backyard for promising fossil sites right from my laptop. To top it off, imaging and radiographic devices can see through some kinds of rock and allow us to visualize the bones inside." 
• "Ideal to preserve fossils are sedimentary rocks: limestones, sandstones, siltstones, and shales. Compared with volcanic and metamorphic rocks, these are formed by more gentle processes, including the action of rivers, lakes, and seas. Not only are animals likely to live in such environments, but the sedimentary processes make these rocks more likely to preserve fossils."
• "The best places to look are tohse 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." 
• "So here is the trick to designing a new fossil expedition: find rocks that are of the right age, of the right type (sedimentary), and well exposed, and we are in business. Ideal fossil-hunting sites have little soil cover and little 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 Arctic deserts, such as Greenland." 
• "At no time is this more sharply felt than when the helicopter drops one off for the first time in some godforsaken part of the Arctic totally alone. The first thought is of polar bears. I can't tell you how many times I've scanned the landscape looking for white specks that move. This anxiety can make you see things. In our first week in the Arctic, one of the crew saw a moving white speck. It looked like a polar bear about a quarter mile away. We scrambled like Keystone Kops for our guns, flares, and whistles until we discovered that 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." 
• "With twenty-four hours of daylight in the Arctic summer, we did not have to worry about the setting sun, so we grabbed chocolate bars and set off for Jason's site." 
• "As discoverers of the creature, Ted, Farish, and I had the privilege of giving it a formal scientific name. We wanted the name to reflect the fish's provenance in the Nunavut Territory of the Arctic and the debt we owed to the Inuit people for permission to work there. We engaged the Nunavut Council of Elders, formally known as the Inuit Qaujimajatuqangit Katimajiit, to come up with a name in the Inuktitut language... I sent them a picture of the fossil, and the elders came up with two suggestions, Siksagiaq and Tiktaalik. We went with Tiktaalik for its relative ease of pronunciation for the non-Inuktitut-speaking tongue and because of its meaning in Inuktitut: 'large freshwater fish.'"

YIF Chapter two: Getting a Grip

• "In the months before I did my first human dissection, I readied myself by trying to envision what I would see, how I would react, and what I would feel. It turned out that my imagined world in o way prepared me for the experience. The moment when we removed the sheet and saw the body for the first time wasn't nearly as stressful as I'd expected. We were to dissect the chest, so we exposed it while leaving the head, arms, and legs wrapped in preservative-drenched gauze. The tissues did not look very human. Having been treated with a number of preservatives, the body didn't bleed when cut, and the skin and internal organs had the consistency of rubber. I began to think that the cadaver looked morel like a doll than a human." 
• "This comfortable illusion [of things being 'all very mechanical, detached, and scientific'] was rudely shattered when I uncovered the hand. As I unwrapped the gauze from the fingers-- as I saw the joints, fingertips, and fingernails for the first time-- I uncovered emotions that had been concealed during the previous few weeks. This was no doll or mannequin; this had once been a living person, who used that hand to carry and caress." 
• "All creatures with limbs, whether those limbs are wings, flippers, or hands, have a common design. One bone, the humerus in the arm or the femur in the leg, articulates with two bones, which attach to a series of small blobs, which connect with the fingers or toes. This pattern underlies the architecture of all limbs. Want to make a bat wing? Make the fingers really long. Make a horse? Elongate the middle fingers and toes and reduce and lose the outer ones. How about a frog leg? Elongate the bones of the leg and fuse several of them together." 
• "There is a major difference between Owen's theory and that of Darwin: Darwin's theory allows us to make very precise predictions." 
• "A seemingly trivial pattern in the fins of these fish had a profound impact on science. The fins of lungfish have at their base a single bone that attaches to the shoulder. To anatomists, the comparison was obvious. Our upper arm has a single bone, and that single bone, the humerus, attaches to our shoulder. In the lungfish, we have a fish with a humerus. And, curiously, it is not just any fish; it is a fish that also has lungs. Coincidence?"
• "The earliest limbs arose to help animals swim, not walk."
• "Preparators use dental tools to scratch at the rocks we find in the field and thereby expose the fossils inside. It can take months, if not years, for a preparator to turn a big fossil-filled boulder like ours into a beautiful, research-quality specimen." 
• "When we study the structure of these joints to assess how one bone moves against another, we see that Tiktaalik was specialized for a rather extraordinary function: it was capable of doing push-ups." 
• "It is no exaggeration to say that this was a fish-eat-fish world. The strategies to succeed in this setting were pretty obvious: get big, get armor, or get out of the water. It looks as if our distant ancestors avoided the fight." 
• "When Tiktaalik bent its elbow, the end of its radius would rotate, or pronate, relative to the elbow. Refinements of this ability are seen in amphibians and reptiles, where the end of the humerus becomes a true ball, much like our own." 
• "We are not separate from the rest of the living world; we are part of it down to our bones and, as we will see shortly, even our genes." 

