COMPARATIVE EMBRYOLOGY: THE VERTEBRATE BODY http://www.pbs.org/wgbh/evolution/library/04/2/l_042_03.html
Even before Darwin proposed the theory of evolution through natural selection, Ernst von Baer claimed that the more closely related any two species are, the more similar their development. His trea- tise (1828) set the stage for linking the study of ontogeny, the development of the individual through a single life cycle, to phylogeny, the relatedness of species through descent from a common ancestor. When Darwin brought together the diverse lines of evidence to demonstrate that new species arose from previous species, he included the findings from studies on embryos.
Von Baer, who discovered the mammalian egg as part of his detailed studies on animal develop- ment, observed that vertebrate animals, during the early stages of their embryological development, seem to have a common design, whereas the adult forms show difference. Arm buds from different species, for example, are virtually indistinguishable when they first form on the embryo, yet they may develop into a wing, an arm, or a flipper. In the early stages of growth when vital organs originate, the developmental sequences, or ontogeny, of all vertebrates are very similar. As the fertilized egg transforms into an adult, the general vertebrate plan is modified during growth as each species acquires its adult species pattern.
This plate illustrates six developmental stages (from left to right) of five species of vertebrates - one amphibian (the salamander), one bird (the chicken), and three mammals (the pig, monkey, and human). As you color, note the similarities of body shapes among the five species in the early develop- mental stages. The late fetal/newborn/adult stages reflect the emergence of species-specific body plans as a result of differential growth.
The fertilized eggs (a), or zygotes, are very similar, though they differ slightly in the size of the cell nucleus. The orderly division of the single-celled zygote into a multicelled blastocyst is referred to as cleavage. By the late cleavage stage (b), the embryos look very similar and differ only in their cleav- age patterns, which vary due to the presence of differing amounts of yolk in the egg.
As the body segments form (c), all three mammals remain almost identical. Notice the ancestral gill slits, which in the mammals will later develop into parts of the ear and pharynx. The mammals possess an umbilical cord that leads to the placenta. In contrast, the salamander and the chicken are nourished by yolk.
The early forelimbs begin as buds (d). By the late fetal stage (e), limbs take on their adult shapes. The striking similarities in the late fetal stage between monkey and human reflect their close phylogenetic relationship. The main difference lies in the absence of a tail in the human fetus. (If an ape fetus were substituted for this monkey, it too would lack a tail). The chicken has developed its spe- cialized shell breaker.
The salamander has just hatched into its larval stage (e). It spends the first part of its life in the water, taking in lifegiving oxygen through its feathery gill slits and using its limbs as paddles. Later, the salamander undergoes metamorphosis and acquires its adult form with terrestrial limbs and lungs for breathing air. Only then, as an adult, can it leave the water to live, but not reproduce, on dry land.
The newborn of each species receive quite different treatment The salamander abandons the eggs after she lays them, and the larvae receive no parental care at all. The hen incubates her eggs with body heat while sitting on them in a nest.
The newly hatched chicks receive some protection from the mother hen, but begin immediately to find their own food.
After gestation times of four (pig), six (monkey), and nine months (human), newborn mammals are nourished by their mother's milk and require extended care before they become independent adults.
A comparison of developmental stages among vertebrates led Ernst Haeckel (1834-1919) to propose his famous principle "ontogeny recapitulates phylogeny." A supporter of the idea of evolution, Haeckel claimed that the development of an individual (ontogeny) reflects the stages through which the individual's species has passed during its evolution
(phylogeny). However, the phrase "ontogeny reca- pitulates phylogeny" oversimplifies and misleads by implying that evolution has goals or is directed. Instead, early developmental sequences of all vertebrates are similar due to common ancestry.
All vertebrate embryos follow a common developmental plan due to having a set of genes that gives the same instructions for development. As each organism grows, it diverges according to its species way of life. Human embryonic development is similar to that of other vertebrates, more like that of other mammals than nonmammals, and most similar to that of other primates. From the study of ontogeny, we discover clues about the transformation of species through evolutionary change.

Every living being carries within it evidence of more than 3.5 billion years of evolutionary change and adaptation by its ancestors. And it just so happens that much of the evidence we humans carry is most obvious —to the eye, at least—during the stages of life that take place inside the womb. So if you watch developing embryos through the lens of evolutionary biology, they can carry you on even more amazing journeys —outward to the odyssey of life's history, and inward, into the invisible world of genes.
Ernst von Haeckel, an early champion of evolutionary theory, was the best-known scientist to propose that similarities among embryos contain important information. Specifically, Haeckel proposed that "ontogeny recapitulates phylogeny." This pithy bit of jargon, when translated into English, asserts that as an embryo develops, it passes through stages that are equivalent to the adult forms of its ancestors. For example, according to Haeckel, a human embryo would pass through a stage in which it has features of an adult fish, then features of an adult amphibian, and so forth.
That would be a mighty tall order, of course, for at least two reasons. First, many adult animals
(including extinct species) are highly specialized, and carry scores of complicated structures that would have to be assembled and disassembled as an embryo progresses from one stage to another. Second, any species alive today has an awful lot of ancestors that stretch back over billions of years. To pass through the adult stages of all of them would make for a long, tortuous (and wasteful) embryonic life!
