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RESPIRATION AND THE BODY PLANS OF ANIMAL LIFE

In the late eighteenth and early nineteenth centuries one preoccupation of naturalists (whom we would now call “scientists”) was in classifying the hugely diverse assemblage of life on Earth into groups called “taxa.” The basic unit of classification was called a “species,” and it was defined based on members of the same species being able to interbreed. For many species however, the demonstration of successful interbreeding was impossible (especially for animals from the deep sea or from continents far from Europe, the site of most of this work and of course for all the fossil forms now extinct). For these latter animals classification into a species was based entirely on similarity of morphology. But it was recognized early on (especially by the eighteenth-century Swedish naturalist C. Linnaeus) that many different species, while not interbreeding, were so morphologically similar to others that all should be included in some “taxon” more inclusive than the species concept. Soon a hierarchical system was in place, with the following categories: species were members of a “genus,” which in turn was a member of a “family,” then “order,” “class,” “phylum,” and, finally, “kingdom.”

The distinction between each of these units was arbitrary unlike a species, which has an objective definition (interbreeding). However, one of the highest categories, the phylum, soon received its own defining aspect: members of a phylum shared a distinct suite of characters



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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere 1 RESPIRATION AND THE BODY PLANS OF ANIMAL LIFE In the late eighteenth and early nineteenth centuries one preoccupation of naturalists (whom we would now call “scientists”) was in classifying the hugely diverse assemblage of life on Earth into groups called “taxa.” The basic unit of classification was called a “species,” and it was defined based on members of the same species being able to interbreed. For many species however, the demonstration of successful interbreeding was impossible (especially for animals from the deep sea or from continents far from Europe, the site of most of this work and of course for all the fossil forms now extinct). For these latter animals classification into a species was based entirely on similarity of morphology. But it was recognized early on (especially by the eighteenth-century Swedish naturalist C. Linnaeus) that many different species, while not interbreeding, were so morphologically similar to others that all should be included in some “taxon” more inclusive than the species concept. Soon a hierarchical system was in place, with the following categories: species were members of a “genus,” which in turn was a member of a “family,” then “order,” “class,” “phylum,” and, finally, “kingdom.” The distinction between each of these units was arbitrary unlike a species, which has an objective definition (interbreeding). However, one of the highest categories, the phylum, soon received its own defining aspect: members of a phylum shared a distinct suite of characters

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere that could be called a “body plan.” For example, all vertebrates have a backbone with a nerve cord, so this characteristic becomes the body plan of all vertebrates. All sponges show only two cell layers with a similar kind of cell allowing them to pump water through the body. This is another kind of body plan. Ultimately, the naturalists could find only 32 distinct kinds of body plans among animals and these became formalized later as the 37 animal phyla. Other examples of phyla are arthropods, all with a body plan with a jointed exoskeleton; Cnidaria, all with two cell layers and tentacles with stinging cells called nematocysts; and mollusks, with a soft body but a hard calcium carbonate shell at some time in their life. The concept of the phylum has changed little since then. For example, one of the best modern descriptions of body plans comes from James Valentine in On the Origin of Phyla: The body plans of phyla have been much admired as representing exquisite products of evolution in which form and function are combined into architectures of great aesthetic appeal. While the phyla seem relatively simple in their basic designs, most contain branches that form important variations on their structural themes and some body types display remarkable embellishments in their morphological details. Presumably these variants reflect something of the ranges of ecological roles and environmental conditions in which the various phyla have evolved and functioned. Why do the various phyla of life on Earth have the body plans they do? In other words, why did animals evolve the respective body plans seen today? Surely the answers lie in adaptations to conditions on Earth at the time of the evolution of the various animal body plans, no earlier than about 600 million years ago. It was a world different from today, with more oceans and less land surface, higher temperatures, more ultraviolet radiation, more atmospheric carbon dioxide, and less oxygen. There were no large predators or herbivores, and hence predation and competition to the emerging animals were only from their own kind. So what drove the body plans that emerged? My contention is that respiration was perhaps the most important driver of animal body plans. And yet in Rudy Raff’s The Shape of Life and James Valentine’s On the Origin of Phyla, two recent excellent treatments of this topic, respiration gets only a brief mention as a driving factor in the first and is not even listed in the index of the second. The emphasis