YIF Chapter three: Handy Genes

• "My laboratory is split directly in two: half is devoted to fossils, the other half to embryos and DNA. Life in my lab can be schizophrenic. The locked cabinet that holds Tiktaalik specimens is adjacent to the freezer containing our precious DNA samples." 
• "Experiments with DNA have enormous potential to reveal inner fish. What if you could do an experiment in which you treated the embryo of a fish with various chemicals and actually changed its body, making part of its fin look like a hand? What if you could show that the genes that build a fish's fin are virtually the same as those that build our hands?"
• "A skin cell is different from a neuron because different genes are active in each cell. When a gene is turned on, it makes a protein that can affect what the cell looks like and how it behaves. Therefore, to understand what makes a cell in the eye different from a cell in the bones of the hand, we need to know about the genetic switches that control the activity of genes in each cell and tissue." 
• "Like a concerto of composed of individual notes played by many instruments, our bodies are a composition of individual genes turning on and off inside each cell during our development." 
• "All the genetic switches that make fingers, arm bones, and toes do their thing during the third to eighth week after conception. Limbs begin their development as tiny buds that extend from our embryonic bodies. The buds grow over two weeks, until the tip forms a little paddle." 
• "The first embryologists interested in limbs in the 1930s and 1940s faced several problems. They needed an organism in which the limbs were accessible for observation and experiment. The embryo had to be relatively large, so that they could perform surgical procedures on it. Importantly, the embryo had to grow in a protected place, in a container that sheltered it from jostling and other environmental disturbances. Also, and critically, the embryos had to be abundant and available year-round. The obvious solution to this scientific need is at your local grocery store: chicken eggs." 
• "In the 1950s and 1960s a number of biologists, including Edgar Zwilling and John Saunders, did extraordinarily creative experiments on chicken eggs to understand how the pattern of the skeleton forms. This was an era of slice and dice. Embryos were cut up and various tissues moved about to see what effect this had on development. The approach involved very careful microsurgery, manipulating patches of tissue no more than a millimeter thick... They discovered that two little patches of tissue essentially control the development of the pattern of bones inside limbs. A strip of tissue at the extreme end of the limb bud is essential for all limb development. Remove it, and development stops. Remove it early, as we are left with only an upper arm, or a piece of an arm. Remove it slightly later, and we end up with an upper arm and a forearm. Remove it even later, and the arm is almost complete, except that the digits are short and deformed." 
• "Randy Dahn entered my laboratory with a simple but very elegant idea: treat skate embryos just the way Cliff Tabin treated chicken eggs. Randy's goal was to perform all the experiments on skates that chicken biologists had performed on chicken eggs, from Saunders and Zwilling's tissue surgeries all the way to Cliff Tabin's gene experiments. Skates develop in an egg with a kind of shell and a yolk. Skates even have big embryos, just as chickens do." 
• "Randy wanted to determine how different the apparatus is that builds our hands. How deep is our connection to the rest of life? Is the recipe that builds our hands new, or does it, too, have deep roots in other creatures? If so, how deep?"
• "There is a deeper beauty to these experiments on limbs and fins. Tabin's lab used work in flies to find a gene in chickens that tells us about human birth defects. Randy used the Tabin lab discovery to tell us something about our connections to skates... The connections among living creatures run deep." 

YIF Chapter five: Getting ahead

• "It was the middle of the night and I was alone in the lab. I also happened to be surrounded by the bodies of twenty-five human beings under sheets." 
• "The trigeminal's branches do two major things: they control muscles, and they carry sensory information from much of our face back to our brain. The muscles controlled by the trigeminal nerve include those we use to chew as well as tiny muscles deep inside the ear. The trigeminal is also the major nerve for sensation in the face." 
• "My building was constructed in 1896, and the utilities reflect an old design that has been jury-rigged further with each innovation. If you want to understand the wiring and plumbing in my building, you have to understand its history, how it was renovated for each new generation of scientists." 
• "The fundamental blueprint of heads helps us make sense of one of the apocryphal tales in anatomy. In 1820, so the story goes, Johannes Goethe was walking through th Jewish cemetery in Venice when he spotted the decomposing skeleton of a ram. The vertebrae were exposed and above them lay a damaged skull. Goethe, in a moment of epiphany, saw that the breaks in the skull made it look like a gnarled mess of vertebrae. To Goethe, this revealed the essential pattern within: the head is made up of vertebrae that fused and grew a vault to hold our brains and sense organs. This was a revolutionary idea because it linked heads and bodies as two versions of the fundamental plan." 
• "The take-home message of many a lawyer joke is that lawyers are an especially voracious kind of shark Teaching embryology during one of the recurring vogues for these jokes, I remember thinking that the joke is on all of us. We're all modified sharks-- or worse, there is a lawyer inside each of us." 