Biologists have known for decades that ontogeny doesn't strictly recapitulate phylogeny —at least not in the precise way that Haeckel thought it did. Haeckel was wrong in his insistence that embryos resemble ancestral adults. But many embryos do pass through stages during which they look a lot like embryos of their ancestors —and therefore, embryos of related species. And many scientists agree that events during development are vitally important in evolution. Leigh von Valen, a prominent modern evolutionary thinker, went so far as to suggest that ".. evolution is the control of development by ecology." The subject is fascinating, complicated, and not at all easy to summarize. (Stephen Jay Gould devoted several years and a lengthy book to the topic.) But here are a few important points to think about.
The embryos (fishes, birds, pigs and humans) in NOVA's "Odyssey of Life - The Ultimate Journey" resemble each other because they all belong to animals that biologists call vertebrates. Any textbook can tell you that, but what does grouping us together that way actually mean? The simple answer is that we all share common ancestors who evolved a successful body plan based on a backbone, two pairs of limbs, and body systems set up in a certain basic manner. But what does that mean? And what does it have to do with the importance of embryos in evolution?
Think about it this way. Each major animal group has evolved a unique combination of particular bodyparts that perform essential functions. Take, for example, the fact that all animals must breathe. Many land animals use lungs like ours, but insects and spiders use quite different devices. Some aquatic animals use various styles of gills, while others just let oxygen and carbon dioxide pass across soft, wet skin. You can think of lungs, gills, and other body parts that help animals breathe as the "breathing tool" component of their bodypart kits. There are similar "tools" for feeding, movement, defense, reproduction, and so on.
The intriguing point is that among all the millions of animal species alive today, there are only a couple of dozen really different body-part tool kits. Each is the hallmark of a major animal group —a collection of related species that biologists usually call a Phylum. Mollusks —snails, clams, octopi and their kin—are one such group.
Insects and their relatives are another. But with only two dozen or so basic body plans, where do the many thousands of species within each group come from? You can think of each group's basic body plan as the biological equivalent of a major musical theme. The slightly different body plans of species within each group are like variations on that theme. Just where do these themes and variations come from? Here's where things get interesting.
An embryo grows and develops under the control of its genes. Some genes work fairly simply, directing cells to churn out products and assemble those products into structures. But these relatively simple genes couldn't produce a complex organism by themselves. Their actions are coordinated by master control genes that act like orchestra conductors —determining which genes are turned on and which are turned off, in what cells, at what stages in development, and for what lengths of time. Of course, the task of orchestrating the entire process of constructing a fish, pig, or human makes directing the most complex musical score look like playing with nursery rhymes!

This is one reason why entirely new basic body plans don't evolve very often. Each body-part is assembled by a group of genes acting under the direction of particular control genes. Those control genes are themselves controlled by higher level control genes. And those genes are controlled by still higher-level control genes. (In some ways, these controls-within-controls are set up almost like a military chain of command.) The long and the short of it is that making major changes in body-part tool kits requires wholesale shakeups in these complex genetic programs. And in order to survive the test of natural selection, these shake ups need to happen in ways that don't introduce any fatal flaws.
So it isn't surprising that completely new body plans haven't evolved very often. In fact, these sorts of shakeups have occurred only a few times in the entire 3.5 billion year history of life. The best-known was the "Cambrian
Explosion"—a period roughly 600 million years ago during which the basic body plans of most major groups of living organisms (and those of many extinct groups) arose. Of course, those original body plans were controlled by genetic programs that have been passed down over time to species alive today.
How does all this explain why vertebrates pass through an early stage that resembles a fish embryo? As Nietzsche once wrote, "Ye have made your way from the worm to man, and much within you is still worm." Our "fish-like" early stages are directed by parts of the same genetic program that built early fishes—some of the first members of our branch of the animal kingdom. By the time fishes evolved, genetic control of development was already a very complicated business, because fishes are complex animals. And once a genetic program passes a certain level of complexity, it becomes difficult for major changes early on not to have "domino effects" that knock things out of kilter down the line.
So, over millions of years, evolution operated mainly by adding on to and fiddling around with later stages in development, rather than by making radical changes in genetic programs that substituted one type of body part for another. The result is that some aspects of the earliest stages in the human developmental program remain rather similar to those found in living fishes.
It is even more fascinating, however, to realize that minor modifications in the timing and ordering of events during embryonic life can produce enormous differences in adults. In fact, nearly all the sorts of evolutionary changes most of us usually think about—ancient fishes giving rise to amphibians, amphibians to reptiles, dinosaurs to birds, and so on—have occurred through relatively small changes in timing and orchestration of genetic controls during development.
That's how ancient limbs evolved into wings, or feet into flippers. It is also how ape-like ancestors evolved into humans.
Why do humans share an astonishing 98% of our genes with chimpanzees? Because, when it comes to differences between such closely related species, timing is everything!