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere here on respiration is due to new views about the nature of the atmosphere at the time of animal origins. While many biologists have sought the origin of body plans comprising the various phyla, a question dealing with time, others have wondered why there are the number and kinds of phyla that there are. Why not 50 or 100 or just one? Why not animals with wheels? Stephen Jay Gould famously wondered if Earth would recapitulate its evolutionary history in approximately the same fashion—and thus end up with the same phyla—if we could somehow “replay the tape” of life on Earth. Given the same origin for our planet, would evolution play out through approximately the same history, or would forces of chance result in a wholly different assemblage of animals? While such an event could never take place, the question is more than academic. The new field of astrobiology is making clear that Earth is far from unique and that we can expect to find numerous Earth-like planets in space. How closely will Earth’s history of life be replicated on any other world? In contrast to Gould’s speculations, Cambridge paleontologist Simon Conway Morris has written that the process of convergence will recreate, at least under similar physical conditions, an assemblage of life forms that might appear wholly familiar to us. After all, in a medium of water and in an atmosphere with composition and pressure similar to that on Earth, the optimum ways to swim or fly—or respire—will, through naturally selected evolution, dictate the structures of organisms conducting these activities. But to what degree? Rudy Raff addresses this question when he states: We do not yet know the history of events that produced the body plans that appeared in the Cambrian. We don’t know whether there is something inevitable about them. So what shapes body plans? While it is clear that body plans have evolved for the multitude of functions required of any animal, is there any single function that is of overriding importance in design? It turns out that there might be. The fossil and genetic records strongly suggest that the various phyla first originated as bottom-dwelling marine organisms and that most, early on, evolved ways of moving across the substrate. Only later did animals evolve body plans that allowed burrowing within the bottom sediment and others that allowed swim-

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere ming above the bottom. While there are many extant body plans that are not primarily involved in locomotion (sponges are a good example), most phyla are mobile either as adults or in early growth stages and, clearly, the need to move has affected the body design of many phyla. The integration of skeletons and locomotion also was important in resultant body plans. Thus we have at least one answer as to why the phyla have the shapes and designs that they do: these were responses to the challenge of attaining movement, first on sea bottoms. We see clear manifestation of this in body plans incorporating streamlining and in the evolution of anterior and posterior regions on the body. But there are other body plans that initially seem to be related to movement but that actually are not. One of these is segmentation, where the body shows a repetitive grouping of smaller units, such as that seen in annelid worms and arthropods. Segmentation does allow a certain kind of movement such as in worms. And, with appendages attached, segmentation leads to other body plans. But is locomotion the primary reason for segmentation? Chapter 3 will return to segmentation and present a new hypothesis for its origin and use. OXYGEN, ENERGY, AND ANIMAL LIFE Why do organisms bother with oxygen at all? Today there are huge areas of Earth, most underwater, that have little oxygen, so a body plan that helps an animal to live in low-oxygen environments would be very useful. But no animals use this kind of body plan. Why not? Aerobic respiration, the chemical reactions of metabolism in the presence of oxygen, yields up to 10 times more energy than does anaerobic respiration, a kind of respiration used by many bacteria. Fermentation is an example of how to get energy without oxygen. Complex life requires vast amounts of energy to meet its needs. For example, the formation of large molecules from smaller molecules in the synthesis of nucleic acids, lipids, and proteins involves a large input of free energy, just as the acquisition of energy requires the formation of specific cells or molecules, such as the chlorophyll molecule in plants—which takes energy. There is an old adage: it takes money to make money. This same idea can be analogized to energy.

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere While simple microbial life can derive its energy from a variety of sources, the choices decrease as life increases in size and complexity, simply because so much more energy is required. With the evolution of bodies capable of locomotion, the requirements increase yet again: an organism that moves can require 10 times more energy than a stationary organism. So a need of complex life (multicellular life, such as animal life) is a great deal of easily acquired energy. Only metabolisms using oxygen seem to give enough for animal life. Where can such energy be found? Only in chemical bonds, it turns out. When some kinds of chemical bonds are broken, energy is released, and organisms have evolved ways to capture some (never all) of this released energy. There are many kinds of specific chemical bonds among the giant chemistry storehouse of naturally occurring compounds in the universe, but only a few have been harnessed by life. Of all combinations of elements in the periodic table, the hydrogen-fluoride and hydrogen-hydroxyl bonds yield the most energetic reactions per electron transfer, and this is because of the way hydrogen’s electron is incorporated. (The specifics of this reaction are beyond the scope of this book: interested readers should refer to any text on physical chemistry). Of these, reactions with fluorine are marginally better than those with oxygen but fluorine has a huge disadvantage for life: it is biologically useless because it explodes when it comes into contact with organic molecules. The next best is oxygen; when present in an atmosphere or in water as dissolved oxygen it allows life to utilize the most energy-rich reactions commonly available. There are two necessary functions of oxygen in aerobic life. The first, which accounts for most oxygen use, is to serve as a terminal electron acceptor in the energy production of aerobic metabolism—the energy extraction process that requires oxygen to “burn” sugar into energy. The second is its role in the biosynthesis of many enzymes necessary for life. More than 200 different enzymes are now known that require oxygen as part of their synthesis. Molecules that require oxygen include sterols, some fatty acids, and, most importantly, blood pigments necessary for respiration and the synthesis of mineral skeletons, such as shell or bone, which cannot be completed in the absence of oxygen for chemical reasons of bonding.

