Monday, February 24, 2014



The basic physical laws of the Universe gave rise to the elements, and on this planet the elements gave rise to life. Simple one-celled organisms evolved, and gradually complexity evolved within some of their lines of descent. Certain kinds of cells unconsciously began to associate with each other and form colonies of cells that had the effect of enhancing their members’ survival prospects. Gradually, there evolved true multicellular life forms, the first of which we know of was an algae. Other colonies of cells adhered to each other in epithelia and engaged in heterotrophy, sexual reproduction, and aerobic respiration. These were the first true animals, and these small but enormously important beings would ultimately give rise to all the subsequent members of the Kingdom Animalia, of which we are a part. It is to the evolution and spread of the animals, therefore, that we will now turn our attention. Scientists speak of the spread of a life form as its radiation. As the processes of natural selection choose the reproductive winners and losers in various ecosystems, speciation occurs. In evolutionary terms, this is known as adaptive radiation, as new forms appear in an environment, often including multiple variations on the ancestral populations’ genotypes. The massive upheavals in the Earth’s climate and the constant movements of the continental landmasses, with their attendant earthquakes, volcanism, mountain building, and changes in the absorption of sunlight over various regions of the Earth’s surface, were the great engines of change that helped drive the evolution and radiation of the animal kingdom. The changes in the various environments of the Earth interacted with the variability inherent in the genetic composition of particular populations to produce an amazing variety of animal life. As is the case with every step in our chronology, this development did not guarantee the rise of consciousness; it simply made such a rise more probable.

The Rise of Cell Specialization and Selective Gene Expression

Each cell in an animal’s body, with the exception of gametes (sex cells) and mature red blood cells in vertebrates, contains a full complement of the animal’s DNA, the complete instructions for building the animal in question. Yet animals are a system of systems, comprised of specialized organs that perform all the tasks necessary for the survival and potential reproduction of the animal. How do the cells that comprise these organs “know” how to form particular kinds of organs when the animal is in an embryonic state, and how do they “know” how to reproduce into particular kinds of cells once an animal is born and matured? How do they “know” what parts of their genetic material to activate and what parts not to activate? In other words, why are they specialists, why do they possess the ability to engage in selective gene expression? (In the process of gene expression, you will recall, genetic information from DNA is first transcribed by messenger RNA and then translated with the aid of transfer RNA and ribosomal RNA, a process that synthesizes first amino acids and then proteins.) What factors favored the rise of cell specialization to begin with?

One researcher hypothesizes that cell specialization, by allowing for the expression of fewer genes, protected genetic material from the influence of mutagenic agents in the environment, and was therefore reinforced by natural selection.1  Another researcher has an intriguing hypothesis: when a colony of cells grows large enough, it can “afford” to have certain cells engage in more specialized tasks, an event which of course happens completely by stochastic means. If the “experiment” in specialization fails, the colony can absorb this failed innovation without too much disruption. This gives larger organisms an evolutionary pathway not open to simpler, smaller ones. They can take more “risks”, and by doing so potentially reap greater rewards.2 (Would it be stretching this example too far to say that human societies operate in the same way? The larger a human society and the more divided its work, the more it can afford to let innovators and experimenters engage in activities not directly related to the group’s survival.)

If cell specialization is indeed in part a function of an organism’s size, that specialization, by definition, survives by enhancing the organism’s reproductive chances. This involves the evolution of “cellular altruism”, as certain cells specialize in such a manner so as to facilitate the reproduction of other cells, even as they themselves will not be reproduced. The complexity that arose from this increasing tendency toward specialization is not “irreducibly complex”, despite the assertions of some misguided individuals. It emerged in small increments over time, and its innovations were simple.3 This is not to say that all of these increments have been discovered, nor that all the mechanisms that underlie specialization have been elucidated. As one research scientist has put it,

Such transitions require the reorganization of fitness, by which we mean the transfer of fitness from the old lower-level individual to the new higher level, and the specialization of lower-level units in fitness components of the new higher-level individual. It is a major challenge to understand why (environmental selective pressures) and how (underlying genetics, population structure, physiology, and development) the basic features of an evolutionary individual, such as fitness heritability, indivisibility, and evolvability, shift their reference from the old level to the new level.4

What causes changes in gene expression at the molecular level? Research indicates that selection is at work even in the translation process itself. Certain codons (triplets of bases along a molecule of DNA or messenger RNA that code for a specific amino acid) seem to be translated more readily, and there may some sort of relationship between the length of a gene and the kinds of codons that are “preferred”. It appears that concentrations of transfer RNA (tRNA) in amino acids can vary as well, affecting the course of protein synthesis. This in turn can open a path for evolutionary change within proteins, one that can result in phenotypic changes in a developing organism. In other words, even at the molecular level, there is enough variability to allow natural selection to make its typically blind “choice”.5