YIF Chapter six: The Best-Laid (Body) Plans

• "We are a package of about two trillion cells assembled in a very precise way." 
• "Don't even bother trying to compare your body plan with a sponge. You could try, but the mere fact that you were trying would reveal something more psychiatric than anatomical." 
• "All organs in the chicken can be traced to one of three layers of tissue in the developing embryo. These three layers became known as the germ layers." 
• "Think of a balloon pushed into a wall: this flattened disk becomes the human embryo. Our entire body forms from only the top of this ball, the part that is mushed into the wall. The part of the blastocyst below the disk covers the yolk. At this stage of development, we look like a Frisbee, a simple two-layered disk... Cells devide and move, causing tissues to fold in on themselves. Eventually, as tissues move and fold, we become a tube with a glded swelling at the head end and another at the tail. If we were to cut ourselves in half right about now, 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." 
• "The names of these three all-important layers are derived from their position: the outer layer is called ectoderm, the inner layer endoderm, and the middle layer mesoderm. Ectoderm forms much of the outer part of the body (the skin) and the nervous system. Endoderm, the inside layer, forms many of the inner structures of the body, including our digestive tract and numerous glands associated with it. The middle layer, the mesoderm, forms tissue in between the guts and skin, including much of our skeleton and our muscles." 
• "Baby hair is remarkable stuff, soft, thin, and pliant, it made the ideal material for tying up a tiny sphere such as a newt egg." 
• "Draw a line from the mouth to the base of the animal [a sea anemone]. Biologists have given that line a name: the oral-aboral axis." 

YIF Chapter eleven: The Meaning of It All

• "The articulation of truly great ideas, of the laws of nature, begins with simple premises that all of us see every day. From simple beginnings, ideas like these extend to explain the really big stuff, like the movement of the stars or the workings of time. In that spirit, I can share with you one true law that all of us can agree upon. This law is so profound that most of us take it completely for granted. Yet it is the starting point for almost everything we do in paleontology, developmental biology, and genetics. This biological 'law of everything' is that every living thing on the planet had parents... To put it in a more precise form: every living thing sprang from some parental genetic information." 
• "The extension of this law is where its power comes in. Here it is, in all its beauty: all of us are modified descendants of our parents or parental genetic information." 
• Species distinctions are not distinct. Are rock layers? 
• "Tiktaalik is a wonderful intermediate between fish and their land-living descendants, but the odds of it being our exact ancestor are very remote. It is more like a cousin of our ancestor. No sane paleontologist would ever claim that he or she had discovered 'The Ancestor.'"
• "Our fish-to-human framework is so strongly supported that we no longer try to marshal evidence for it-- doing so would be like dropping a ball fifty times to test the theory of gravity." 
• "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 us." 
• "We can dress up a fish only so much without paying a price." 
• "Cats can be stimulated to hiccup by sending an electrical impulse to a small patch of tissue in their brain steam." 
• "Stop the hiccups in the first five to ten hics, and you have a chance of ending the bout altogether. Miss that window, and the bout of hiccups can persist for an average of about sixty hics. Inhaling carbon dioxide (by breathing into the classic paper bag) and stretching the body wall (taking a big inhalation and holding it) can end hiccups early in some of us. But not all. Some cases of pathological hiccups can be extremely prolonged. The longest uninterrupted hiccups in a person lasted from 1922 to 1990." 
• "Tadpoles use this pattern generator when they breathe with gills. In that circumstance, they want to pump water into their mouth and throat and across the gill,s but they do not want the water to enter their lungs. To prevent it from doing so, they close the glottis, the flap that closes off the breathing tube. And to close the glottis, tadpoles have a central pattern generator in their brain steam so that an inspiration is followed immediately by a closing glottis. They can breathe with their gills thanks to an extended form of hiccup." 
• "Slit the belly of a shark from mouth to tail. The first thing you'll see is liver, a lot of it. The liver of a shark is gigantic. Some zoologists believe that a large liver contributes to the buoyancy of the shark." 
• "Our gonads begin their development in the same place as a shark's: up near our livers. As they grow and develop, our gonads descend. In females, the ovaries descend from the midsection to lie near the uterus and fallopian tubes. This ensures that the egg does not have far to travel to be fertilized. In males, the descent goes farther." 
• "Mitochondria carry this bacterial past inside of them: with an entire genetic structure and cellular microstructure similar to bacteria, it is generally accepted that they originally arose from free-living microbes over a billion years ago." 
• "The bacterial past can be used to our advantage in studying the diseases of mitochrondria-- in fact, some of the best experimental models for these diseases are bacteria."