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere First, let’s look at energy production. All cells on Earth need energy to run their cellular machinery. This energy comes from the chemical reaction that changes the molecule adenosine triphosphate (ATP) to adenosine diphosphate (ADP) and a free phosphorus atom through a pathway involving water (part of the water molecule is required to allow the chemical reaction to run). The splitting off of this single phosphorus atom releases energy that is utilized by the cell. There is no life on earth without ATP, and cells on Earth cannot live without a constant splitting of ATP into ADP. But organisms do not take in ATP. ATP has to be made, by bonding the phosphorus atom back on to ADP to make ATP. Organisms cannot either find or take ADP or ATP from other organisms by eating them. This involves an oxidation-reduction reaction. The ADP gains an electron and thus receives stored energy. At the same time, the electron donor is oxidized. While there is a wide range of chemical electron acceptors, the one that is most energetically favorable is oxygen and the species that use oxygen in this way. For animals the energy needed to start this ball rolling is the sugar called glucose. In the presence of oxygen, glucose is split, and the eventual product from several chemical reactions down the road is ATP. Organisms using this glucose plus oxygen chemical reaction to produce ATP from ADP (by splitting oxygen-hydrogen bonds) are said to use aerobic respiration. There is a chemical waste product of all of this—carbon dioxide. Cells using this chemical pathway can make much more ATP than cells that do not over the same time period. For example, an animal that “burns” glucose by using oxygen makes more ATP per unit of time than does a bacterium using fermentation. All animals on Earth use this oxygen-mediated kind of cellular respiration. All animal cells thus need a constant supply of oxygen; without it they quickly die. Every body plan has its own way of getting the life-giving molecule, and this acquisition process is part of the foundation of any animal’s design. Now, let’s look at other molecules of life that require oxygen, particularly those involved in oxygen and carbon dioxide movement to cells, called respiratory pigments. Respiratory pigments are used to help acquire oxygen from either air or water. They are formed from metal ions attached to organic compounds. Hemoglobin is the most

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere familiar to us as it is the molecule/pigment that we use. It exists in a number of forms and is found throughout the animal kingdom in many (but not all) phyla, including vertebrates, echinoderms, flatworms, mollusks, insects, crustaceans, annelids, nematodes, and ciliates. Other pigments include hemocyanin, a copper-containing pigment found in gastropods, crustaceans, cephalopods, and chelicerates; and hemerythrin, the iron-containing pigment found in sipunculans, polychaetes, and priapulans. All of these pigments bind oxygen more strongly when oxygen levels are high (in lungs or gills) and release it when oxygen levels are low (in respiring tissues). This occurs because in areas of low oxygen the chemical bond holding oxygen to the respiratory pigment molecule breaks more easily than it would in high-oxygen concentrations. Moreover, oxygen uptake is further facilitated in the respiratory structures where levels are low (and thus alkaline pH), and oxygen release is facilitated at actively respiring tissues where there is excess carbon dioxide and thus an acid pH. We’ve seen that oxygen is critical, from a chemical perspective, in four necessary/useful functions of animal life. Indeed, we do not see animal life in oxygen-free zones. OXYGEN- AND ANIMAL-FREE ZONES So how important is oxygen to animal and plant life on our planet? This question is perhaps best answered by looking at where animals do—and don’t—live on Earth. One of our most powerful methods in deducing the biology of any organism is in looking at the extremes that limit its life, for instance the upper and lower temperatures or chemical compositions an organism can withstand. In particular: at what level of oxygen are organisms never found? It is not hard to find such places. On any beach, for instance, digging down into the sand with a shovel takes one quickly from the upper sandy layers, usually populated by a diversity of invertebrate animals, to a deeper, dark stratum that is both foul smelling and almost devoid of animal life. Usually it is necessary to dig no more than a