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Edwin Grant Conklin
In early times and among primitive peoples all phenomena were regarded as supernatural. The rising and setting of the sun, the sweet influence of the Pleiades, the coming and going of the winds, storms, lightning, thunder -- all the phenomena of life, birth, and death -- were supposed to be directly controlled by gods or spirits. In the course of centuries many such events were seen to be natural — that is, lawful or orderly -- and were more or less understood, so that gradually the supernatural withdrew to the misty mountain tops of origins. During the last two or three centuries enlightened people everywhere have come to realize that ordinary phenomena occur in accordance with natural laws.
But in the matter of beginnings and origins the opinion is still widely held that they do not happen in accordance with nature, but only in response to supernatural action.
Even such a constantly recurring phenomenon as the origin of the individual human being was by many regarded as a supernatural phenomenon until a little more than a hundred years ago; and even today many intelligent people believe that the mind and soul of every person is supernaturally created, though few, if any, would go so far as to maintain that the body is supernaturally created, as some of the "preformationists" did in the eighteenth century... These speculations reached their culmination in the works of Charles Bonnet (1748-1773), the distinguished natural philosopher of Geneva, in which he denied all new formation, all development or generation, and held that in the original creation of the progenitor of each species God created at one stroke all the individuals that would ever come from that progenitor.
Thus every individual in the world was supernaturally created.
Ontogeny, or the origin of individuals, and phylogeny, or the origin of races, are two aspects of one and the same thing, namely, organic development. There is a remarkable parallelism between the two, and in particular the factors or causes of development are essentially the same in both. Just as the earth rotates on its axis and revolves in its orbit and the whole solar system moves through space in accordance with the law of gravity, so organisms undergo development as embryos, as species, and as larger groups according to the law of organic evolution.
It was Ernst Haeckel, in his Generelle Morphologie (1866) and in many later books, who announced that
"Ontogeny is a short recapitulation of Phylogeny" -- that is, the successive embryonic stages in the development of an animal correspond to the successive adult stages of the phylum to which it belongs. This is Haeckel's Fundamental Law of
Biogeny ("Biogenetisches Grundgesetzt"), which is more frequently called the theory of embryonic recapitulation.
All vertebrates, from fishes to mammals, pass through a fish-like stage in their development in which they have (1) gill slits, (2) five or six pairs of aortic arches, (3) a simple tubular heart with one auricle and one ventricle, (4) a notochord
(the basis of the backbone in higher vertebrates), (5) a primitive type of kidney (the pronephros), etc. These organs persist throughout life in the lowest fishes, but they undergo many changes in higher forms.
The fundamental resemblances or homologies between embryos, larvae, and adults which have been cited above are just as genuine homologies as those between adult structures, and the only natural explanation that has ever been found for such homologies is inheritance from common ancestors.
The origin of the individual (ontogeny) is not only a key to the conditions and causes of the origin of the race
(phylogeny) but is also an actual evolution -- that is, an origin of new forms by transformation from old ones. In the long series of stages which an egg passes through in its transformation into a mature animal one sees not only an actual evolution -- the evolution of an individual — but also, more or less obscurely, a repetition of the stages of the long-past evolution of the ancestors of the species.
Man no less than other mammals develops from a fertilized egg, which passes through cleavage, blastula, and gastrula stages. The human embryo has gill slits and aortic arches, which undergo exactly the same transformations that take place in other mammals. Man's heart is at first like that of a fish, consisting of one auricle and one ventricle. His backbone begins as a notochord, is next a segmented cartilaginous rod, then each segment or vertebra consists of five separate bones, and finally each fuses into a single bone. He has in the course of his development three different pairs of kidneys, first a pronephros (or fore-kidney) , like that of the lower fishes, then a mesonephros (or mid-kidney) , like that of the frogs, and finally a metanephros (or hind-kidney) like that of reptiles, birds, and mammals, which alone survives in the adult. His brain, eye, ear, in fact, all his organs, pass through stages in development that are characteristic of lower vertebrates. Even in those adult features that are distinctively human, such as the peculiar form of the hand and the foot, the number of bones in the ankle and wrist, the number of pairs of ribs, the absence of a tail and the relative hairlessness of the skin -- in all these respects the human foetus resembles anthropoid apes more than adult man.
Why are not these and a hundred other structures made directly? Why this roundabout process of making a man? There is no answer but evolution.
Embryology bears indubitable testimony to the truth of evolution; ancestral history is repeated in individual

history, but the record is like an ancient palimpsest that has been erased and written over again and again. Traces of the old record are still there; some are obscure, some are almost entirely obliterated, but wherever they are decipherable they, tell the old, old story of the common origin of animal and man -- their similarities and their kinship.
What bearings do these scientific evidences as to the origin of individuals and species have on religious faith? It might satisfy our pride to believe that every human being sprang into existence fully formed and armed, like Minerva, from the brain of Jove, but however pleasing such a belief might be it could not be held by sane and enlightened people. We know well that every human being, even the greatest that ever trod the earth, was once a baby, an embryo, a germ cell, and this knowledge has not destroyed our belief in the dignity of man nor in the existence of God.