There are other considerations as well. The material that makes up a cell nucleus, the chromatin, consists of DNA and proteins known as histones. Histones bind tightly to DNA, making it very compact, since they and DNA have opposite electrical charges. (Once again we see how the simple rules that govern the physical world affect every area of reality.) The chemistry of histones can be affected by such processes as acetylation (the addition of an acetyl group), methylation (the addition of a methyl group), or phosphorylation (the addition of a phosphate group).6 There is evidence that such changes in histones may in turn bring about changes in the chromatin structure itself, and hence in the genes found along the length of the DNA. Such changes may hint at the existence of a histone code that regulates other proteins. This process may represent yet another layer of variation that exists, and may gave us insights into the evolution of a phenomenon known as an epigenome, the genes that regulate other genes in an organism.Gene expression is controlled by the epigenome, which activates some genes while silencing others. The key genes in the epigenome are known as homeobox genes. Their function has been described by one biologist in the following manner:

Since their discovery in 1983, homeobox genes, and the proteins they encode, the homeodomain proteins, have turned out to play important roles in the developmental processes of many multicellular organisms. While certainly not the only developmental control genes, they have been shown to play crucial roles from the earliest steps in embryogenesis … to the very latest steps in cell differentiation…They have a wide phylogenetic distribution, having been found in baker's yeast, plants, and all animal phyla that have been examined so far. Since their original discovery, hundreds of homeobox genes have been described.8

The fact that homeobox genes are found in such a diverse array of life forms means that this kind of regulatory gene complex is in all probability very, very ancient. We see evidence of this in the early evolution of animals. In the evolving animal kingdom, there was a split that emerged very early on between bilaterians, animals that are bilaterally symmetrical, which is to say possessing distinct and similar sides and identifiable anterior and posterior ends, and cnidarians, sac-like animals that are radially symmetrical. Certain gene clusters arising from the ancestral homeobox genes are so ancient that they actually pre-date the split between the two basic body types.9 (This would make their lineage in animals more than 520 million years old.) It was the evolution of the first forms of these regulatory genes and then the evolution of diverse types of them that made possible the tremendous variety of distinct animals that have appeared on this planet, and yet animals that have retained, across huge sections of the animal kingdom, a great many homologies.

It is cell specialization that has allowed animals to evolve the internal and external structures they possess. Beginning with the simplest specializations in the simplest organisms, specialization became enormously elaborated over the course of hundreds of millions of years, creating systems within systems that facilitated the reproductive success of countless organisms—until external environmental changes caused the adaptations that had evolved in those organisms to become obsolete. This obsolescence was the harbinger of extinction. Ancestral groups were wiped out, leaving only their descendant groups, if any. It would probably be most accurate, in my view, to think of selective gene expression and cell specialization as mutually reinforcing phenomena, as natural selection blindly favored organisms that were subdivided into useful specialized areas, and the genes in the DNA that enabled this specialization were “rewarded” by greater frequency of expression. Specialization worked. Large organisms could “experiment” with greater and greater levels of specialization. Starting at least 1.6 billion ybp, beginning with the appearance of the first true multicellular life forms, such experiments have been carried out ceaselessly in the laboratory of the Earth’s evolving biosphere.

The Origins of Sentience

Living things are open systems by definition, exchanging energy-matter in various ways with the environment in which they live, using the energy acquired to both facilitate their own survival and to perpetuate their genetic material. With the advent of multicellular animals, a new survival requirement arose: the ability to feel the world and respond to it. Natural selection began producing feedback loops, at the start nothing more than simple chemical responses to the environment. As these feedback loops, buttressed by reproductive success, became part of more elaborately-organized synergistically-functioning networks, sensation emerged. Plants respond to the world; animals (at least in some sense) experience the world and respond to it. In that element of experience lies a crucial distinction that sets animals apart. Animals, being heterotrophic, have a greater level of interactivity with the rest of the physical world than plants which, with a few notable exceptions, obtain the energy necessary for their survival from the more passive processes of photosynthesis. And although there are completely sedentary animals living in environments which expose them to adequate amounts of nutrients, most animals are mobile and therefore need some way to move about in three spatial dimensions. In the course of these movements, they need information. (Information is here defined as a kind of energy the detection of which by a living thing is capable of causing a modification of the living being’s behavior.)  Living animals need information about:

1.  Their own status as physical entities, both for their survival and for the maintenance of their internal equilibrium. 

2.  Their position relative to other objects, information they need in order to navigate. 

3.  The presence and location of food and other resources.

4.  Possible threats from other animals or other potential environmental danger.

The possession of this information is not optional—it is the sine qua non of a mobile animal’s physical survival on this planet. Natural selection, therefore, favored those animals which acquired, by means of favorable mutations, electrochemical ways of obtaining this information—nervous systems.

A nervous system is the individual animal’s only contact with the real reality. Particular kinds of nervous systems create distinct versions of that reality, or at minimum emphasize certain key aspects of it. Nervous systems are a mass of sensory feedback loops, engaged in endless signaling and/or self-corrective activity, sending electrochemical messages that are coordinated and acted upon (to some extent) in a central organ—a brain—of some kind. Cell specializations conducive to the ability to gather information about the environment evolved, and with them, sentience—the ability to experience the world as a distinct set of physical sensations that are interpreted by an animal as feeling.

As animal life evolved, more complex organisms needed (and were characterized by the possession of) correspondingly more complex nervous systems, especially if the organisms were very mobile and situated in hostile environments. Natural selection tends to favor efficiency in the gathering and use of information, rewarding facility in these areas with increasingly likely survival odds. What energies constitute this vital information? Most lineages of animals evolved the means to detect ranges within the light spectrum. Most lineages of animals evolved the means to detect wave frequencies in the air or water that are interpreted as sound. Most animal lineages evolved ways of detecting the presence of certain chemicals in the environment that are interpreted as smell. Most animal lineages evolved a means of testing the edibility of plants or other animals that is interpreted as a sense of taste. Some animals evolved highly specialized sensory apparatuses that allow them to detect the presence of an electrical field. It could be said that proprioception, the ability of an animal to orientate its limbs in space, represents a sense of equal importance to the others. And there are many other senses which, it could be argued, have their own distinct modes of operation. But of all the senses, the ability to detect energies from the environment that are interpreted as touch or feeling is perhaps the most vital. The most basic rules of animal life, it could be argued, are these: Stimuli an animal finds pleasant attract it; unpleasant stimuli drive it away; the range of relatively neutral stimuli with which an animal is surrounded constitutes its ordinary sensory environment, an environment which may or may not be agreeable to other animals.

It is necessary for animals to know when they are being injured in some way so that they can engage in response activities. If the injury is being inflicted by another animal, they can fight it or flee from it. Injury, and the pain arising from it, force an animal to take action. This suffering runs on a continuum ranging from mild irritation to intolerable agony. Truly, pain is the curse of the animal kingdom. And the pain response within an animal can be brutally persistent—it keeps signaling long after the information it has sent has been acted upon. But without it, animals would suffer constant injuries without realizing it. Further, its reduction signals healing and the body’s ability to resume normal activity. In animals with more elaborated nervous systems, the continuous action of feedback loops saying “touch this/don’t touch that” forms the basis of a routine which is internalized and which guides the animal’s movements when the animal is awake.  (We will examine various aspects of this subject more deeply in a subsequent volume.) Suffering is a hard form of instruction, but it is a very powerful one.

More broadly, the ability to suffer—which goes back deep in the history of the animal kingdom—can be said to be the basis of moral consciousness in humans. We will elaborate on this point at some length elsewhere, but here let it suffice to say that if we are aware of our own potential for suffering and recognize in others an approximately equal capacity for it, we have established the fundamental basis of moral sensibility. Sentience in the other animals, in my view, also gives them a moral claim upon us, at minimum to show humaneness to them even as we hold them captive and kill them for our food. All of these various issues have roots that go back hundreds of millions of years, when animal life began to feel the world.

In general, from whence did nervous systems arise? In his 1976 study of the brain, Steven Rose addressed this question. He discussed the tendency of even one-celled organisms to exhibit “behaviors”. In explaining the response of bacteria to the presence of nutrients in their immediate environment, he pointed out how the structures on the surfaces of bacteria known as chemoreceptors must sense in some way the location of the nutrient in relation to the bacterium and cause it to move toward the food source. This action could be effected by a change in the electrical potential of the cells.10 The evolutionary advantage of such a property is obvious, and in the operation of this simple electrochemical system of “communication” we see, perhaps, the deep origin of the electrochemical operation of our own highly advanced nervous systems. John Morgan Allman points to the example of Escherichia coli in this regard:

E. coli has more than a dozen different types of receptors on its surface. Some are specialized for the detection of different nutrients, such as particular types of sugar, which provide energy, or amino acids, which are the building blocks of proteins; other receptors are responsive to toxins, such as heavy-metal ions.11

So even single-celled life forms show a remarkable sensitivity to external stimuli. As clusters of single cells formed colonies, and then evolved increasingly sophisticated interconnections among themselves, nervous systems began to emerge. The key principle that governs the evolution of nervous systems across broad ranges of animal life is the conservation of genomes and structures. For example, there are certain marked similarities in the sensory apparatuses of arthropods and vertebrates, such as the similarities between the sensory bristles of flies and the hair cells in the inner ear of vertebrates. There are also similarities among insects, roundworms, and vertebrates in the genes that produce various kinds of neurons. The presence of these features in such widely divergent taxa indicates their origin was in a very ancient common ancestor. They have been conserved because they were useful.12  I would like to reserve the detailed examination of the evolution of the vertebrate nervous system for the chapter on the evolution of the human brain. But it must be reiterated: with the rise of animals, and the emergence of nervous systems, energy-matter could now sense the world of which it was a part. Specifically, the evolution of sentience was to put life on wholly new paths, and establish the foundation from which consciousness could arise. The world could now be felt. Because of that development, the world could later be consciously changed.

Fossil Evidence of the Earliest Animal Life

As we go back deeper in time, it is no surprise that the physical evidence of animal life becomes harder and harder to find. We must suppose that the very earliest animal life was no bigger than meiofauna—extremely small animals that would have left only trace chemical evidence and no fossilized remains whatsoever. So what is the earliest fossil evidence yet uncovered (to this date)? In 2010, researchers from Princeton University discovered what appear to be primitive sponge-like animals dated at 650 million ybp. The animals are indeed quite small, but they are larger than the smallest extant meiofauna.13 And research sponsored by the National Science Foundation has uncovered a biomarker (chemical evidence characteristic of organisms) particular to demosponges, estimated to be 635 million years old.14 Some scientists believe the Cryogenian Era of global glaciation extended to 635 million ybp. (Others put the end date at around 650 million ybp.) If those using the 635 million year estimate are correct, there may have been animals that survived some of the worst glaciation in the Earth’s history, albeit near the end of that period.

Genetic analysis of an utterly simple animal life form known as Placozoa has given intriguing indications that these little animals, which lack a nervous system (just as the sponges do) are quite possibly the animal the ancient forms of which formed the base of the animal kingdom. Placozoa in fact may have possessed, even before the split between the  bilaterians and cnidarians, the basic genetic “toolkit” that influenced the development of both groups.15 Unfortunately, no fossil forms of Placozoa have been uncovered, which is unsurprising given that this animal is composed exclusively of soft tissue.

The Ediacaran Fauna

There is a significant amount of physical evidence for the animal life that appeared during the Ediacaran Period, which stretched from 635 million to 542 million ybp.16 Often, this length of time is referred to in the literature as the Vendian Period, and it is the last period of the Proterozoic Era. The life forms characteristic of this time were first discovered in southeastern Australia. Since then they have been discovered on every continent except Antarctica. The evidence of these earliest animals is usually in the form of impressions that have been fossilized. The organisms often resemble those of the phylum Cnidaria, which includes the jellyfish and corals. Other examples appear to be similar (superficially) to arthropods (segmented-like animals, common examples of which are insects, centipedes, and scorpions) annelids (segmented worms), and echinoderms (starfish-like animals).17 They appear to have definitely existed by around 565 million ybp. All are invertebrates, animals that lack a spinal column. Some scientists question whether there are true living descendants of the Ediacaran organisms, but others  are confident the descendants of these humble animals are still among us. Given the somewhat complex body features of many of these specimens, we must infer that there were more rudimentary forms of animal life that preceded them. As one paleontologist has expressed it, the fact that the Ediacaran fauna form “a fully integrated ecosystem” with several advanced types means that animal life may have appeared soon after the end of the Cryogenian Period.18

The Cambrian “Explosion”: An Acceleration or an Eruption?

The Cambrian Period stretched from 542 million to around 488 million ybp.19 A great many new life forms evolved during this time, and in many places in the literature one sees this abundance of new organisms referred to as the Cambrian “Explosion”. The term is misleading, in the view of some. If we consider many of the Ediacaran Fauna and the Cambrian fauna to form a continuous group, it took tens of millions of years for all the new forms to appear. It might be useful, as Donald Prothero puts it, to refer rather to the Cambrian “Slow Fuse”.20 Yet, as Stephen Gould argued, by the end of a period of 100 million years every phylum that still exists had appeared, and no others have evolved  since that time.21 So perhaps this period can be thought of as an eruption, if one remembers that “eruption” is a relative term when thinking in geological time scales. In the context of the long billions of years in which life on Earth was dominated by single-celled organisms, the appearance of so many new forms in a “mere” tens of millions of years might indeed seem revolutionary. In effect, during the Cambrian, we see a proliferation of new body plans, new ways to organize a living thing, many of which are still present in vast numbers in the biosphere, and evidence of increasing cell specialization during this period of relatively rapid change.

What kinds of animals appeared during this period of evolutionary history? All Cambrian life forms were ocean dwellers, living on a planet where the position and extent of the landmasses were drastically different from what they are now. What were once sea beds are now often parts of the dry land. So there are many locales on the Earth where Cambrian fossils have been discovered. But a few sites are particularly outstanding. One of our major sources of knowledge concerning the Cambrian fauna is located in the Chengjiang region, in the vicinity of  Kunming in the eastern part of Yunnan Province in southern China. The Chengjiang fauna date from about 515 million to 520 million ybp. (Some sources extend their earliest appearance to 530 million ybp.) Extensive analysis and exploration of this Konservat Lagerst├Ątte—a German term that simply means a location that contains a highly diverse and/or exceptionally well-preserved trove of specimens—has been done since 1984. Researchers have identified 228 different species, although some of them cannot be readily assigned to a particular phylum. More than a third of the species appear to belong to Arthropoda; about 12% of them are Porifera (sponges); then, in descending frequency, species are a part of Priapulida (predatory worm-like animals), Lobopodia (another kind of worm-like animal), and perhaps most significantly, Chordata, to which about 4% of the species belong. About a third of the phyla are present in concentrations lower than Chordata.22 The specimens from the phylum Chordata—chordates—are members of the phylum that includes humans. The Chengjiang chordates include two primitive vertebrates, backboned animals, as well, Myllokunmingia fengjiaoa and Haikouichthys ercaicunensis, which is highly significant.23

Equally impressive is the evidence we have from the Burgess Shale of eastern British Columbia, the specimens of which were deposited around 500 million ybp. This rare glimpse into the Cambrian world was discovered in 1909 by Charles D. Walcott of the Smithsonian Institution, who did exceptionally thorough and important work on the site.24 Many of the specimens uncovered and examined by Walcott, the indefatigable Simon Conway Morris, and other researchers, have an unusually high degree of preservation, with evidence of soft body tissue that is usually lost through decay. Among the animals in the Burgess collection there are arthropods (including crustaceans of many kinds and the well-known animals called trilobites), a host of often beautifully-shaped sponges, strange-looking worms, conical-shaped shell-covered animals called hyoliths, mollusks, various members of Cnidaria, and a member of the phylum Chordata.25 The Burgess chordate is known as Pikaia gracilens, which was at first thought to be a worm, but which later was definitely shown to be a member of our phylum.

The level of oxygen gas in seawater is one one-hundredth what it is in the atmosphere. Since no marine animal can obtain its oxygen by splitting water molecules, marine life depends on gaseous oxygen in the ocean. All such animals survive by passing dissolved gaseous oxygen through their bodies. (Obviously marine mammalians do not pass oxygen through slits in their bodies, as do other marine forms.)26 This fact took on great relevance about 499 million ybp, as a mass extinction struck the Cambrian fauna at that time. The extinction appears to have been triggered by a sharp decline in the gaseous oxygen content of the world ocean, although the exact cause of this abrupt decline is not yet known. Excessive concentrations of sulphur, a phenomenon known as euxinia, appear to have been a factor, and there is evidence of a major disruption in the world’s carbon cycle at that time.27 The loss of life forms was enormous. But among the phyla that survived were the chordates.

At the end of his popular work on the Burgess Shale, Stephen Jay Gould discussed the significance of the survival of the chordates:

And so, if you wish to ask the question of the ages—why do humans exist?—a major part of the answer, touching those aspects that science can treat at all, must be: because Pikaia survived the Burgess decimation. [The Cambrian extinction]28

Of course, the chordates found in Chengjiang predate Pikaia. But Gould’s point remains. Because primitive chordates survived the mass extinction, all the animals that ultimately evolved from them would come to be. There were no biological guarantees that animals like ourselves would ever exist. Gould often emphasized the highly contingent nature of evolution, and pointed out that the course of evolution could have taken innumerable turns different from the ones it actually did. Start the whole process over 100 times, and it is likely you would see 100 different outcomes. Random chance and chains of unanticipated consequences allowed our deep ancestors to continue, making the rise of consciousness as we know it a greater possibility. The Cambrian extinction was a massive selection pressure. For whatever reasons, the little animals with spinal cords were able to meet the challenge—without ever realizing they had done so.

Issues Concerning the Use of Molecular Calibration in the Estimation of Life Form Divergences

When scientists are being as careful as possible to not go beyond their evidence, overturn established hypotheses without the best causes, or employ excessively complex explanations of phenomena, it is said that they are being parsimonious. As a layperson in this area, I feel it is my responsibility to be especially careful, to display great parsimony. There has been, in the life sciences, a vigorous debate, one that has lasted many years, about the techniques used to determine when certain lineages of organisms diverged from a common ancestral population. Molecular evolutionists use certain fixed points, known divergences in the fossil record, as reference points, or points of calibration, for their estimates of when earlier divergences occurred. They hold that the rate of molecular change in proteins is regular enough that their estimates can be used with confidence. However, other scientists, confronted with estimates of genetic divergences that go far beyond the actual physical evidence in our possession, have challenged these techniques. I must emphasize that no scientist questions the basic technique for measuring genetic “distance” that we touched on in the chapter on life.  It is, rather, the chronology of these divergences that is at issue. For example, we have seen that primitive vertebrates were uncovered at Chengjiang, and that these fauna are estimated to be somewhere around 520 million years old. Yet, on the basis of calculations of molecular change, a very serious estimate has been made that the mean date at which urochordates (a primitive type of chordate) and vertebrates diverged from a common population was 794 million ybp29more than 270 million years before the earliest vertebrates for which we have tangible evidence. Findings such as this (not this specific one) have been sharply criticized on methodological and statistical grounds.30 While the molecular researchers offer plausible explanations for the huge gap between the postulated molecular dates of urochordate/vertebrate divergence and the actual fossil evidence, I am constrained to point out that the genetic evidence seems to be converging on either the sponges or Placozoa as the first identifiable members of Animalia.31 And as we have seen, evidence of sponges in the fossil record goes back no more than 650 million years. Therefore, I will wait to see fossil evidence of vertebrates almost 800 million years old. Until then, I will remain parsimonious. 
Hypotheses Concerning the Evolution of the Vertebrates

When we are seeking the evolutionary history of a group of life forms, we are trying to establish their phylogeny. What is the phylogeny of the vertebrates, the animals that now dominate so much of the biosphere, and which include humans? There is a superphylum, a very large group of animals, that includes an immense array of organisms ranging from starfish to worms to vertebrates. All of these animals share the designation deuterostomes. They are united by certain embryological traits they all have in common. The common ancestor of deuterostomes is now thought to have possessed pharyngeal slits—openings in the body of the kind that eventually evolved into gills in fish—and a segmented mesoderm. (The mesoderm is a layer of cells in embryos out of which numerous structures, such as bone and musculature, develop.)32 It was out of the deuterostomes that chordates emerged. The characteristics of a chordate include the possession of a dorsal nerve cord (nerve fibers that run the length of what we might consider an animal’s back and which connect its “brain”, however primitive, with the rest of its body), a notochord (a rod-like structure made out of cartilage that supports the nerve cord), and the possession of pharyngeal slits in the embryonic stage.33 There is no evidence that the ancestor of the deuterostomes possessed a  notochord, so we think that such a structure evolved in chordates and is exclusive to them.34  There are three subphyla of Chordata. Members of a particular subphylum, Craniata, have skulls in which the brain and various sensory organs are located. This subphylum contains the great majority of all chordates. In almost all members of Craniata (with one exception) the embryonic notochord becomes a column of vertebrae.35 It was the evolution of this transformation that established the vertebrates. How might this have come about?

Sometimes it’s useful for scientists studying a taxon of animals to look at close relatives of the taxon to study why the close relatives lack certain traits the subject taxon possesses. Such is the case with a humble animal known as amphioxus. Amphioxus is the closest genetically-related invertebrate to the vertebrates. It may seem like an odd way to say it, but why aren’t amphioxi (commonly known as lancelets) vertebrates? They appear to have several similarities to vertebrates in their nervous systems, and they share certain important genes with vertebrates. But they apparently lack a single key structure in their neural cord that vertebrates have. Further, not all of the important genes they share with vertebrates are expressed in the same manner.36 Vertebrate embryos have a structure called a neural crest. This structure is an area that exists in the early stages of vertebrate embryo development, when the embryo possesses a neural tube (which becomes a spinal cord). It is from the neural crest that neural crest cells are disseminated. It is these cells that help create, in conjunction with other kinds of cells, such structures as the head, the face, teeth, limbs, and sense organs.37 All of the physical features many people tend to think of when they think of animals are the products of these cells. Amphioxus never develops a neural crest, even though it has much of the same genetic inheritance as vertebrates.

Yet, there seems to have been more at work in the split between amphioxus and the vertebrates than differing structures and unexpressed genes. There is a phenomenon called genome duplication, an example of polyploidy (the reproduction of multiple copies of the same genome), that appears to have had a major effect on the evolution of Craniata (and on many phylogenies throughout nature). It is not unusual for duplicate copies of individual genes to be made during meiosis. Such genes are often referred to as paralogous genes. It is less common for an entire genome to be duplicated, but occasionally an organism receives a double set of parental chromosomes. The significance of gene duplication in evolution is being studied widely in the biological sciences, and the mechanisms by which this occurs are being elucidated.38 Many scientists conclude that genome duplication has occurred twice in the evolution of vertebrates, relatively early in the history of the vertebrate subphylum.39 There is however, not a complete consensus of opinion on this point. Evidence in support of this contention can be found in the Hox clusters present in vertebrates. A Hox cluster is a group of homeobox genes that are important in the formation of an animal’s physical structure from head to tail.40 Vertebrates have four of these clusters; amphioxus has one.41 This greater genetic sophistication and complexity has had major consequences. 

It is these four clusters of Hox genes that form all the various kinds of vertebrae found in the subphylum Craniata—the vertebrates. To oversimplify the matter, Hox genes are why you and I have backbones in the first place. It is the possession of these Hox clusters that truly differentiates us from the invertebrates.

The Evolution and Significance of the Skeleton

Through the presence of minerals in their body chemistry, many taxa of animals have  evolved skeletons. Skeletons fall into two general varieties. Exoskeletons are shell-like structures that encompass all or most of the soft tissues that comprise an animal’s interior. Endoskeletons are the kind of skeleton that we associate with animals like us, an interior scaffold surrounded by and connected to the musculature, the skin, and other features. The possession of a skeleton confers certain obvious advantages on its possessor. An exoskeleton, a feature found in the arthropods, is a first line of defense against the ravages of the external world. However, its characteristics tend to put limits on the sizes its possessors can attain (even though there were some formidable arthropods swimming in prehistoric oceans). Marine invertebrates, such as squids, can attain a very large size. But the true behemoths of the natural world have been and are the largest members of the endoskeleton-possessing subphylum Craniata. Endoskeleton-possessing animals display an astounding range of sizes and shapes, from the smallest vertebrate fishes to the largest whales. It is an organizational arrangement that has been tremendously successful in the history of life. From where does it derive?  

Bone itself is formed by what are known as osteocytes, cells that specialize in the mineralization of certain kinds of protein. (Osteocytes are derived in turn from neural crest cells.) The chief mineral found in bone is a kind of calcium. The first examples of bone-like structures that appear in the fossil record appear to be parts of what scientists call the dermal skeleton, the first bony structures that evolved to surround both the brain and those sensory organs found in the head. These bone-like structures include spongy kinds of bone tissue, thin layers of primitive bone called lamellae, and the earliest outcroppings of what could called tooth-like objects.42 Many scientists are zeroing in on an extinct group of very small animals, called conodonts, which are now thought to have been vertebrates (having previously been considered invertebrate chordates). Conodonts flourished for more than 150 million years, and appear to have been the first animals to have tooth-like protrusions in the mouth.43 Some researchers have concluded that the vertebrate skeleton itself may have its beginning in this early conodont dentition.44

The first vertebrates were jawless fishes. The advent of the jaw was a momentous step. Jaws are an example of how certain body parts can be “repurposed”, so to speak. It now appears that the vertebrate jaw evolved from the bones that formed the gill arches in jawless fish.45 Coupled with the evolution of the first true teeth, this produced an animal far more capable of food gathering, particularly as the jaw continued to be “rewarded” and refined by natural selection and became a true instrument of predation in many fish.

The bones that comprise the skull, the bones that form the vertebrae, and the ribs are known as the axial skeleton. All of the selection pressures that caused the emergence of the vertebrate body axis, an integrated system of bones, muscle, and connective tissue, are not yet known. But we do know that this interdependent arrangement allows the body to bend, it allows the body to absorb and utilize physical forces, and in the air-breathing vertebrates that ultimately evolved, it helped facilitate lung function. In the fish that evolved in ancient seas, the possession of an efficient body axis, along with the evolution of fins, meant greater maneuverability, bigger physical size, and increased speed through the water. It was a tremendous advantage. 46 It worked. It was perpetuated.

From the physical structures of the earliest fin-possessing fish would ultimately evolve the appendicular skeleton—the bones of the pelvic girdle that support the lower limbs, the bones of the pectoral girdle that support the upper limbs, and the limb bones themselves. This process will be examined, briefly, in the chapter The Animal Kingdom Begins to Colonize the Land.  Suffice it to say, however, that we owe our ability to move about on the dry land to the structures that evolved to facilitate the ability to move about in the ocean. Once again, we see the interconnectedness of life on the Earth, and gain insight into the enormously long heritage that gave rise to us.

The degree of bone-hardening, or ossification, differs among the vertebrates. There are whole taxa of fish that are completely cartilaginous. Cartilage has a specific gravity (density in relation to the density of water) only about half that of bone. Sharks, for example, have no bone, and never developed a swim bladder to facilitate their buoyancy. The possession of bones and swim bladders proved to be a tremendous advantage. There are now fewer than 800 species of cartilaginous fish, as opposed to almost 21,000 species of fish possessing a bony anatomy.47 We must conclude, therefore, that by making a greater structural sophistication possible, bone proved to be adaptively superior, and while most vertebrates contain both bone and cartilage, bone is the material “favored” by natural selection for the construction of durable animals.

Other General Considerations

Animals more developed than cnidarians, ctenophores, and some kinds of worms possess a body cavity, known technically as a coelom. The coelom arises in the mesoderm during an animal’s embryonic stage. (Most animals are what is called triploblastic, which means they have three distinct cell layers in their embryonic structures.) The mesoderm itself splits into two layers. One layer becomes the animal’s outer body wall and the other gives rise to the internal organs. The space they create is the coelom.48 The coelom’s significance is great. It is the ability of bodies to form an interior that allows for the rise and interaction of all organ-based systems within an animal, and all of the “higher” animals are made possible by it. The evolutionary origins of the coelom are a matter of differing opinions, but there is some evidence from a Precambrian Lagerst├Ątte in the Doushantuo formation (600 million to 580 million ybp) of southern China of a bilaterian that may have possessed a coelom. If this is true, it would be the earliest example of which we know.49

A discussion of all hypotheses concerning the evolution of animal sensory apparatuses is beyond the scope of this chapter, but it is of interest to consider the role the evolution of eyes played in the Cambrian “Explosion”. Contrary to the uninformed opinion of some, eyes can evolve complex structure rather readily, starting simply from photosensitive skin cells. Arthropods that had structurally advanced eyes have been uncovered in Australia. The specimens are dated at approximately 515 million ybp, and the unusually well-preserved eyes are of a kind typical of predatory animals. The evolution of eyes therefore was a tremendous advantage to the populations in which this occurred, and no doubt was an element of the unceasing struggle of the heterotrophs to find something to eat—or to keep from being eaten.50

Fish generally reproduce by means of external fertilization, meaning that a female deposits a layer of eggs on an underwater surface and a male releases sperm in order to fertilize the eggs—a chancy reproductive proposition. But a Devonian Period class of fish known as the Placodermi appears to have been the first vertebrate group to evolve one of the most momentous abilities in the history of the Animal Kingdom—internal fertilization. Internal fertilization involves the insemination of a female’s egg inside of her body, followed either by the laying of an egg (oviparity) or the internal development of offspring, culminating in birth. In scientific parlance, the process of gestation and birth is known as viviparity. Remarkable fossil evidence from Western Australia has revealed the presence of embryos inside fish of the placoderm genus Incisoscutum. There are also structures within these fish that are associated with copulatory abilities. Dated at 380 million ybp, this is the earliest evidence yet seen of the method of sexual reproduction that would ultimately come to be the dominant one among the mammals—like us.51 There is evidence that internal fertilization evolved independently several times in the history of animal life.

If it were possible to observe the fauna of the Cambrian ocean, the arthropods known as trilobites would be seen in abundance. These segmented animals, many of which were just a few centimeters in length, had well-developed eyes and hard shells for their defense. They were among the survivors of the Cambrian extinction. They were also astonishingly long-lived as a subphylum. Trilobites have been found as far back as 570 million ybp, and the last specimens didn’t die out until around 225 million ybp. Few animals have had greater success in the history of life than that.52

The Geography and Climate of the Earth From the Late Proterozoic to the  Middle Paleozoic World

The late Proterozoic landmasses were relatively sparse. Supercontinent Rodinia had broken up, and the world’s land was distributed in a roughly even manner both north and south of the Equator. By the time of the Cambrian Period, in the early Paleozoic Era, there was a much greater landmass on the Earth.53 In the early Cambrian, about 535 million ybp, the vast bulk of the Earth’s landmass was south of the equator. What was to be South America was connected to Africa, India, and several other major landmasses in a supercontinent geologists call Gondwana. A smaller landmass named Laurentia, which was to be the physical foundation of North America, straddled the Equator. Baltica, which was to be the foundation of much of Europe, and Siberia, were smaller, disconnected landmasses among several others of relatively small size. By the late Cambrian, at 500 million ybp, Siberia and Laurentia had moved farther north, but were still largely in the southern hemisphere. What is now North Africa was at or near the South Pole. Not until 400 million ybp were there significant landmasses of any size in the northern hemisphere, in a geologic period called the Early Devonian. Gondwana was still the largest landmass, and Laurentia, Baltica, and another landmass had coalesced to form a continent geologists refer to Laurussia.54

The Ediacaran Fauna had faced tough climatic conditions, as the late Proterozoic was characterized by extensive glaciation. By the middle Paleozoic Era there is reason to believe the global climate had grown significantly warmer, with average temperatures in the Cambrian and Ordovician Periods believed to have been in the vicinity of 25 degrees Centigrade (around 77 degrees Fahrenheit).55 The massive shifting of continental-sized landmasses and the tremendous fluctuations of climate underscore again the non-equilibrium inherent in the story of this planet, a non-equilibrium that was to challenge, again and again, the descendants of the Cambrian Period’s inhabitants.

On the Cusp of the Next Transformation

Were we somehow able to view the life forms of the Cambrian Period ocean (prior to the extinction event), we would see an astounding array of animal life, most of which would be utterly unfamiliar to us. By the middle of the Devonian Period, around 400 million ybp, we would see the ocean teeming with a wide variety of fishes. The photosynthetic life of the Cambrian Period ocean, primarily algae of various kinds, some of them multicellular forms a few inches long at best, most of them single-celled organisms, would not have impressed us very much. But these sunlight-eating life forms were about to transform the entire planet Earth. The next great revolution that was to shake the history of life was now at hand: the evolution and movement of true plant life onto the dry land of the world. 

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