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere foot or so to arrive at this darker regime, whose only animal life is made up of worms or clams with tubes or burrows that penetrate upward into the sea itself when the tide is high. If we continue to dig, we soon lose even these hardy colonists and find ourselves in a world devoid of animals. It is not devoid of life: rich colonies of microbial bacteria inhabit this world, but animals are nonexistent. The blackness of this subterranean world tells us volumes about the chemical nature of this region. The black compounds and minerals found here are characteristic of a reducing environment as contrasted to an oxidizing one. A reducing environment is one in which oxygen is in short supply and any that somehow arrives is quickly involved in a chemical reaction. The reduction of chemical compounds in the sediment leads to the distinctive color, because many of the compounds contain carbon, which in substances like coal has a black color, and metals such as iron and lead, which in reduced states have minerals that are also dark in color, caused by the near absence of oxygen. It is the lack of oxygen that precludes animal life. It is not just the sand that covers a reducing, anoxic world. Water itself can be virtually devoid of dissolved oxygen. Today there are large regions of the Gulf of Mexico that are composed of water volumes essentially lacking in oxygen, and the Black Sea in Asia, between Turkey and the old Soviet Union, is the largest known water body that has oxygen at very low levels. In both areas animal life is rare or absent, depending on the level of dissolved oxygen in the water. We live in an oxygenated atmosphere. So how could places like the bottom of the Black Sea have little or no oxygen? It has an anoxic bottom because, unlike the larger oceans of the present-day, the Black Sea is composed of highly stratified, rather than mixed (from top to bottom), packages of seawater. Its relatively small size and more importantly, a low number of highly energetic storms or constant strong winds allows the seawater to settle into distinct strata based on their density. The lesson from the Black Sea is that, because of oceanographic conditions, even in a world with a highly oxygenated atmosphere there can be anoxic seas. And even large stretches of ocean considered “oxic” today could change. For example, because of phosphate- and

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere nitrate-rich runoff from the Mississippi River valley region, large areas of the Gulf of Mexico are undergoing eutrification. This rather stagnant body of water is being fertilized to the point that large, oxygen-free water masses are becoming a yearly phenomenon. Eutrification occurs when nutrients allow such lavish growths of plankton that all available oxygen in the water column is used up and cannot be replenished rapidly enough by ocean-air contact to avoid the formation of deadly, oxygen-free water masses. As these stagnant and anoxic body masses move into shallow waters, they kill off all benthic, or bottom-living, invertebrates, irrespective of whether they live on or in the sediment. Many invertebrates have very slow growth rates, and hence these relatively new oxygen-free zones are radically changing the nature of the sea bottom in important ways. Natural selection must be working in the Gulf of Mexico by favoring those organisms that have best adapted for living in low-oxygen conditions, but in the long history of life on Earth no animal has ever evolved a way to live in zero oxygen. Low-oxygen water masses have been part of the oceans since the beginning of animal life. While low water-oxygen levels were exacerbated during times when the atmosphere itself had lower oxygen content than today, they are always present and thus there is always stimulus for selection for living in lowered-oxygen conditions. Today the oceans are mixed; the heat gradient between the warm tropics and cold polar regions creates the ocean circulation systems, which are composed of both surface currents and deeper, so-called thermohaline circulation systems, where cold, salt-rich, highly oxygenated bottom water is moved through the deeper oceans beneath warmer, fresher-water masses. This movement tends to oxygenate the oceans. But during past times of warmer climates, when there was much less of a heat gradient, the oceans were stratified, just as the Black Sea is today. There was a permanent presence of an oxygenated surface region atop an essentially worldwide, anoxic ocean at depth. Much of the Mesozoic was like this, and those of us who have collected Mesozoic marine rocks can attest to how widespread the dark anoxic ocean sediments from those times are. Usually such strata are fossil-free.

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere OXYGEN IN WATER AND AIR Because animals are obligated to harvest oxygen from the atmosphere or from a watery medium, they are affected by the varying concentrations of oxygen in air and water. There is no way that sufficient oxygen can be gained by eating food or drinking liquid with oxygen contained in it. And because animals are obligated to dispose of the waste products of respiration, chiefly carbon dioxide and water vapor, they are affected by the varying concentrations of carbon dioxide in air and water as well. What are the factors that influence the concentrations of oxygen and carbon dioxide in air and water? First, water: At most there is only about 7 milliliters of oxygen per liter of water, but this is affected by many factors, including temperature and salinity (water pressure does not matter). The temperature of water plays a major role in the amount of oxygen that can be held dissolved in water. Colder water holds more oxygen than warm water. Because seawater contains such a large amount of dissolved solutes, there is less “room” among the water molecules for oxygen to squeeze in for gases to dissolve into seawater. At equal temperatures, then, a well-mixed body of fresh water will hold more oxygen than an equivalent volume of seawater. Well-mixed indicates that the water has the same characteristics from top to bottom, unlike, say, places such as the Black Sea as we saw above. Oxygen and carbon dioxide also have different solubility in water. Carbon dioxide is far more soluble in water than is oxygen. However, even with this property there is never so much carbon dioxide in the water as to poison animals. Now air: At present a liter of air contains 209 milliliters of oxygen at room temperature and at sea level. But with altitude, the amount of oxygen drops off. At the top of Mount Everest there is only one-third the air pressure that there is at sea level and hence the amount of oxygen is only a third. At any altitude the amount of oxygen diminishes as temperature rises. To acquire an equal amount of oxygen, an animal living in liquid and getting its oxygen entirely from the liquid medium it lives in must process 30 times more seawater than an equivalent air breather. If breathing expends much energy for a particular animal, living in water

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere is far more “expensive” than living in air, and at first glance it looks like life in air is a more promising physiology than life in water. But here the high dissolution rate of carbon dioxide in water comes to the aid of the water livers. Air breathers have a more difficult time ridding themselves of carbon dioxide from their blood than do their water-living cousins. OXYGEN AND ANIMAL RESPIRATION The great differences in the behavior of oxygen and carbon dioxide in fresh and salty water compared to air have dictated the anatomy of many of the special respiratory structures found throughout the animal kingdom today and in the past as well. And another difference between the special respiratory structures used by water and air breathers is due to a fundamental law of chemistry. Both oxygen and carbon dioxide molecules are larger than a water molecule, so that any membrane that allows these gases to diffuse across it will also leak water. This has no consequence for an animal in water because if the animal becomes dehydrated, it can easily adsorb necessary water from its surrounding medium. However, in air the need to allow gas in lets water out. This leads to desiccation, a leading cause of death in both animals and plants to this day. Only in animals living in very moist environments, such as earthworms in moist soil, is this fundamental property inconsequential. For all other animals in dryer environments, some kind of impermeable body coating is needed to halt desiccation, but there have to be places where gas can come in as well. Size also plays a part in the anatomy of respiratory structures. Very small animals can extract all the oxygen they need through passive diffusion, since if an animal is small enough its entire body is the respiratory structure. Five factors control any sort of diffusion: the solubility of the gas in question, the temperature at which the animal lives (or the body temperature it maintains), the surface area available for gas exchange, the difference in partial pressure of gases on either side of the respiratory structure, and the thickness of the barrier itself. Each of these factors has a say in dictating the anatomy of a respiratory structure, or, if the animal is small enough, the nature of body anatomy itself.

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere But because volume increases so much faster than surface area on an enlarging animal (or an evolutionary lineage undergoing a size increase), animals quickly move into size ranges that require special adaptation to acquire oxygen. The ratio of surface area to volume is a particularly insightful way to understand why special respiratory structures needed to evolve. The volume of a spherical organism grows according to diameter cubed, while its surface area grows according to diameter squared. Volume thus increases faster than surface area as diameter increases; the enlarging organisms soon reach the point where oxygen will not be able to enter all of the organism’s cells fast enough. Organisms can increase the critical surface area to volume ratios by changing their body plans from squat and compact to elongated. Aquatic forms with large surface areas include the numerous worm-shaped phyla. Similarly, changing the shape of the body to include numerous protrusions, fleshy spines, leafy additions, and even invaginations on the surface of the body increases the surface area to volume ratio. This class of adaptation is found in the gas exchange structures of both terrestrial and aquatic organisms. Most aquatic organisms, however, that rely on either basic body shape, small size, or simple evaginations or invaginations are limited to a life with limited locomotion, since, as we saw, locomotion requires great amounts of energy. They will be sluggish and slow moving and unable to support much in the way of nervous tissue, which, it turns out, is a large consumer of oxygen due to the many chemical reactions constantly taking place by signaling nerve cells. There is no better example than flatworms, small animals that are very sluggish and have only the most primitive kinds of nervous system. There is a difference in how much oxygen specific cell types require, and nervous tissue has the most voracious appetite for oxygen. Drowning victims die not from death of muscle or fat but from death of nerve cells. Thus, any group needing or evolving complex behaviors, such as locomotion or processing sensory input with their attendant nerve cells, very quickly has a need for an efficient source of delivering oxygen to nerve cells, among others.

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere KINDS OF RESPIRATORY ORGANS In general, respiratory organs are broadly classified as gills (evaginations), which are used in water, or lungs (invaginations), which are used in air. Respiratory organs evolved for water usually will not work in air and vice versa. The densities of the two media are so different that vastly different structures must be employed. That no animal has ever evolved an organ that could work both in air and water equally well suggests that it just cannot be done with biological material. We’ll need to look at how gills and lungs acquire oxygen and dispose of carbon dioxide. First, gills. As we have seen, if an aquatic animal is small enough relative to its oxygen requirements, no gill is needed. Oxygen simply diffuses across the outer body wall into the organism. But with greater size, this method is insufficient. Larger organisms are faced with some alternatives. The first is to produce tissue that has a high surface area to volume ratio and then connect this organ—this gill—to the rest of the body via some circulatory system. We can call this a passive gill, because it depends on contact with the medium to bring necessary oxy- Illustration of two kinds of gills. On the left is a passive gill: it is a located outside of the main body and depends on the passive uptake of oxygen in the surrounding water. On the right is a “pump gill”, where the gill is enclosed by a shell, and water is actively pumped over the gill. This is a much better method for gaining oxygen from water.

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere gen. It extends into the water, oxygen diffuses across its boundary into the blood or body fluid, and this oxygenated fluid is then passed inward to the interior cells. Salamander tadpoles, with their feathery gills, are a good example of this type of structure in vertebrates, while echinoids and nudibranch gastropods, among many others, are examples among the invertebrates. A disadvantage is that these types of gills are tasty targets for predators and, if nipped off, the wounded organism, assuming it survives the attack, would probably die anyway from lack of oxygen. Gills only work if there is a thin barrier between the water and the animal’s blood and thus gills cannot be armored. Therefore, one common modification to this system is to place the gills within the body or build some kind of body armor over the delicate gills. Early mollusks used this trick, enclosing their gills (technically called ctenidia) with a space at the back of the body called a mantle cavity and then building a shell over the cavity and visceral mass. Crabs and many other modern arthropods also use this modification. Yet while hiding the gills out of predators’ reach protects these delicate structures, it reduces the efficiency of respiratory exchange by reducing free exposure to water. Another problem is that the water that has already been processed for its oxygen could be reprocessed, thereby using up the organism’s valuable energy and risking its oxygen starvation. To get around this, many animal groups evolved elaborate methods both to ensure that a sufficient volume of water is available to pass over the gill surface for the oxygen needs of the organism and to ensure that the water entering the gill region is not recirculated. For instance, while the shell of a gastropod, bivalve, or crab is typically explained as a compromise to allow defense and locomotion, in our discussion these same shells are considered part of the respiratory system, since some of their design specifically allows a more efficient or higher-volume passage of water over gills. Two separate types of adaptations beyond simply increasing the surface area to volume ratio can increase the efficiency of gills. These are the second set of alternative approaches facing a larger aquatic animal. One increases the water flow over the gills; the other ensures that recirculation of already respired water is minimized. Increasing the water flow available to the gills can be done in sev-

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere eral ways. The simplest would be for the animal to position itself in high current areas, so that more water naturally passes over the respiratory structure. Many sessile invertebrates use this adaptation today, and certainly it must have been used in the past. A more direct adaptation is through pump gills, which actively use some mechanical means of pumping water across the gill membranes or respiratory exchange surface, such as by increasing the pressure differential between the water volumes on either side of the gill. At least three different sets of morphological adaptations would have to be evolved for this to work. First, there must be a space in the body in which to situate the gill so as to maximize the efficiency of water movement over the gill. Second, a circulation system must be evolved to maximize the gas transport and oxygen capture-efficiency of the gill itself—it is no use having a very efficient gill if the oxygen-laden blood cannot be carried to the cells of the body, often located far from the gill. Finally, some morphological structure must be built to maximize the flow of water across the gill through active pumping of some sort, such as through the evolution of cilia or flagella. Therefore, one way of categorizing gill types is to break out external from internal gill systems. An external gill, such as that in many salamander tadpoles, is in direct contact with water but does not have any mechanism for increasing the water flow over the gill, or for ensuring that already processed water is not recirculated over the gill. Those two capabilities, however, are possible in internal gills. If the gill is placed within some body or shell cavity, it is possible to create a pressure differential on either side of the gill that causes water to cross the gill surface at a higher rate than would occur if the gill is passively in contact with water. Such internal and “powered” gill systems are found in marine bivalves, which pump water into the space with the gills and then actively pump the deoxygenated, carbon dioxide–laden, respired water back out of the shell. The variables that control oxygen uptake are the thickness of the tissue making up the gill surface, for this will control the adsorption rate of oxygen (more correctly the diffusion of oxygen across a biological membrane), and the size of the gill. The larger the surface area, the more oxygen that will be adsorbed. But since the amount of oxygen

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere being acquired is a function of the rate at which water passes over the gill, the evolution of a water pump effectively increases the surface area. Another gill adaptation to increase oxygen uptake is the use of “countercurrent” systems, used by organisms with very high metabolic rates, such as fish. Their high metabolic needs occur because of their exercise, which occurs during locomotion. Since most fish swim for some periods each day, they need more oxygen than similarly sized but unmoving animals. Countercurrent flows are the most efficient way to extract something from a fluid. In fish gills, which utilize a countercurrent system, blood flows forward against the current of oxygenated seawater crossing the gill. In other words, as the fish brings in water across the gill, usually in a front-to-back direction, blood is pumped through the gill going the opposite direction—back to front. The blood being pumped across these gills has just come back from the body, and it is rich in bicarbonate ions that have been chemically changed from carbon dioxide to bicarbonate for the ride. When this bicarbonate-rich blood reaches the gills (or lungs) the bicarbonate is transformed back to carbon dioxide. There it encounters an environment with very little carbon dioxide. Because of this, it is pulled out of solution by diffusion and as a gas is expelled from the body. As in gills, respiratory structures for air (lungs) involve the principle of exchanging oxygen and carbon dioxide. Often there is some morphological adaptation to force air at a higher pressure than atmospheric ambient pressure, and this entails the use of a “pump” of some kind. Animals do this in many ways. Our own solution is to use a series of muscles, the diaphragm, to inflate our lungs. Because air is far less dense than water, an equal volume of air contains many thousand times fewer molecules of oxygen than does the same volume of normally oxygenated water. Lungs therefore usually have much larger surface areas and, to do this, all are internal. Like powered gills, the animal uses some morphological mechanism to pump air into the lung chamber. Passive contact with air will not work for most larger animals and hence the many adaptations for “breathing”—the pumping of air into the lung chambers.

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere RESPIRATORY SYSTEMS A respiratory system can be defined as an assemblage of integrated cells and organ and tissue structures that deliver oxygen to the various cells in an animal’s body and then remove carbon dioxide from the body. Respiratory systems are highly variable across the animal kingdom, incorporating specific morphologies involved in gas exchange, such as our own lungs and the gills of fish, but gas exchange is just the first part of the respiratory cycle. Oxygen has to be transported to the cells, and thus the animal’s circulatory system is a major part of the respiration complex. Our blood, with its iron-bearing red blood cells, evolved specifically for oxygen and carbon dioxide transport, and the blood itself is classified as a tissue. The primary purpose of the heart in vertebrates, and larger invertebrates, is to take the blood or other medium, such as coelomic fluid, to every part of the body with speed. These fluids also take food material to the cells, so there is an overlapping of functions. And because the red blood cells are so important in respiration, we can say that their production, in the marrow of long bones in our body, is also a part of the respiratory system. In the evolutionary pathway to an efficient respiratory system it is not just the primary oxygen acquisition organ that must be changed but also the entire system. Here is one example of just such a required change, one that we will revisit in more detail in Chapter 6 but that Illustration of a lung system. Air goes into body, where oxygen and carbon dioxide exchange takes place.

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere here can serve as an example of how complex it is to change a respiratory system. As we will see, the late Paleozoic was a time of rapidly falling oxygen, which diminished in volume relative to the gases in the atmosphere to the point that it seems to have affected the survivability of many groups of animals. This oxygen fall has been partially blamed for the great Permian extinction. Therapsids, or mammal-like reptiles, were major victims of this extinction, but one genus of this group not only survived the extinction but actually flourished. The genus Lystrosaurus, which appears in the final throes of the mass extinction, differed from other therapsids in having an enormous, barrel-like chest with larger lungs. The hypothesis is that this group evolved larger lungs in response to dropping oxygen levels and thereby survived the oxygen fall. But increasing lung size would not have been the only evolutionary adaptation. The larger lungs, with their new size and shape, would necessitate changes in the morphology of the blood vessels servicing the lungs. Even if these changes involved only repositioning of the aorta and major blood vessels going to the lungs, there would necessarily have been wholesale changes in chest morphology, probably involving the heart as well. And there may have been even more radical and extensive adaptation in response to this, perhaps including the first evolution of endothermy, or warm-bloodedness, as evidenced by changes in the series of bones in the nose that allow warm air to go in and out of the body and that at the same time reduce water loss caused by breathing. In the entire history of the therapsids, themselves consisting of hundreds of individual species, the evolutionary changes resulting in the origination of Lystrosaurus in the late Permian represent the most radical morphological change in the formation of a new genus known from the entire history of the group. Evolution happens all the time in animals, and many of the changes commonly seen are overall size increase or, among mammals, changes in tooth morphology. But here it is suggested that respiratory changes usually require the most extensive morphological transformations. In the example of the Permian-Triassic Lystrosaurus, increasing the oxygen-acquisition process can involve increasing the size of the lungs. But other respiratory system adaptations are to increase breathing rate

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere or to modify the fashion by which air is delivered to the lungs. As we will see, both adaptations have appeared in land animals in times of low oxygen. What specific kinds of respiratory systems are observable in animals, and how have they changed over time? How can these various kinds of respiratory systems be compared one to another? The hypothesis that changing oxygen levels through time provoked the most radical evolutionary changes in animals of all evolutionary stimuli would be supported if it could be shown that those animals with more efficient lungs were more successful (at the level of individual survival anyway; “successful” has many meanings and could equally refer to success as measured by diversity as well) in times of low or lowering oxygen than those with less efficient respiratory systems. The problem of relating efficiency of respiration to successful survival is a difficult one, made even more vexing by the fact that most animals double up functions. For instance, bivalved mollusks use their gills for both respiration and food acquisition. If we see changes in the gills over time, are these respiratory adaptations or increases in feeding efficiency? We will return to this question, but first let’s note a simpler case. Our own lungs provide such a case: they are used exclusively for oxygen acquisition and carbon dioxide excretion. This is typical of vertebrates, but, as we shall see, respiratory structures often double as feeding organs in many invertebrates. First, we need to quantify respiratory system efficiency. One way of measuring efficiency of a respiratory system is to compare the rate at which oxygen is captured from either water or air and then transported to the body. There is a good deal of literature in the field of physiology that has been concerned with this question, so that much is known at least for many groups of vertebrates. Unfortunately, far less is known about invertebrates. One well-known result involves the relative efficiency of mammals and birds. At rest the bird respiratory system, as measured by the amount of oxygen delivered to the body over a given amount of time, is at least 33 percent more efficient than any mammal lung. The lungs of high-altitude South American mammals such as Vicuna and Alpaca are among the best that mammals have mustered, but even they pale

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere when compared to the efficiency of even low-altitude bird lungs. (It should be noted that this kind of study of birds is still in its infancy, with many questions on the relative efficiency of lungs found in various-sized birds and from different habitat types just beginning.) How can this difference be explained? While perhaps the blood of mammals and birds is sufficiently different to allow the avians to transport oxygen more efficiency, the likely cause is the radically different lung morphology that birds have compared to mammals. Fundamentally, it is the amount of dissolved oxygen in the blood that is to be compared. Physiologists insert instruments into the blood (ow!) and directly measure how much oxygen is present. In many respiratory organs this value is related to the rate and volume of oxygen-bearing medium that comes in contact with the blood at the gas absorption sites. It is this process that can be most easily shaped and changed by evolution. To highlight the various possibilities among existing and some extinct organisms, a table of respiratory organs for various body plans is shown in the Appendix at the back of the book. The appendix is but a short list of taxa, mostly generalized at higher taxonomic levels, but it illustrates the great variety of respiratory styles across the animal kingdom. As we profile the various groups of animals making up the specific events in the history of life, we can ask whether a specific group first evolved in a high- or low-oxygen world (compared to the present-day) and if respiratory adaptations of any kind can be observed during or immediately after times of oxygen content change in the atmosphere, either up or down. The difficulty is that respiratory organs are composed of mainly nonpreservable soft parts. However, because of the high degree of integration of skeletal parts and respiration found in so many groups, respiratory adaptations often can be inferred or directly observed. MOLECULE OF ANIMAL LIFE Oxygen is thus essential for animal life, and animal life consequently has evolved a host of structures for its acquisition. Because Earth has widely varying oxygen concentrations in different environments, some

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere of the differences shown in the Appendix are related to living in different oxygen regimes. But we must take into account a new variable as well. Not only does oxygen concentration vary from place to place, it has also varied through time. It seems possible that an organism’s type of respiratory system could be related to the oxygen levels present on Earth when that organism first evolved. Some animals first appeared when atmospheric oxygen was much higher than now, some under just the opposite condition. Chapter 2 looks at the history of oxygen in Earth’s atmosphere and oceans and how this molecule’s history has been studied.

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Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere