"According to the widely accepted scientific account, the universe erupted 15 billion years ago in an explosion called the 'Big Bang' and has been expanding and cooling ever since. Later there gradually emerged the conditions necessary for the formation of atoms, still later the condensation of galaxies and stars, and about 10 billion years later the formation of planets. In our own solar system and on earth (formed about 4.5 billion years ago), the conditions have been favorable to the emergence of life. While there is little consensus among scientists about how the origin of this first microscopic life is to be explained, there is general agreement among them that the first organism dwelt on this planet about 3.5 - 4 billion years ago. Since it has been demonstrated that all living organisms on earth are genetically related, it is virtually certain that all living organisms have descended from this first organism. Converging evidence from many studies in the physical and biological sciences furnishes mounting support for some theory of evolution to account for the development and diversification of life on earth, while controversy continues over the pace and mechanisms of evolution. While the story of human origins is complex and subject to revision, physical anthropology and molecular biology combine to make a convincing case for the origin of the human species in Africa about 150,000 years ago in a humanoid population of common genetic lineage. However it is to be explained, the decisive factor in human origins was a continually increasing brain size, culminating in that of homo sapiens. With the development of the human brain, the nature and rate of evolution were permanently altered: with the introduction of the uniquely human factors of consciousness, intentionality, freedom and creativity, biological evolution was recast as social and cultural evolution." (From the International Theological Commission, headed by then Joseph Cardinal Ratzinger now Pope Benedict XVI, statement "Communion and Stewardship: Human Persons Created in the Image of God," plenary sessions held in Rome 2000-2002, published July 2004)

The purpose of this article is to reveal the scientific evidence in favor of an old earth and (more controversial) macroevolution (defined as "the theory of universal common descent with gradual modification"). Much of my material I have borrowed from the comprehensive TalkOrigins.org site, as well as the books I have listed below. I will be quoting a young-earth Catholic creationist (who takes the first chapters of the book of Genesis quite literally) and respond to some of his criticisms and confusion over science, Catholic theology, and the Bible.

see also Part 1: The Scientific Evidence for an Old Earth

The Evidence for Evolution

• Definition of Evolution
• Evidence for Macroevolution
• Unique Universal Phylogenetic Tree
• Transitional Forms and the Tree of Life
• Geological Time Scale and the Fossil Record
• History: Anatomical Vestiges and Atavisms
• Embryology
• Biogeography
• Opportunistic Nature and Evolutionary Constraint
• Anatomic/Molecular Paralogy
• Anatomic/Molecular Analogy
• Suboptimal Function
• Molecular Sequence Evidence
• Cytochrome c Studies
• Pseudogenes
• Conclusion

Transitional Fossils (below, being updated)

• Catholics and "No Transitional Fossils" Claim
• Fossil Evidence Intro
• Origin of Life
• Invertebrates to Vertebrates ("Cambrian explosion")
• Primitive fish to sharks
• Primitive fish to bony fish
• Fish to Tetrapods ("amphibians")
• Tetrapods to Reptiles
• Reptiles and Dinosaurs
• Reptiles to Mammals
• Reptiles to Birds
• Transitions among Mammals
• Horses (and Perissodactyls)
• Giraffes (and Artiodactyls)
• Whales
• Elephants
• Primates, Hominids, and Us

Reply to a Catholic Creationist (below, updated Dec 2008)

Bibliography (updated July 2010)

Definition of Evolution

Let's remember what Pope John Paul II stated to the Pontifical Academy of Sciences in 1996.

"Today, almost half a century after the publication of the [Pope Pius XII Humani Generis] Encyclical, new knowledge has led to the recognition of more than a hypothesis in the theory of evolution. It is indeed remarkable that this theory has been progressively accepted by researchers, following a series of discoveries in various fields of knowledge. The convergence, neither sought nor fabricated, of the results of work that was conducted independently is in itself a significant argument in favor of this theory."

Now let's find out why he might say this. What is the scientific evidence for macroevolution? First, a simple definition: "Macroevolution is the theory of universal common descent with gradual modification." Or as Douglas Theobald in his "29+ Evidences for Macroevolution" further defines:

"Common descent is a general descriptive theory that proposes to explain the origins of living organisms....Because it is so well supported scientifically, macroevolution is often called the 'fact of evolution' by biologists. The theory specifically postulates that all of the earth's known biota are genealogically related, much in the same way that siblings or cousins are related to one another. Thus, macroevolutionary processes necessarily entail the transformation of one species into another and, consequently, the origin of higher taxa."

Stephen Jay Gould of Harvard explains why evolution is considered both a fact and a theory.

"Well evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts don't go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's in this century, but apples didn't suspend themselves in midair, pending the outcome....In science "fact" can only mean 'confirmed to such a degree that it would be perverse to withhold provisional consent.' I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. Evolutionists have been very clear about this distinction of fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred." (Stephen Jay Gould "Evolution as Fact and Theory" in Discover magazine, May 1981)

This article will lay out some of the best evidence for macroevolution while not delving into natural selection, punctuated equilibrium, or the various proposed "mechanisms" of evolution. In Finding Darwin's God (1999) Kenneth Miller has written a fabulous book that presents the evidence for evolution and responds to prominent critics from various perspectives (young-earth creationists represented by Duane Gish/Henry Morris/ICR in the chapter "God the Charlatan"; progressive creationists like Phillip E. Johnson in "God the Magician"; and intelligent design advocates like Michael Behe in "God the Mechanic"). Dr. Miller says to deny the evidence for evolution that we see from natural history and propose "intelligent design" in its place is to posit a Creator who mimics evolution.

"Is it any wonder that biologists are unable to take intelligent design seriously? Over and over again, the imposition of intelligent design on the facts of natural history requires us to imagine a designer who creates successive forms that mimic evolution. Magicians are master illusionists, and if this magical designer had anything in mind, it must have been to cast the illusion of evolution and nothing else....Like it or not, intelligent design requires us to believe that the past was a time of magic in which species appeared out of nothing. That magic began with the dawn of life on this planet, and continued unabated for more than a billion years, bringing a grand parade of living things into existence. Throughout this time, novel organisms sprang into existence one after another, transforming the earth and producing eras in which organisms now long extinct dominated the planet." (Kenneth Miller, from chapter 4 "God the Magician" in Finding Darwin's God, page 99, 100)

It should be noted that the biologist Miller considers himself an "orthodox Catholic" as well as an "orthodox Darwinist" (from his appearance on the 2001 PBS special on evolution). He sees no problem reconciling his Catholic faith with the Darwinian theory of evolution.

Another Catholic writing on evolutionary theory, but from the "intelligent design" standpoint, is Michael Behe, the biochemist from Lehigh University. Young-earth creationists (whether Catholic or evangelical), thinking they had an ally in their fight against science, were no doubt very disappointed when they read this from Behe at the beginning of his book (supposedly) challenging evolution:

"Evolution is a controversial topic, so it is necessary to address a few basic questions at the beginning of the book. Many people think that questioning Darwinian evolution must be equivalent to espousing creationism. As commonly understood, creationism involves belief in an earth formed only about ten thousand years ago, an interpretation of the Bible that is still very popular. For the record, I have no reason to doubt that the universe is the billions of years old that physicists say it is. Further, I find the idea of common descent (that all organisms share a common ancestor) fairly convincing, and have no particular reason to doubt it. I greatly respect the work of my colleagues who study the development and behavior of organisms within an evolutionary framework, and I think that evolutionary biologists have contributed enormously to our understanding of the world. Although Darwin's mechanism -- natural selection working on variation -- might explain many things, however, I do not believe it explains molecular life." (Michael Behe, Darwin's Black Box, page 5)

So Behe himself does not doubt evolution (descent with modification from a common ancestor), he challenges the idea that the current mechanisms of evolution can explain the "irreducible complexity" of life at the molecular level. I don't intend to critique Behe's theory of "intelligent design." The purpose of this article is to lay out the basic scientific evidence for an old earth and macroevolution. Kenneth Miller has critiqued Behe's book (see chapter 5 of Finding Darwin's God, "God the Mechanic") and Behe has responded (see Behe's appendix in Science and Evidence for Design in the Universe titled "Answering Scientific Criticisms of Intelligent Design" and the Access Research Network Behe page online). See also Kenneth Miller's Evolution Page at Brown University. One can read the replies back and forth from both sides and decide if "intelligent design" is a valid argument against evolution.

Evidence for Macroevolution

Now I will outline some of the evidence for macroevolution.

Adapted from the detailed TalkOrigins "29+ Evidences for Macroevolution" (from November 2002 version) by Douglas Theobald, Ph.D.

Universal common descent is the hypothesis that all living organisms are the lineal descendants of one original living species. All the diversity of life, both past and present, was originated by normal reproductive processes observable today. Thus, all extant species are related in a strict genealogical sense. More specifically, macroevolution is proposed to occur on a geological timescale and in a gradual manner. "Gradualness" has little to do with the rate or tempo of evolution; it is a mode of change that is dependent on population phenomena. The truth of macroevolution is not assumed a priori in this discussion. Simply put, the hypothesis of common descent, combined with modern biological knowledge, is used to deduce predictions; these predictions are then compared to the real world in order see how the hypothesis fairs in light of the observable evidence. Without assuming the truth of universal common descent, it is highly probable that the hypothesis will indeed fail for most of these predictions -- and this is exactly why many of these predictions are such strong evidence for common descent.

The Unique Universal Phylogenetic Tree

Descent from a common ancestor entails a process of branching and divergence of species, in common with any genealogical process. The macroevolutionary prediction of a unique, historical universal phylogenetic tree (the "Tree of Life") is the most important, powerful, and basic conclusion from the hypothesis of universal common descent. If modern species have descended from ancestral ones in this tree-like, branching manner, a rigorous classification of species should reflect their divergence and it should be possible to infer the true historical tree that traces their paths of descent. Cladistics is a method used to determine the standard phylogenetic tree based on morphology by classifying organisms according to their shared derived characters (proposed by taxonomist Willi Hennig in 1950).

According to the theory of common descent, modern living organisms, with all their incredible differences, are the progeny of one single species in the distant past. In spite of the extensive variation of form and function among organisms, several fundamental criteria characterize all life: (1) replication, (2) information flow in continuity of kind, (3) catalysis, and (4) energy utilization (metabolism). These four functions are required to generate a physical historical process that can be described by a phylogenetic tree.

A basic prediction of the genealogical relatedness of all life, combined with the constraint of gradualism, is that organisms should be very similar in the particular mechanisms and structures that execute these four basic life processes. All known living things use polymers to perform these four basic functions: polynucleotides, polypeptides, and polysaccharides. All known life uses the same polymer, polynucleotide (DNA or RNA), for storing species specific information. All known organisms base replication on the duplication of this molecule. In all known organisms, enzymatic catalysis is based on the abilities provided by protein molecules which are constructed with the same subset of 22 amino acids (even though there are 293 naturally occurring amino acids). All known organisms, with extremely rare exceptions, use the same genetic code for transmitting information from the genetic material to the catalytic material. All known organisms use extremely similar, if not the same, metabolic pathways and metabolic enzymes in processing energy-containing molecules.

If there is one historical phylogenetic tree which unites all species in an objective genealogy, all separate lines of evidence should converge on the same tree. And indeed, independently derived phylogenetic trees of all organisms match each other with an extremely high degree of statistical significance. There are over 10⁴¹ different possible ways to arrange the 30 major taxa represented into a phylogenetic tree (picture above). Speaking quantitatively, independent morphological and molecular measurements have determined the standard phylogenetic tree to better than 41 decimal places, which is a much greater precision and accuracy than that of even the most well-determined physical constants. For comparison, the charge of the electron is known to only seven decimal places, the Planck constant is known to only eight decimal places, the mass of the neutron, proton, and electron are all known to only nine decimal places, and the universal gravitational constant has been determined to only three decimal places.

Transitional Forms and the Tree of Life

Any fossilized animals found should conform to the standard phylogenetic tree. If all organisms are united by descent from a common ancestor, then there is one single true historical phylogeny for all organisms, just like there is one single true historical genealogy for any individual human. It directly follows that if there is a unique universal phylogeny, then all organisms fit in that phylogeny uniquely. We have found a quite complete set of dinosaur (reptile)-to-bird transitional fossils with no morphological gaps, represented by Eoraptor, Herrerasaurus, Ceratosaurus, Allosaurus, Compsognathus, Sinosauropteryx, Protarchaeopteryx, Caudipteryx, Velociraptor, Sinovenator, Beipiaosaurus, Sinornithosaurus, Microraptor, Archaeopteryx, Rahonavis, Confuciusornis, Sinornis, Patagopteryx, Hesperornis, Apsaravis, Ichthyornis, and Columba, among many others. We also have an exquisitely complete series of fossils for the reptile-to-mammal intermediates, ranging from the pelycosauria, therapsida, cynodonta, up to primitive mammalia.

Based upon the consensus of numerous phylogenetic analyses, Pan troglodytes (the chimpanzee) is the closest living relative of humans. Thus, we expect that organisms lived in the past which were intermediate in morphology between humans and chimpanzees. Over the past century, many spectacular paleontological finds have identified such transitional hominid fossils. Another impressive example of incontrovertible transitional forms predicted to exist by evolutionary biologists is the collection of land mammal-to-whale fossil intermediates. Whales, of course, are sea animals with flippers. Since they are also mammals, the consensus phylogeny indicates that whales and dolphins evolved from land mammals with legs. In recent years, we have found several transitional forms of whales with legs, both capable and incapable of terrestrial locomotion (for some pictures and more details, see "Transitional Fossils" below).

The reptile-bird intermediates date from the Upper Jurassic and Lower Cretaceous (about 150 million years ago), whereas pelycosauria and therapsida (reptile-mammal intermediates) are older and date from the Carboniferous and the Permian (about 250 to 350 million years ago, see the Geological Time Scale at right). This is precisely what should be observed if the fossil record matches the standard phylogenetic tree. The most scientifically rigorous method of confirming this is to demonstrate a positive correlation between phylogeny and stratigraphy (the strata or rocks of the geologic column where fossils are found throughout the world), i.e. a positive correlation between the order of taxa in a phylogenetic tree and the geological order in which those taxa first appear and last appear (whether for living or extinct intermediates).

The Geological Time Scale and Fossil Record

The geological periods where the major groups of organisms appeared can be divided as follows (see also Kenneth Miller, Finding Darwin's God, page 39) : Ma = Millions of years ago

CENOZOIC

Quaternary 1.5-present Ma -- modern humans appear (Homo sapiens sapiens)
Tertiary 65-1.5 Ma -- Mammals and birds and teleost fish dominant

MESOZOIC 

Cretaceous 144-65 Ma -- Dinosaurs dominant, small mammals, birds
Jurassic 213-144 Ma -- Dinosaurs dominant, first mammals, then first birds
Triassic 248-213 Ma -- Mammalian reptiles dominant, first dinosaurs

PALEOZOIC

Permian 286-248 Ma -- Amphibians dominant, first mammal-like reptiles
Pennsylvanian 320-286 Ma -- Amphibians dominant, first reptiles
Carboniferous (includes Penn and Miss periods)
Mississippian 360-320 Ma -- big terrestrial amphibians, fishes
Devonian 408-360 Ma -- Fish dominant, first amphibians
Silurian 438-408 Ma -- first ray-finned and lobe-finned fish
Ordovician 505-438 Ma -- more jawless fishes
Cambrian 570-505 Ma -- first jawless fishes

Within the error inherent in the fossil record, prokaryotes should appear first, followed by simple multicellular animals like sponges and starfish, then lampreys, fish, amphibians, reptiles, then mammals, etc. Studies from the past ten years addressing this very issue have confirmed that there is indeed a positive correlation between phylogeny and stratigraphy, with statistical significance. Using three different measures of phylogeny-stratigraphy correlation [the RCI, GER, and SCI], a high positive correlation was found between the standard phylogenetic tree and the stratigraphic range of the same taxa, with very high statistical significance (P < 0.0001).

It would be highly inconsistent if the chronological order were reversed in the reptile-bird and reptile-mammal example. More generally, the strongest falsification of this prediction would be the finding that there was a negative correlation between stratigraphy and the phylogenetic tree that describes the genealogical relatedness of all living organisms.

History: Anatomical Vestiges and Atavisms

Some of the more renowned evidences for evolution are the various nonfunctional or rudimentary vestigial characters, both anatomical and molecular, which are found throughout biology. During macroevolutionary history, functions necessarily have been gained and lost. Thus, from common descent and the constraint of gradualism, we predict that many organisms should display vestigial structures, which are structural remnants of lost functions.

There are many examples of rudimentary and nonfunctional characters carried by organisms, and these can very often be explained in terms of evolutionary histories: (1) snakes such as pythons (which are legless snakes) carry vestigial pelvises hidden beneath their skin; (2) some lizards carry rudimentary, nonfunctional legs underneath their skin, undetectable from the outside; (3) many cave dwelling animals, such as the fish Astyanax mexicanus (the Mexican tetra) and the salamander species Typhlotriton spelaeus and Proteus anguinus, are blind yet have rudimentary, vestigial eyes; (4) dandelions reproduce without reproduction (a condition known as apomixis), yet they retain flowers and produce pollen (which are useless); (5) over 90% of all adult humans develop third molars (otherwise known as wisdom teeth), and in one-third they are malformed and impacted (these useless structures point to our ancestors who were herbivorous, and molar teeth were required for chewing and grinding plant material, but now in human beings can cause significant pain and increased risk for injury, etc); (6) there are many examples of flightless beetles (such as the weevils of the genus Lucanidae) which retain perfectly formed wings housed underneath fused wing covers. All of these examples can be explained in terms of the beneficial functions and structures of the organisms' predicted ancestors.

Anatomical atavisms are closely related conceptually to vestigial structures. An atavism is the reappearance of a lost character specific to a remote evolutionary ancestor and not observed in the parents or recent ancestors of the organism displaying the atavistic character. As with vestigial structures, no organism can have an atavistic structure that was not previously found in one of its ancestors.

Probably the most well known case of atavism is found in the whales. According to the standard phylogenetic tree, whales are known to be the descendants of terrestrial mammals that had hindlimbs. Thus, we expect the possibility that rare mutant whales might occasionally develop atavistic hindlimbs. In fact, there are many cases where whales have been found with rudimentary atavistic hindlimbs in the wild: hindlimbs have been found in baleen whales, humpback whales, and in many specimens of sperm whales. Most of these examples are of whales with femurs, tibia, and fibulae; however, some even include feet with complete digits.

Other famous examples of atavisms exist, including (1) rare formation of extra toes in horses (2nd and 4th digits), similar to what is seen in the archaic horses Mesohippus and Merychippus; (2) atavistic thigh muscles in birds and sparrows (Passeriform); (3) hyoid muscles in dogs; (4) wings in earwigs (normally wingless); (5) atavistic fibulae in birds (the fibulae are normally extremely reduced); (6) extra toes in guinea pigs and salamanders; (6) the atavistic dew claw in many dogs; and (7) various atavisms in humans -- such as the "true human tail." Concerning the latter, more than 100 cases of human tails have been reported in the medical literature and less than one-third of these are medically known as "pseudo-tails" (which are not true tails). True human tails are complex structures which have muscle, blood vessels, occasional vertebrae and cartilage, can move and contract, and they are occasionally inherited.

Vestigial characters are also found at the molecular level: (1) the L-gulano-g-lactone oxidase gene, the gene required for Vitamin C synthesis, was found in humans and guinea pigs, and in other primates (chimpanzees, orangutans, and macaques), exactly as predicted by evolutionary theory (it exists as a pseudogene, present but incapable of functioning); (2) multiple odorant receptor genes; (3) the RT6 protein gene; (4) the galactosyl transferase gene; and (5) the tyrosinase-related gene (TYRL). We share these vestigial genes with other primates, and the mutations that made these genes nonfunctional are also shared with several other primates.

Embryology

Embryology and developmental biology have provided some fascinating insights into evolutionary pathways. Since the cladistic morphological classification of species is generally based on derived characters of adult organisms, embryology and developmental studies provide a nearly independent body of evidence. From embryological studies it is known that two bones of a developing reptile eventually form the quadrate and the articular bones in the hinge of the adult reptilian jaw. Accordingly, there is a very complete series of fossil intermediates in which these structures are clearly modified from the reptilian jaw to the mammalian ear.

Early in development, mammalian embryos temporarily have pharyngeal pouches, which are morphologically indistinguishable from aquatic vertebrate gill pouches. This evolutionary relic reflects the fact that mammalian ancestors were once aquatic gill-breathing vertebrates. The arches between the gills, called branchial arches, were present in jawless fish and some of these branchial arches later evolved into the bones of the jaw, and, eventually, into the bones of the inner ear.

Many species of snakes and legless lizards (such as the "slow worm") initially develop limb buds in their embryonic development, only to reabsorb them before hatching. Similarly, modern adult whales, dolphins, and porpoises have no hind legs. Even so, hind legs, complete with various leg bones, nerves, and blood vessels, temporarily appear in the cetacean fetus and subsequently degenerate before birth.

Mammals evolved from a reptile-like ancestor, and placental mammals (like humans and dogs) have lost the egg-tooth and caruncle (and eggshell). However, monotremes, such as the platypus and echidna, are primitive mammals that have both an egg-tooth and a caruncle, even though the monotreme eggshell is thin and leathery. Most strikingly, during marsupial development, an eggshell forms transiently and then is reabsorbed before live birth. Though they have no need for it, several marsupial newborns (such as baby Brushtail possums, koalas, and bandicoots) retain a vestigial caruncle as a clear indicator of their reptilian, oviparous ancestry.

The fossil record has confirmed that birds once had teeth, as demonstrated by the fossils of many birds with teeth including Archaeopteryx. Furthermore, this predicted possibility has been confirmed experimentally in a modern bird, the chicken. Kollar and Fisher transplanted a small piece of mammalian mesenchymal tissue (which forms teeth) underneath the beak-forming epithelial layer of a developing chick. Intriguingly, they observed that the chicken epithelium secreted dental enamel and directed the adjacent mesenchyme to form teeth. This would have been impossible unless the chicken still retained the genes and developmental pathway for making teeth. Thus, chickens have not yet completely lost the genes coding for tooth development (two of Stephen Jay Gould's popular books are titled Hen's Teeth and Horse's Toes and The Panda's Thumb which explain some of this past evolutionary history).

Present and Past Biogeography

Common ancestors originate in a particular geographical location. Thus, the spatial and geographical distribution of species should be consistent with their predicted genealogical relationships. The standard phylogenetic tree predicts that new species must originate close to the older species from which they are derived. Closely related contemporary species should be close geographically, regardless of their habitat or specific adaptations (if not, there should be a good explanation, such as extreme mobility in the case of birds, sea animals, or human intervention).

Examples of present biogeography supporting evolutionary theory are (1) marsupials (kangaroos, etc) which only inhabit Australia (exceptions such as some South American species and the opossum are explained by continental drift); (2) conversely, placental mammals are virtually absent on Australia, despite the fact that many would flourish there (humans introduced most of the few placentals found on Australia); (3) the southern reaches of South America and Africa and all of Australia share lungfishes, ostrich-like birds (ratite birds), and leptodactylid frogs -- all of which occur nowhere else; (4) alligators, some related species of giant salamander, and magnolias only occur in Eastern North America and East Asia (which were once spatially close in the Laurasian continent); (5) indigenous Cacti (Cactus plant) only inhabit the Americas, while Saharan and Australian vegetation is very distantly related (mostly Euphorbiaceae); (6) members of the closely related pineapple family inhabit many diverse habitats (such as rainforest, alpine, and desert areas), but only in the American tropics, not African or Asian tropics, etc.

As for past biogeography, we find the earliest marsupial fossils (e.g. Alphadon) from the Late Cretaceous, when South America, Antarctica, and Australia were still connected. Additionally, the earliest ancestors of modern marsupials are actually found on North America. The obvious paleontological deduction is that extinct marsupial fossil organisms should be found on South America and Antarctica, since marsupials must have traversed these continents to reach their present day location in Australia. Interestingly, we have found marsupial fossils on both South America and on Antarctica. This is an astounding macroevolutionary confirmation, given that no marsupials live on Antarctica now.

The Equidae (i.e. horse) fossil record is very complete (though extremely complex) and makes very good geographical sense, without any large spatial jumps between intermediates. Every single one of the fossil ancestors of the modern horse are found on the North American continent. Finally, the theory of common descent predicts that we may find early hominid fossils on the African continent. Numerous transitional fossils between humans and the great apes have been found in southern and eastern Africa. Examples include Ardipithecus ramidus, Australopithecus anamensis, Australopithecus afarensis, Australopithecus garhi, Kenyanthropus platyops, Kenyanthropus rudolfensis, Homo habilis, and a host of other transitionals thought to be less related to Homo sapiens, such as the robust australopithicenes.

The Opportunistic Nature of Evolution and Evolutionary Constraint

The principle of evolutionary opportunism is closely related to evolutionary history and to the effects of contingency. Descent with gradual modification means that new organisms can only use and modify what they initially are given; they are slaves to their history. New structures and functions must be recruited from previous, older structures. One major consequence of the constraint of gradualism is the predicted existence of "paralogy": similarity of structure despite difference in function.

Anatomical and Molecular Paralogy

There are countless examples of paralogy in living and extinct species -- the same bones in the same relative positions are used in primate hands, bat wings, bird wings, pterosaur wings, whale and penguin flippers, horse legs, the digging forelimbs of moles, and webbed amphibian legs. All of these characters have similar structures that perform various different functions. The standard phylogenetic tree shows why these species have these same structures, i.e. they have common ancestors that had these structures. The fossil record shows a general chronological progression of intermediate forms between theropod dinosaurs and modern birds, in which theropod structures were modified into modern bird structures.

On the molecular level, the existence of paralogy is quite impressive. Many proteins of very different function have strikingly similar amino acid sequences and three-dimensional structures. A frequently cited example is lysozyme and a-lactalbumin. A-Lactalbumin is very similar structurally to lysozyme, even though its function is very different (it is involved in mammalian lactose synthesis in the mammary gland). On a grander scale, a stunning confirmation of these evolutionary predictions has come from an analysis of Saccharomyces cerevisiae (baker's yeast) and Caenorhabditis elegans (a worm). The genes used by the yeast, a unicellular organism, are mostly genes dealing directly with core biochemical functions that all organisms must perform. From an evolutionary perspective, we would expect these genes to be ancient. Thus it was expected and shown that the worm contains a great majority of these genes. In contrast, the extra genes used by the worm, which deal with multicellularity, should be more recently evolved. Phylogenetic analysis has shown that this is exactly the case. An even larger study of the known eukaryotic genomes has further demonstrated that paralogy is rampant in nature, and that true structural innovation is relatively rare ("Comparative Genomics of the Eukaryotes" [2000] Science 287: 2204-2218).

Anatomical and Molecular Analogy

A corollary of the principle of evolutionary opportunism is analogy. Analogy is the case where different structures perform the same or similar functions in different species. Two distinct species have different histories and different structures; if both species evolve the same new function, they may recruit different structures to perform this new function. Analogy also must conform to the principle of structural continuity; analogy must be explained in terms of the structures of predicted ancestors. There are many anatomical examples of functional analogy. One case is the vertebrate eye and the cephalopod eye. Another is the case of American and Saharan desert plants, which use different structures for the same functions needed to live in dry, arid regions. By contrast, we would not expect newly discovered species of dolphins, whales, penguins, or any close mammalian relatives to have gills (a possible analogy with fish), since their immediate ancestors lacked gills or gill-like structures from which they could be derived.

A familiar molecular example is the case of the three proteases subtilisin, carboxy peptidase II, and chymotrypsin. These three proteins are all serine proteases (i.e. they degrade other proteins in digestion). They have the same function, the same catalytic residues in their active sites, and they have the same catalytic mechanism. Yet they have no sequence or structural similarity. Another molecular example is that of DNA polymerases. Rat polymerase � has obviously evolved from nucleotidyl transferases by mutating to catalyze several nucleotide additions instead of just one -- which nicely illustrates why analogy is ultimately also paralogy.

Suboptimal Function

Another consequence of evolutionary opportunism is the existence of apparent suboptimal function. This does not refer to a structure functioning poorly. It simply means that a structure with a more efficient design (usually with less superfluous complexity), could perform the same final function equally as well. Structures with suboptimal function should have a gradualistic historical evolutionary explanation, based on the opportunistic recruitment of ancestral structures.

For example, the mammalian gastrointestinal tract crosses the respiratory system. Functionally, this is suboptimal; it would be beneficial if we could breathe and swallow simultaneously. However, there is a good historical evolutionary reason for this arrangement. The Osteolepiformes (Devonian lungfish), from which mammals evolved, swallowed air to breathe. Only later did the ancestors of mammals recruit the olfactory nares of fish for the function of breathing on land. Another anatomical example of suboptimal function is the inverted mammalian retina, with its blind spot. In order to deal with the many problems inherent in an inverted retina, the vertebrate eye utilizes various complex compensatory structures and mechanisms. In contrast with mammalian eyes, cephalopod eyes have very different underlying retinal structures (e.g. they are verted, not inverted), and they have no blind spots. This strongly suggests that mammals also could have eyes without blind spots.

With the recent sequencing of the human genome, we have found that less than 2% of the DNA in the human genome is used for making proteins (International Human Genome Sequencing Consortium 2001). A full 45% of our genome is composed of transposons, which serve no known function for the individual (except to cause a significant fraction of genetic illnesses and cancers). Twenty percent of the human genome are pseudogenes. They also serve no function for the individual. A remarkable example is the glyceraldehyde-3-phosphate dehydrogenase (GDPH) gene. In humans, there is one functional GDPH gene, but there are at least twenty GDPH pseudogenes. In mice, there are approximately 200 GDPH pseudogenes, none of which are necessary. In addition to one or two functional copies, there are between 20 and 30 pseudogenes of cytochrome c in both humans and the rat.

A lot of wasted energy is expended in dealing with this useless DNA; however, all these molecular examples also have convincing explanations based on evolutionary histories.

The Molecular Sequence Evidence

The molecular sequence evidence gives the most impressive and irrefutable evidence for the genealogical relatedness of all life. The nature of molecular sequences allows for extremely impressive probability calculations that demonstrate how well the predictions of common descent with modification actually match empirical observation. There are several categories and independent lines of molecular sequence evidence useful for determining phylogenetic relationships. Studies of functional elements include ribosomal RNA, ubiquitous proteins, and mitochondrial DNA comparisons; studies of nonfunctional elements include comparisons of pseudogenes, endogenous retroviral genes, and mobile genetic elements (such as introns, transposons, or retroelements).

Cytochrome c Studies

Cytochrome c is an essential and ubiquitous protein found in all organisms, including eukaryotes and bacteria. The mitochondria of cells contain cytochrome c, where it transports electrons in the fundamental metabolic process of oxidative phosphorylation. The oxygen we breathe is used to generate energy in this process. Using an ubiquitous gene such as cytochrome c, there is no reason to assume that two different organisms should have the same protein sequence or even similar protein sequences, unless the two organisms are genealogically related. Hubert Yockey has done a careful study in which he calculated that there are a minimum of 2.3 x 10⁹³ possible functional cytochrome c protein sequences, based on genetic mutational analyses (Yockey, H.P. [Cambridge Univ Press, 1992] Information Theory and Molecular Biology, Chapter 6). For perspective, the number 10⁹³ is about one billion times larger than the number of atoms in the visible universe. Thus, functional cytochrome c sequences are virtually unlimited in number, and there is no a priori reason for two different species to have the same, or even mildly similar, cytochrome c protein sequences.

From the theory of common descent and our standard phylogenetic tree we know that humans and chimpanzees are quite closely related. We therefore predict, in spite of the odds, that human and chimpanzee cytochrome c sequences should be much more similar than, say, human and yeast cytochrome c -- simply due to inheritance. This has been confirmed: Humans and chimpanzees have the exact same cytochrome c protein sequence. In the absence of common descent, the chance of this occurrence is conservatively less than 10^-93 (1 out of 10⁹³). Thus, the high degree of similarity in these proteins is a spectacular corroboration of the theory of common descent. Furthermore, human and chimpanzee cytochrome c proteins differ by about 10 amino acids from all other mammals. The chance of this occurring in the absence of a hereditary mechanism is less than 10^-29.

Further, bat cytochrome c is much more similar to human cytochrome c than to hummingbird cytochrome c; porpoise cytochrome c is much more similar to human cytochrome c than to shark cytochrome c. The phylogenetic tree constructed from the cytochrome c data exactly recapitulates the relationships of major taxa as determined by the completely independent morphological data. Why would two organisms have such similar ubiquitous proteins when the odds are astronomically against it? We know of only one reason for why two organisms would have two similar protein sequences in the absence of functional necessity: heredity. Thus, in such cases we can confidently deduce that the two organisms are genealogically related.

Like protein sequence similarity, the DNA sequence similarity of two ubiquitous genes also implies common ancestry. If chimps and humans are truly genealogically related, we predict that the difference between their respective cytochrome c gene DNA sequences should be less than 3% -- probably even much less, due to the essential function of the cytochrome c gene. As mentioned above, the cytochrome c proteins in chimps and humans are exactly identical. The clincher is that the two DNA sequences that code for cytochrome c in humans and chimps differ by only one base (a 0.3% difference), even though there are 10⁴⁹ different sequences that could code for this protein. The combined effects of DNA coding redundancy and protein sequence redundancy make DNA sequence comparisons doubly redundant; DNA sequences of ubiquitous proteins are completely uncorrelated with phenotype, but they are strongly causally correlated with heredity. This is why DNA sequence phylogenies are considered so robust.

Pseudogenes

Other nonfunctional molecular examples that provide evidence of common ancestry are pseudogenes. Pseudogenes are very closely related to their functional counterparts (in primary sequence and often in chromosomal location), except that either they have faulty regulatory sequences or they have internal stops that keep the protein from being made. They are functionless and do not affect an organism's phenotype when deleted. Finding the same pseudogene in the same chromosomal location in two species is strong evidence of common ancestry.

This also has been confirmed: there are very many examples of shared pseudogenes between primates and humans. One is the ψη-globin gene, a hemoglobin pseudogene. It is shared among the primates only, in the exact chromosomal location, with the same mutations that render it nonfunctional. Another example is the steroid 21-hydroxylase gene. Humans have two copies of the steroid 21-hydroxylase gene, a functional one and a nonfunctional pseudogene. Chimps and humans both share the same eight bp deletion in this pseudogene that renders it nonfunctional.

Conclusion

These previous points are all evidence of macroevolution alone; the evidence and the conclusion are independent of any specific gradualistic explanatory mechanisms for the origin and evolution of macroevolutionary adaptations and variation. This is why scientists call universal common descent the "fact of evolution." None of the evidence above assumes that natural selection is true or that it is sufficient for generating adaptations or the differences between species and other taxa. Thus, the macroevolutionary conclusion stands, regardless of the mechanism.

Adapted from the detailed TalkOrigins "29+ Evidences for Macroevolution" (from November 2002 version) by Douglas Theobald, Ph.D.

Transitional Fossils (being updated)

First, some Catholic writers on the false "No Transitional Fossils" claim:

KARL KEATING of Catholic Answers:

"The writer quoted prominent biologists -- evolutionists to a man -- who affirm that the missing links are still missing. The fossil record, they say, fails to show even one clear example of species A turning into species B. It shows many examples of one species disappearing and being replaced by another, but that is not the same thing. It also shows the development of minor variations within species but never a transition from one species into another. As one might expect, this is awkward for Darwin's theory, which holds that species develop from one another through a long series of minute changes. The quoted biologists do not reject evolution itself, but they say that the scheme given in the Origin of Species is not supported by the fossil record....I am not a biologist, and I do not have sufficient interest in the question of speciation to work up a knowledgeable conclusion on my own. But what does interest me is that people who are biologists and who do have demonstrated sufficient interest have come to opposite conclusions. One group says the links are missing, and the other says they have been found. It is not possible that both groups are correct, since the same link cannot be both missing and found." (Karl Keating, "At Ease Please," This Rock magazine, July-Aug 2006)

ROBIN BERNHOFT of Kolbe Center for Creation:

"The fossil record is equally hostile to Darwin....He expected that many fossils would be found of species intermediate between ancestral organisms and their descendants and admitted that if such fossils could not be found it would disprove his theory. By Darwin's own criterion his theory has been disproved. In the past one hundred fifty years, the fossil record has become nearly complete, yet there are still no intermediate fossils. Scientists have found fossils of 97.7 percent of land vertebrates worldwide, and almost one hundred percent in North America, and still they have not found the intermediate fossils Darwin said had to be there in order for his theory to be true....What you find in the fossil record is the sudden appearance, 600 million years ago in the 'Cambrian Explosion,' of a wide range of mature fossils. Some of these lasted for a while, then died out. Others have survived into the present. None changed into anything else. Later, other fossils appeared abruptly in their mature forms, persisted, then either died out or survived to the present. None changed into anything else. There are no intermediate forms....The fossil record provides no evidence that any species was ancestral to any other species and no evidence of intermediate forms showing ancestral relationship.....Finally, there is no scientific evidence that microevolution -- the adaptation of species to environmental change -- can generate macroevolution -- the development of new species." (Robin Bernhoft, "Confronting Creation's Complexities: Darwinism Isn't Fit to Survive," This Rock magazine, Sept 2003)

GERARD KEANE of Kolbe Center for Creation:

"In reality, not only are the required intermediate forms between the various species absent from the fossil record, but also many such supposed forms are conceptually untenable. Evolution Theory now stands exposed as both the worst mistake made in science and the most enduring myth of modern times....If Evolution really did occur down through the ages, an ample number of transitional creatures should by now have been found among the immense number of fossils now unearthed....Vast numbers of fossils identical to creatures alive today have been found, but not a trace of transitional forms. The fossil record is devoid of 'missing links' grading up from simple to more complex creatures." (Gerard Keane, Creation Rediscovered [Tan Books, 1999], pages xxvi, 103, 105)

AMY WELBORN, blogger and author of "Prove It" series of books, she outlines three "basic problems" with evolution, the first one is:

"While 'microevolution' the development or disappearance of traits within a species is an acknowledged fact, the broader Darwinian scheme 'macroevolution' which proposes that the diversity of living creatures comes from one organism adapting so much it became a whole other species, suffers from a serious lack of evidence at this point. There is absolutely no evidence from the fossil record of evolution between species. No 'transitional' or 'intermediate' forms exist. The missing link is still missing." (Amy Welborn, Prove It! God [2000],  page 46)

GEORGE SIM JOHNSTON, author of Did Darwin Get It Right?

"The publication of the Origin sent whole armies of paleontologists into the folds of the earth to find the 'innumerable' transitional links that Darwin said must be there. What did this army find? The answer appears to be -- nothing. The fossil evidence does not support the idea that species evolved by minute gradations....The fossil record shows exactly what it shows in Darwin's day -- that species appear suddenly in a fully developed state and change little or not at all before disappearing...." (George Sim Johnston, Did Darwin Get It Right? Catholics and the Theory of Evolution [1998], page 29-30)

"...about 550 million years ago, came biology's Big Bang. It occurred at the beginning of the Cambrian era. There was an explosion of highly organized life-forms -- mollusks, jellyfish, trilobites -- for which not a single ancestral fossil can be found in the earlier rocks....The Precambrian strata, moreover, are perfectly suited for the imprinting of fossils. In some locations, there are over five thousand feet of unbroken layers of sedimentary rock; but they do not contain the innumerable transitional species that Darwin maintained to be there. They are, in fact, an evolutionary blank....More importantly, there are no transitional forms, no gradations to speak of, leading up to these complex animals....This compacting of the Cambrian explosion [he places it at only 5 million years] is a major problem for orthodox Darwinists." (Johnston, page 30, 32)

"In recent years paleontologists have retreated from simple connect-the-dot scenarios linking earlier and later species. Instead of ladders, they now talk of bushes. What we see in the fossils, according to this view, are only the twigs, the end products of evolution, while the key transitional forms that would give a clue about the origin of major animal and plant groups remain hidden. The gaps on the evolutionary trees occur at just the points where the crucial changes had to take place. The direct ancestors of all the major groups -- reptiles, mammals, flowering plants -- are missing. There are no fossil grandparent of the monkeys, for example....[quotes Don Johanson]....The same is true of bats, elephants, and turtles: They all simply burst upon the scene -- de novo, as it were." (Johnston, page 35)

FR. MITCH PACWA on "Mother Angelica Live" (Nov 1996)

"Darwin's theory has also been rejected by scientists. And that, one of the things that is important about that, you know, Darwin said there would be all kinds of missing links, from one species to another. Never have any missing links been found. The theory didn't work. The hypothesis failed." (Fr. Mitch Pacwa, "Mother Angelica Live" Nov 1996 -- LISTEN TO THIS)

Next, we are about to see how wrong these Catholics are on the science. It's always best to read the actual paleontological literature, rather than "quotes" from other creationists.

The Fossil Evidence for Evolution

The following data is adapted from the detailed TalkOrigins "Transitional Vertebrate Fossils FAQ" (1994-1997) by Kathleen Hunt, and updated from the book Evolution: What the Fossils Say and Why It Matters by paleontologist / geologist Donald R. Prothero (Columbia Univ Press, 2007).

Abbreviations used: Ma = millions of years ago (Ga = billion), or My = millions of years, where appropriate.

Please consult the following books for the full paleontological evidence, pictures and descriptions of transitionals (also the Bibliography at end):

• Vertebrate Paleontology and Evolution by Robert L. Carroll (1988) -- older source and I have double-checked the references made to it
• Evolution: What the Fossils Say and Why It Matters by Donald R. Prothero (2007) -- updates Carroll and responds to many bad "creationist" arguments and errors
• also Invertebrate Paleontology and Evolution by E.N.K. Clarkson (1979, 1998 4th edition) -- discusses the pre-Cambrian to Cambrian fossils
• also The Fossil Record 2 edited by M.J. Benton (1993) -- over 800 large pages that lists virtually all the known fossils from the animal invertebrates, animal vertebrates, plants and other organisms

Carroll begins his comprehensive 1988 book on vertebrate paleontology, evolution and the fossil record:

"During the past 20 years [i.e. 1968-1988], our knowledge of fossil vertebrates has increased immensely. Entirely new groups of jawless fish, sharks, amphibians, and dinosaurs have been discovered, and the major transitions between amphibians and reptiles, reptiles and mammals, and dinosaurs and birds have been thoroughly studied. Evidence from both paleontology and molecular biology provides much new information on the initial radiation of both birds and placental mammals." (Carroll, page xiii preface).

Prothero updates us on the fossil record and evolution in the 20 years since Carroll's book:

"But the past 20 years [i.e. 1987-2007] have produced some of the greatest discoveries of all, including incredible fossils that show how whales, manatees, and seals evolved from land mammals, where elephants, horses, and rhinos come from, and how the first backboned animals evolved. We now have an amazing diversity of fossil humans, including specimens that show that we walked upright on two feet almost 7 million years ago, long before we acquired large brains. In addition to all this fossil evidence, we have new evidence from molecules as well that enables us to decipher the details of the family tree of life as never before....The fossil record is an amazing testimony to the power of evolution, with documentation of evolutionary transitions that Darwin could have only dreamed about....The fossil record is now one of the strongest lines of evidence for evolution, completely reversing its subordinate status only 150 years ago. Instead of the embarrassingly poor record that Darwin faced in 1859, we now have an embarrassment of riches." (Prothero [2007], page xix-xx)

A couple of definitions and distinctions to keep in mind (from Prothero, page 82ff, 124ff):

• while intermediate forms and transitional fossils between species are rare, there are many transitionals between larger groups (i.e. Classes such as Fish to Tetrapods, Reptiles to Mammals, etc);
• an important concept is the distinction between a lineal ancestor (i.e. direct ancestors such as father and mother, grandparents, great-grandparents, etc) and a collateral ancestor (uncles and aunts, great uncles/aunts, cousins or "close relatives," etc), e.g. Archaeopteryx (front cover of Prothero) has many transitional features between living birds and Mesozoic dinosaurs, so if it was not direct it was certainly a collateral ancestor;
• there is really no such thing as a "missing link" : evolution is not about life climbing the "ladder of nature" or a "great chain of being" from "lower" to "higher" organisms; instead evolution is more like a "bush" with many lineages branching from one another, with "ancestors" living alongside their "descendants"; the classification of life forms a natural bushy or tree-like pattern;
• we do not need to have every single transitional fossil connecting several species to show evolutionary transformation; a sequence of related species that are stable through time nevertheless forms an evolutionary transformation series even though not every transitional fossil has been preserved, e.g. the evolution of sand dollars from sea urchins (Prothero, page 190), etc;
• creationists challenge "evolutionists" to present a "perfect 10" transitional fossil : this shows a misunderstanding of evolution and transitional forms since there is no general conversion of all parts of a transitional form at the same time; genetics does not produce a smooth gradation of all features, but characteristics of an intermediate will be mixed, a pattern of descendents called mosaic evolution (i.e. normally "cousins" of an ancestor, not lineal or direct descendants due to the "incompleteness" or spottiness of the fossil record and the multiple splitting off of species);
• since evolution is a bush, not a ladder, organisms evolve but they do not always "move up the ladder"; species may retain primitive features for hundreds of millions of years, and not every anatomical feature of an animal evolves at the same time; some parts may be quite "advanced" while others retain their "primitive" state; this is the idea of mosaic evolution and this is what we want for a transitional fossil.

Now I will cover many of the known and confirmed "transitional fossils" -- including some species-to-species transitions -- with a few pictures where appropriate. First we begin with the controversial "origin of life" --

The Origin of Life on Earth

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Transitions from Invertebrates to Vertebrates (and the "Cambrian explosion")

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From the book On the Origin of Phyla by James W. Valentine (Univ of Chicago Press, 2004) :

"The title of this book, modeled on that of the greatest biological work ever written, is in homage to the greatest biologist who has ever lived. Darwin puzzled over but could not cover the ground that is reviewed here, simply because the relevant fossils, genes, and their molecules, and even the body-plans of many of the phyla, were quite unknown in his day. Nevertheless, the evidence from these many additional sources of data simply confirm that Darwin was correct in his conclusions that all living things have descended from a common ancestor and can be placed within a tree of life, and that the principle process guiding their descent has been natural selection. And he was correct in so much more." (Valentine, On the Origin of Phyla, preface page xxiii)

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Transitions from primitive fish to sharks, skates, rays

Picture below is an early shark from the late Devonian, Cladoselache (from Carroll, page 65).

• Cladoselache (late Devonian) -- Magnificent early shark fossils
• Tristychius and similar hybodonts (early Mississippian) -- Primitive proto-sharks with broad-based fins
• Ctenacanthus and similar ctenacanthids (late Devonian) -- Primitive, slow sharks with broad-based shark-like fins and spines
• Paleospinax (early Jurassic) -- More advanced features such as detached upper jaw, but retains primitive ctenacanthid features such as two dorsal spines, primitive teeth
• Spathobatis (late Jurassic) -- First proto-ray
• Protospinax (late Jurassic) -- A very early shark/skate

Picture to the right is a modern reef shark, photo by Bob Whorton and SharkTrust.org

Transitions from primitive fish to bony fish

Picture below-right is the early Devonian Palaeoniscoid Moythomasia, this genus shows the well-developed fulcral scales on the caudal fin that are characteristic of chondrostean fishes (from Carroll, page 92).

• Acanthodians (Silurian) -- A puzzling group of spiny fish with similarities to early bony fish
• Palaeoniscoids, e.g. Cheirolepis, Mimia (early Devonian) -- Primitive bony ray-finned fishes that gave rise to the vast majority of living fish, heavy acanthodian-type scales, acanthodian-like skull, and big notochord
• Canobius, Aeduella (Carboniferous) -- Later paleoniscoids with smaller, more advanced jaws
• Parasemionotus (early Triassic) -- "Holostean" fish with modified cheeks but still many primitive features, almost exactly intermediate between the late paleoniscoids and first teleosts, most of these fish lived in seasonal rivers and had lungs (which first evolved in fish)
• Oreochima and similar pholidophorids (late Triassic) -- The most primitive teleosts, with lighter scales (almost cycloid), partially ossified vertebrae, more advanced cheeks/jaws
• Leptolepis and similar leptolepids (Jurassic) -- More advanced with fully ossified vertebrae and cycloid scales, the Jurassic leptolepids radiated into the modern teleosts (the massive, successful group of fishes that are almost totally dominant today), lung transformed into swim bladder

Transitions from fishes to first amphibians (tetrapods)

• Paleoniscoids again, e.g. Cheirolepis -- These ancient bony fish probably gave rise both to modern ray-finned and lobe-finned fish
• Osteolepis (mid-Devonian) -- One of the earliest crossopterygian lobe-finned fishes, sharing characters with the lungfish, had paired fins with a leg-like arrangement of major limb bones, capable of flexing at the "elbow" and had an early-amphibian-like skull and teeth
• Eusthenopteron, Sterropterygion (mid-late Devonian) -- Early rhipidistian lobe-finned fish roughly intermediate between early crossopterygian fish and the earliest amphibians
• Panderichthys, Elpistostege (mid-late Devonian, about 370 Ma) -- These "panderichthyids" are very tetrapod-like lobe-finned fish, fragmented limbs and teeth from the mid-late Devonian (about 370 Ma)
• Obruchevichthys -- Discovered in 1991 in Scotland, some of the earliest known tetrapod remains
• Tiktaalik roseae ("large shallow water fish") -- a 375-million-year-old large scaly creature with forward fins and the beginnings of digits, proto-wrists, elbows and shoulders, a flat skull like a crocodile, a neck, ribs and other parts similar to tetrapods, discovered by a team led by Neil Shubin of the University of Chicago in sediments of former streambeds in the Canadian Arctic, 600 miles from the North Pole
• Hynerpeton, Acanthostega, Ichthyostega, Tulerpeton (late Devonian) -- A little later, the fin-to-foot transition was almost complete, and we have a set of early tetrapod fossils that clearly did have feet
• Labyrinthodonts, e.g. Pholidogaster, Pteroplax (late Dev/early Miss) -- These larger amphibians still have some icthyostegid fish features, such as skull bone patterns, labyrinthine tooth dentine, presence and pattern of large palatal tusks, the fish skull hinge, pieces of gill structure between cheek and shoulder, and the vertebral structure, but they have lost several other fish features: the fin rays in the tail are gone, the vertebrae are stronger and interlocking, the nasal passage for air intake is well defined

Picture above is the evolution of the earliest terrestrial tetrapods (e.g. Acanthostega) from aquatic lobe-finned fish (e.g. Eusthenopteron) that involved a transformation of the skeleton. Among other changes, the pectoral and pelvic fins became limbs with feet and toes, the vertebrae became interlocking, the tail fin disappeared, the snout elongated, and the bones that covered the gills and throat were lost. Many of Acanthostega's features were undeniably fishlike, including both gills and lungs. [ Source: "Getting a Leg Up on Land" by Jennifer Clack, Scientific American, December 2005 ]

Transitions among amphibians

• Temnospondyls, e.g. Pholidogaster (Mississippian, about 330 Ma) -- A group of large labrinthodont amphibians, transitional between the early amphibians and later
• Archegosaurus decheni (early Permian) -- Intertemporals lost
• Eryops megacephalus (late Penn) -- Occipital condyle splitting in two
• Trematops spp (late Permian) -- Eardrum like modern amphibians
• Amphibamus lyelli (mid-Penn) -- Double occipital condyles, ribs very small
• Doleserpeton annectens or perhaps Schoenfelderpeton (both early Permian) -- first pedicellate teeth (classic trait of modern amphibians)
• Triadobatrachus (early Triassic) -- a proto-frog, with a longer trunk and much less specialized hipbone, and a short tail still present
• Vieraella (early Jurassic) -- first known true frog
• Karaurus (early Jurassic) -- first known salamander

Picture to the right is the oldest known salamander, Karaurus, from the early Jurassic of Russia. When they first appear in the fossil record during the Jurassic, both frogs and salamanders appear essentially modern in their skeletal anatomy (from Carroll, page 180-181).

Transitions from amphibians to first reptiles

• Proterogyrinus or another early anthracosaur (late Mississippian) -- Classic labyrinthodont-amphibian skull and teeth, but with reptilian vertebrae, pelvis, humerus, and digits, still has fish skull hinge, amphibian ankle, 5-toed hand and a 2-3-4-5-3 (almost reptilian) phalangeal count
• Limnoscelis, Tseajaia (late Carboniferous) -- Amphibians apparently derived from the early anthracosaurs, but with additional reptilian features: structure of braincase, reptilian jaw muscle, expanded neural arches
• Solenodonsaurus (mid-Pennsylvanian) -- An incomplete fossil, apparently between the anthracosaurs and the cotylosaurs, loss of palatal fangs, loss of lateral line on head, still just a single sacral vertebra
• Hylonomus, Paleothyris (early Pennsylvanian) -- These are protorothyrids, very early cotylosaurs (primitive reptiles), quite little, lizard-sized animals with amphibian-like skulls (amphibian pineal opening, dermal bone), shoulder, pelvis, limbs, intermediate teeth and vertebrae, rest of skeleton reptilian, with reptilian jaw muscle, no palatal fangs, and spool-shaped vertebral centra, probably no eardrum yet

Many of these new "reptilian" features are also seen in little amphibians (which also sometimes have direct-developing eggs laid on land), so perhaps these features just came along with the small body size of the first reptiles. The major functional difference between the ancient, large amphibians and the first little reptiles is the amniotic egg. Additional differences include stronger legs and girdles, different vertebrae, and stronger jaw muscles.

Transitions among reptiles (and dinosaurs)

• Scutosaurus and other pareiasaurs (mid-Permian) -- Large bulky herbivorous reptiles with turtle-like skull features
• Deltavjatia vjatkensis (Permian) -- A recently discovered pareiasaur with numerous turtle-like skull features
• Proganochelys (late Triassic) -- a primitive turtle, with a fully turtle-like skull, beak, and shell, but with some primitive traits such as rows of little palatal teeth, a still-recognizable clavicle, a simple captorhinid-type jaw musculature, a primitive captorhinid-type ear, a non-retractable neck
• Hylonomus, Paleothyris (early Penn) -- The primitive amniotes described above Petrolacosaurus, Araeoscelis (late Pennsylvanian), first known diapsids
• Apsisaurus (early Permian) -- A more typical diapsid, lost canines
• Claudiosaurus (late Permian) -- An early diapsid with several neodiapsid traits, but still had primitive cervical vertebrae and unossified sternum, probably close to the ancestry of all diapsides (the lizards, snakes, crocs, birds)
• Planocephalosaurus (early Triassic) -- Further along the line that produced the lizards and snakes, loss of some skull bones, teeth, toe bones
• Protorosaurus, Prolacerta (early Triassic) -- Possibly among the very first archosaurs, the line that produced dinosaurs, crocodiles, and birds, may be "cousins" to the archosaurs
• Proterosuchus (early Triassic), also Sphenosuchus  -- First known archosaurs/crocodiles
• Hyperodapedon, Trilophosaurus (late Triassic) -- Early archosaurs

Picture to the left is an early archosaur, Protosuchus, approx one meter long, an early Triassic Protosuchid crocodile. The Protosuchia retain long limbs and probably were basically terrestrial in habit, but they resemble modern crocodiles more closely than sphenosuchids in their general appearance and configuration of the skull (from Carroll, page 280-281).

Several possible cases of gradual evolution (as well as some lineages that showed abrupt appearance or stasis) among the early Permian reptile genera Captorhinus, Protocaptorhinus, Eocaptorhinus, and Romeria are known. Excellent transitional dinosaur fossils from a site in Montana that was a coastal plain in the late Cretaceous include:

• Many transitional ceratopsids between Styracosaurus and Pachyrhinosaurus
• Many transitional lambeosaurids (50 specimens) between Lambeosaurus and Hypacrosaurus
• A transitional pachycephalosaurid between Stegoceras and Pachycephalosaurus
• A transitional tyrannosaurid between Tyrannosaurus and Daspletosaurus

All of these transitional animals lived during the same brief 500,000 years. Before this site was studied, these dinosaur groups were known from the much larger Judith River Formation, where the fossils showed 5 million years of evolutionary stasis, followed by the apparently abrupt appearance of the new forms. It turns out that the sea level rose during that 500,000 years, temporarily burying the Judith River Formation under water, and forcing the dinosaur populations into smaller areas such as the site in Montana. While the populations were isolated in this smaller area, they underwent rapid evolution. When sea level fell again, the new forms spread out to the re-exposed Judith River landscape, thus appearing "suddenly" in the Judith River fossils, with the transitional fossils only existing in the Montana site.

This is an excellent example of punctuated equilibrium (500,000 years is very brief and counts as a "punctuation"), and is a good example of why transitional fossils may only exist in a small area, with the new species appearing "suddenly" in other areas. Also note the discovery of Ianthosaurus, a genus that links the two synapsid families Ophiacodontidae and Edaphosauridae.

Picture above-left is the well-known Tyrannosaurus Rex (artwork by Fabio Pastori), one of the largest meat-eating dinosaurs, sharp teeth reaching lengths of 6 in, height up to 20 ft, length up to 49 ft, weight approx 6.5 US tons, first complete T-rex skeleton was discovered in 1902, many great examples have been unearthed over the last several decades.

Transitions from reptiles to first mammals

This is the best-documented transition between vertebrate classes. So far this series is known only as a series of genera or families; the transitions from species to species are not known. But the family sequence is quite complete. These range from the pelycosauria, therapsida, cynodonta, up to primitive mammalia.

• Paleothyris (early Pennsylvanian) -- An early captorhinomorph reptile, with no temporal fenestrae at all
• Protoclepsydrops haplous (early Pennsylvanian) -- The earliest known synapsid reptile
• Clepsydrops (early Pennsylvanian) -- The second earliest known synapsid
• Archaeothyris (early-mid Pennsylvanian) -- A slightly later ophiacodont
• Varanops (early Permian) -- Temporal fenestra further enlarged, braincase floor shows first mammalian tendencies
• Haptodus (late Pennsylvanian) -- One of the first known sphenacodonts, showing the initiation of sphenacodont features while retaining many primitive features of the ophiacodonts
• Dimetrodon, Sphenacodon or a similar sphenacodont (late Pennsylvanian to early Permian, 270 Ma) -- More advanced pelycosaurs, clearly closely related to the first therapsids
• Biarmosuchia (late Permian) -- A therocephalian, one of the earliest, most primitive therapsids
• Procynosuchus (latest Permian) -- The first known cynodont, a famous group of very mammal-like therapsid reptiles, sometimes considered to be the first mammals
• Dvinia or Permocynodon (latest Permian) -- Another early cynodont, first signs of teeth that are more than simple stabbing points
• Thrinaxodon (early Triassic) -- A more advanced "galesaurid" cynodont, further development of several of the cynodont features seen already
• Cynognathus (early Triassic, 240 Ma) -- Advanced cynodont, temporal fenestra larger, teeth differentiating further, cheek teeth with cusps met in true occlusion for slicing up food
• Diademodon (early Triassic, 240 Ma) -- Temporal fenestra larger still, for still stronger jaw muscles, true bony secondary palate formed exactly as in mammals, but didn't extend quite as far back
• Probelesodon (mid-Triassic; South America) -- Fenestra very large, still separate from eyesocket (with postorbital bar)
• Probainognathus (mid-Triassic, 239-235 Ma, Argentina) -- Larger brain with various skull changes: pineal foramen ("third eye") closes, fusion of some skull plates
• Exaeretodon (mid-late Triassic, 239 Ma, South America) -- Formerly lumped with the herbivorous gomphodont cynodonts, mammalian jaw prong forms, related to eardrum support, three incisors only (mammalian)
• Oligokyphus, Kayentatherium (early Jurassic, 208 Ma) -- These are tritylodontids, an advanced cynodont group, face more mammalian, with changes around eyesocket and cheekbone, full bony secondary palate
• Pachygenelus, Diarthrognathus (earliest Jurassic, 209 Ma) -- These are trithelodontids, a slightly different advanced cynodont group
• Adelobasileus cromptoni (late Triassic, 225 Ma, west Texas) -- A recently discovered fossil proto-mammal from right in the middle of that late Triassic gap, currently the oldest known "mammal"
• Sinoconodon (early Jurassic, 208 Ma) -- The next known very ancient proto-mammal
• Kuehneotherium (early Jurassic, about 205 Ma) -- A slightly later proto-mammal, sometimes considered the first known pantothere (primitive placental-type mammal)
• Eozostrodon, Morganucodon, Haldanodon (early Jurassic, 205 Ma) -- A group of early proto-mammals called morganucodonts, the restructuring of the secondary palate and the floor of the braincase had continued, and was now very mammalian, truly mammalian teeth
• Peramus (late Jurassic, about 155 Ma) -- A "eupantothere" (more advanced placental-type mammal), the closest known relative of the placentals and marsupials
• Endotherium (very latest Jurassic, 147 Ma) -- An advanced eupantothere, fully tribosphenic molars with a well-developed talonid
• Kielantherium and Aegialodon (early Cretaceous) -- More advanced eupantotheres known only from teeth
• Steropodon galmani (early Cretaceous) -- The first known definite monotreme, discovered in 1985
• Vincelestes neuquenianus (early Cretaceous, 135 Ma) -- A probably-placental mammal with some marsupial traits, known from some nice skulls
• Pariadens kirklandi (late Cretaceous, about 95 Ma) -- The first definite marsupial, known only from teeth
• Kennalestes and Asioryctes (late Cretaceous, Mongolia) -- Small, slender animals, eyesocket open behind, simple ring to support eardrum, primitive placental-type brain
• Cimolestes, Procerberus, Gypsonictops (very late Cretaceous) -- Primitive North American placentals with same basic tooth pattern

Transitions from reptiles (dinosaurs) to first birds

In the mid-1800's, this was one of the most significant gaps in vertebrate fossil evolution. No transitional fossils at all were known, and the two groups seemed impossibly different. Then the exciting discovery of Archaeopteryx in 1861 showed clearly that the two groups were in fact related. Since then, other reptile-bird links have been found.

• Coelophysis (late Triassic) -- One of the first theropod dinosaurs, theropods in general show clear general skeletal affinities with birds (long limbs, hollow bones, foot with 3 toes in front and 1 reversed toe behind, long ilium)
• Deinonychus, Oviraptor, and other advanced theropods (late Jurassic, Cretaceous) -- Predatory bipedal advanced theropods, larger, with more bird-like skeletal features
• Lisboasaurus estesi and other "troodontid dinosaur-birds" (mid-Jurassic) -- A bird-like theropod reptile with very bird-like teeth (teeth very like those of early toothed birds, since modern birds have no teeth)
• Archaeopteryx lithographica (late Jurassic, 150 Ma) -- The several known specimens of this deservedly famous fossil show a mosaic of reptilian and avian features, with the reptilian features predominating, the skull and skeleton are basically reptilian (skull, teeth, vertebrae, sternum, ribs, pelvis, tail, digits, claws, generally unfused bones)
• Sinornis santensis ("Chinese bird", early Cretaceous, 138 Ma) -- A recently found little primitive bird with bird traits: short trunk, claws on the toes, flight-specialized shoulders, stronger flight-feather bones, tightly folding wrist, short hand (these traits make it a much better flier than Archaeopteryx), reptilian traits: teeth, stomach ribs, unfused hand bones, reptilian-shaped unfused pelvis (these remaining reptilian traits wouldn't have interfered with flight)
• "Las Hoyas bird" or "Spanish bird" (not yet named, early Cretaceous, 131 Ma) -- Another recently found "little forest flier," still has reptilian pelvis and legs, with bird-like shoulder
• Ambiortus dementjevi (early Cretaceous, 125 Ma) -- The third known "little forest flier," found in 1985
• Hesperornis, Ichthyornis, and other Cretaceous diving birds -- This line of birds became specialized for diving, like modern cormorants, as they lived along saltwater coasts, there are many fossils known, skeleton further modified for flight (fusion of pelvis bones, fusion of hand bones, short fused tail), still had true socketed teeth, a reptilian trait
• the feathered dinosaurs: Sinosauropteryx, Caudipteryx, Beipiaosaurus, Sinornithosaurus, Microraptor and many hundreds of specimens of the bird Confuciusornis

Picture to the left is the famous "Archaeopteryx" --  a transitional link between reptiles and birds -- there are 10 known specimens (some are just feathers, some quite complete) -- see the detailed TalkOrigins Archaeopteryx FAQ -- The exact reptilian ancestor of Archaeopteryx, and the first development of feathers, are unknown. Early bird evolution seems to have involved little forest climbers and then little forest fliers, both of which are guaranteed to leave very bad fossil records (a little animal with acidic forest soil leaves no remains). Archaeopteryx itself is really about the best we could ask for: several specimens have superb feather impressions, it is clearly related to both reptiles and birds, and it clearly shows that the transition is feasible. The Berlin specimen is shown at left (discovered in 1877), the Thermopolis specimen at right (shown under ultraviolet light) is the most recent [ Source: Science, 2 December 2005 ] with the best preserved feet that are turned like a dinosaur's (e.g. Velociraptor).

From the book Dinosaurs of the Air: The Evolution and Loss of Flight in Dinosaurs and Birds by Gregory Paul (John Hopkins Univ Press, 2002) :

"One of the wonderful coincidences of science is that immediately after Charles Darwin published On the Origin of Species, his famous explication of the mechanism behind evolution, dramatic support for his hypothesis appeared in Bavaria. In 1860, a feather and, in 1861, the skeleton of a Mesozoic vertebrate obviously intermediate in form between modern birds and their reptilian ancestors were uncovered in lithographic slate quarries. This vertebrate was, of course, the urvogel (original bird) Archaeopteryx. As our knowledge of fossil birds has expanded in the subsequent fourteen decades, the question of how birds arose has become ever more fascinating. Most paleontologists now agree that birds -- always popular with the public -- happily happen to be the direct descendents of the best-liked group of extinct creatures, the dinosaurs. Of course, public opinion has no relevance to scientific debate, but the broad appeal of a dinosaur-bird link vexes the shrinking minority of researchers who dispute the link....That birds descended from predatory dinosaurs has become far and away the majority view expressed in many additional studies....From China has come the feathered dinosaurs Sinosauropteryx, Caudipteryx, Beipiaosaurus, Sinornithosaurus, and Microraptor as well as many hundreds of specimens of the bird Confuciusornis....the fossils are coming so fast that it was hard to keep up with the new data during preparation of this book...." (Gregory Paul, Dinosaurs of the Air, page 1, 11, 15)

One possible ancestor of Archaeopteryx is Protoavis (Triassic, 225 Ma) -- A highly controversial fossil that may or may not be an extremely early bird. Unfortunately, not enough of the fossil was recovered to determine if it is definitely related to the birds.

Transitions among mammals

Carnivores

• Creodonts -- early placental mammals with minor but interestingly carnivore-like changes in the molars and premolars
• Cimolestes (late Cretaceous) -- This creodont lost the last molar and later enlarged the last upper premolar and first lower molar
• Cimolestes incisus and Cimolestes cerberoides (Cretaceous) -- These are two species that lost their third molar
• Cimolestes sp (Paleocene) -- A later, as yet unnamed species that has very miacid-like teeth
• Simpsonictis tenuis (mid-Paleocene) -- A very early viverravid
• Paroodectes, Vulpavus (early Eocene) -- Early miacids, enlarged carnassials now specialized for shearing
• Viverravus sicarius (mid-Eocene) -- this viverravid may be the ancestral aeluroid

Dogs

• Cynodictis (late Eocene) -- First known arctoid (undifferentiated dog/bear)
• Hesperocyon (early Oligocene) -- A later arctoid, compared to miacids like Paroodectes
• Cynodesmus (Miocene) -- First true dog, the dog lineage continued through Tomarctus (Pliocene) to the modern dogs, wolves, foxes, Canis (Pleistocene)

Bears

• Cynodictis (above)
• Hesperocyon (above)
• Ursavus elmensis (mid-Oligocene) -- A small, heavy doglike animal, intermediate between arctoids and bears
• Protursus simpsoni (Pliocene; also "Indarctos") -- Sheepdog-sized, carnassial teeth have no shearing action, molars are square, shorter tail, heavy limbs, transitional to the modern genus Ursus
• Ursus minimus (Pliocene) -- First little bear, with very bearlike molars, but still had the first premolars, gave rise to the modern black bears (U. americanus and U. thibetanus), smoothly evolved to the next species, U. etruscus
• U. etruscus (late Pliocene) -- A larger bear, similar to our brown bear but with more primitive dentition, in Europe gradually evolved into U. savini
• U. savini (late Pleistocene, 1 Ma) -- Very similar to the brown bear
• U. spelaeus (late Pleistocene) -- The recently extinct giant cave bear, with a highly domed forehead, clearly derived from the European population of U. savini in a smooth transition
• U. arctos (late Pleistocene) -- The brown "grizzly" bear, clearly derived from the Asian population of U. savini about 800,000 years ago, spread into Europe and the New World
• U. maritimus (late Pleistocene) -- The polar bear, very similar to a local population of brown bear, U. arctos beringianus that lived in Kamchatka about 500,000 years ago

The transitions between each of these bear species are very well documented. For most of the transitions there are superb series of transitional specimens leading right across the species boundaries.

Raccoons (procyonids)

• Phlaocyon (Miocene) -- A climbing carnivore with non-shearing carnassials and handlike forepaws, transitional from the arctoids to the procyonids (raccoons), typical raccoons first appeared in the Pliocene

Weasels (mustelids)

• Plesictis (early Oligocene) -- Transitional between miacids and mustelids (weasels)
• Potamotherium (late Oligocene) -- Another early mustelid, but has some puzzling traits

Seals, sea lions and walruses

• Pachycynodon (early Oligocene) -- A bearlike terrestrial carnivore with several sea-lion traits
• Enaliarctos (late Oligocene, California) -- Still had many features of bear-like terrestrial carnivores
• Odobenidae (the walrus family) -- started with Neotherium 14 Ma, then Imagotaria, which is probably ancestral to modern species
• Otariidae (the sea lion family), Pithanotaria (mid- Miocene, 11 Ma) -- small and primitive in many respects
• Thalassoleon (late Miocene) and finally modern sea lions (Pleistocene, about 2 Ma)
• Phocidae (the seal family) -- first known are the primitive and somewhat weasel-like mid-Miocene seals Leptophoca
• Montherium -- Modern seals first appear in the Pliocene, about 4 Ma

Civets (viverrids)

• Stenoplesictis (early Oligocene) -- An early civet-like animal related to the miacids
• Palaeoprionodon (late Oligocene, 30-24 Ma) -- An aeluroid (undifferentiated cat/civet/hyena) with a civet-like skull
• Herpestides (early Miocene, 22 Ma, France) -- Had a distinctly civet-like skull floor

Cats

• Haplogale (late Oligocene, 30 Ma) -- A slightly cat-like aeluroid (cat/civet/hyena)
• Proailurus julieni (early Miocene) -- An aeluroid with a viverrid-ish skull floor that also showed the first cat-like traits
• Proailurus lemanensis (early Miocene, 24 Ma) -- Considered the first true cat, had the first really cat-like skull floor
• Pseudaelurus (early-mid Miocene, 20 Ma) -- A slightly later, more advanced cat
• Dinictis (early Oligocene) -- Transitional from early cats such as Proailurus to modern "feline" cats
• Hoplophoneus (early Oligocene) -- Transitional from early cats to "saber-tooth" cats

Rodents

• Anagale, Barunlestes, or a similar anagalid (mid-late Paleocene) -- A recently discovered order of primitive rodent/lagomorph ancestors from Asia, rabbit-like lower cheek teeth, barunlestes in particular (known so far from just one specimen) has both rodent-like and rabbit-like features, and may be ancestral to both rodents and lagomorphs, lineage apparently split into two groups, a eurymyloid/rodent-like group and a mymotonid/rabbit-like group
• Heomys (mid-late Paleocene, China) -- An early rodent-like eurymyloid, similar overall to Barunlestes but with added rodent/lagomorph features
• Tribosphenomys minutus (late Paleocene, 55 Ma) -- A newer discovery, a small Asian anagalid known from a single jaw found in some fossilized dung, still had rabbit-like cheek teeth, but had fully rodent-like ever-growing first incisors, probably the "ancestral stem" of the rodents (Discover, Feb 1995, page 22)
• Acritoparamys (was "Paramys") atavus (late Paleocene) -- first known primitive rodent
• Paramys and ischyromyid group (late Paleocene) -- Generalized early rodents, mostly squirrel-like skeleton but without the arboreal adaptations
• Protosciurus (early Oligocene) -- An early squirrel with very primitive dentition and jaw muscles, but with the unique ear structure of modern squirrels, fully arboreal
• Sciurus (Miocene) -- the modern squirrel genus, among the rodents, squirrels may be considered "living fossils"
• Paleocastor (Oligocene) -- Early beaver, a burrower, not yet aquatic, modern beavers appear in the Pleistocene
• Eomyids -- later Eocene rodents with a few tooth and eyesocket features that show they had branched off from the squirrel line
• Geomyoids -- primitive rodents and still have squirrel-like jaws, known to have given rise to the mouse family

Lagomorphs (rabbits and hares)

• Barunlestes (above) -- The possible Asian rodent/lagomorph ancestor
• Mimotoma (Paleocene) -- A rabbit-like animal, similar to Barunlestes, but with a rabbit dental formula, changes in the facial bones, and only one layer of enamel on the incisors (unlike the rodents), like rabbits it had two upper incisors, but the second incisor is still large and functional, in modern rabbits it is tiny
• Mimolagus (late Eocene) -- Possesses several more lagomorph-like characters, such as a special enamel layer, possible double upper incisors, and large premolars
• Lushilagus (mid-late Eocene) -- first true lagomorph, teeth very similar to Mimotoma, and modern rabbit and hare teeth could easily have been derived from these teeth, after this the first modern rabbits appeared in the Oligocene

Condylarths (first hoofed animals)

• Protungulatum (latest Cretaceous) -- Transitional between earliest placental mammals and the condylarths (primitive, small hoofed animals), these early, simple insectivore-like small mammals had one new development: their cheek teeth had grinding surfaces instead of simple, pointed cusps, they were the first mammal herbivores

Within a few million years the condylarths split into several slightly different lineages with slightly different teeth, such as oxyclaenids (the most primitive), triisodontines, and phenacodonts (described in other sections). Those first differences amplified over time as the lineages drifted further and further apart, resulting ultimately in such different animals as whales, anteaters, and horses. Says Carroll (1988): "In the case of the cetaceans [whales] and the perissodactyls [horses], their origin among the condylarths has been clearly documented." (page 505) P.D. Gingerich has analyzed the condylarth lineage and species-to-species transitions, for example: "Haplomylus speirianus... gradually became larger over time, ultimately giving rise to a new species Haplomylus scottianus... Hyopsodus latidens also became larger and then smaller, ultimately giving rise to a still smaller species, Hyopsodus simplex." These analyses were based on hundreds of new specimens (505 for Haplomylus, and 869 for Hyopsodus) from Clark's Fork Basin in Wyoming.

Perissodactyls (horses, rhinos, tapirs)

Here we come to the most famous general lineage of all, the horse sequence. It was the first such lineage to be discovered, in the late 1800's, and thus became the most famous. It is a very good sequence that has grown only more detailed and complete over the years, changing mainly by the addition of large side-branches.

• Loxolophus (early Paleocene) -- A primitive condylarth with rather low-crowned molars, probably ancestral to the phenacodontid condylarths
• Tetraclaenodon (mid-Paleocene) -- A more advanced Paleocene condylarth from the phenacodontid family, and almost certainly ancestral to all the perissodactyls (a different order)
• Radinskya yupingae (late Paleocene, China) -- A recently discovered perissodactyl-like condylarth
• Hyracotherium (early Eocene, about 55 Ma, previously "Eohippus") -- The famous "dawn horse," a small, doggish perissodactyl, with an arched back, short neck, omnivore teeth, and short snout, 4 toes in front and 3 behind
• Hyracotherium vassacciense (early Eocene) -- The particular species that probably gave rise to the equids
• Orohippus (mid-Eocene, 50 Ma) -- Small, 4/3 toed, developing browser tooth crests
• Epihippus (late Eocene, 45 Ma) -- Small, 4/3 toed, good tooth crests, browser
• Epihippus (Duchesnehippus) -- A later subgenus with Mesohippus-like teeth
• Mesohippus celer (latest Eocene, 40 Ma) -- Three-toed on all feet, browser, slightly larger
• Mesohippus westoni (early Oligocene) -- A slightly later, more advanced species
• Miohippus assiniboiensis (mid-Oligocene) -- This species split off from early Mesohippus via cladogenetic evolution, after which Miohippus and Mesohippus overlapped for the next 4 my
• Kalobatippus (late Oligocene) -- Three-toed browser w/foot intermediate between Mio and Para
• Parahippus (early Miocene, 23 Ma) -- Three-toed browser/grazer, developing "spring foot"
• Parahippus leonensis (mid-Miocene, 20 Ma) -- Three-toed browser/grazer with the emphasis on grazer
• Merychippus gunteri (mid-Miocene, 18 Ma) -- Three-toed grazer, fully spring-footed with high-crowned teeth
• Merychippus primus (mid-Miocene, 17 Ma) -- Slightly more advanced
• Merychippus spp (mid-late Miocene, 16-15 Ma) -- 3-toed grazers, spring-footed, size of small pony

The line that eventually produced Equus developed as follows: M. primus, M. sejunctus, M. isonesus (these last two still had a mix of primitive, hipparion, and equine features), M. intermontanus, M. stylodontus, M. carrizoensis. These last two looked quite horsey, with quite small side toes, and gave rise to a set of larger three-toed and one-toed horses known as the "true equines."

• Dinohippus (late Miocene, 12 Ma) -- One-toed grazer, spring-footed, very equine feet, teeth, and skull, with straighter teeth and smaller fossae, first was D. spectans, followed by D. interpolatus and D. leidyanus, a slightly later species was D. mexicanus with even straighter teeth and even smaller fossae
• Equus (Plesippus), also called the E. simplicidens group (Pliocene, 4 My) -- Three closely related species of one-toed spring-footed high-crowned grazers, no fossae and very straight teeth, pony size, fully "horsey" body
• Equus (Hippotigris) (Pleistocene) -- Subgenus of modern 1-toed spring-footed grazing zebras
• Equus (Equus) (Pleistocene) -- Subgenus of modern 1-toed spring-footed grazing horses and donkeys
• Homagalax (early Eocene) -- Very like its sister genus Hyracotherium, but had cross-lophs on teeth
• Heptodon (late early Eocene) -- A small early tapiroid showing one more tooth cusp change, split into two lineages
• Helaletes (mid-Eocene) -- which had a short proboscis
• Prototapir (late Oligocene) -- much like modern tapirs but without such a flexible snout
• Miotapirus (early Miocene) -- an almost-modern tapir with a flexible snout
• Tapirus (Pliocene) -- the modern tapir
• Hyrachyus (late Eocene) -- a tapiroid with increased shearing function in its teeth, led to the late Eocene hyracodontids such as Hyracodon (rhino-tapiroids, or "running rhinos")

For more details, see the TalkOrigins Horse Evolution FAQ.

Artiodactyls (pigs, hippos, deer, giraffes, cows)

Carroll (1988) says: "The early evolution of the artiodactyls is fairly well documented by both the dentition and considerable skeletal material and provides the basis for fairly detailed analysis of evolutionary patterns....the origin of nearly all the recognized families can be traced to the late Middle Eocene or the Upper Eocene..." (page 507).

• Chriacus (early Paleocene) -- A primitive oxyclaenid condylarth from the Lower Paleocene
• Diacodexis (early Eocene) -- A rabbit-sized with longer limbs than the condylarths
• Helohyus or a similar helohyid (mid-Eocene) -- Primitive artiodactyl, larger than Diacodexis but with relatively shorter and stouter limbs, with bulbous cusps on the molars
• Anthracotherium and later anthracotheriids (late Eocene) -- A group of heavy artiodactyls that started out dog-size and increased to be hippo-size, later species became amphibious with hippo-like teeth, led to the modern hippos in the early Miocene, 18 Ma
• Propalaeochoerus or a similar cebochoerid/choeropotamid (late Eocene) -- Primitive piglike artiodactyls derived from the helohyids (above)
• Perchoerus (early Oligocene) -- The first known peccary
• Paleochoerus (early Oligocene, 38 Ma) -- first known true pig, apparently ancestral to all modern pigs
• Homacodon and other dichobunids (mid-Eocene) -- similar to Diacodexis but with some advances
• Poebrodon (late Eocene) -- first primitive camelid, like other late Eocene artiodactyls, it had developed crescent-shaped grinding ridges on the cheek teeth, a small, short-necked, four-toed animal with little hooves on each toe
• Poebrotherium (mid-Oligocene) -- A taller camelid with fused arm and leg bones, and missing toes 1, 4, and 5, longer neck, though still much shorter than modern camels
• Mesomeryx (late Eocene) -- A more advanced dichobunid, probably close to the ancestry of the rest of the artiodactyls
• Hypertragulus, Indomeryx or a similar hypertragulid (late Eocene) -- Primitive ruminants with a tendency toward crescent ridges on teeth, high-crowned teeth, and loss of one cusp on the upper molars, long-legged runners and bounders, with many primitive features, but with telltale transitional signs
• Hyemoschus or other tragulids (Oligocene) -- Slightly more advanced ruminants called "tragulids" that have the above features plus loss of part of the first toe, some more bones fused, fibula shaft no longer ossifies
• Archaeomeryx, Leptomeryx (mid-late Eocene) -- Rabbit-sized ruminants, still had small upper incisors, the mastoid bone becomes less and less exposed in these "leptomerycids"
• Bachitherium (early Oligocene) -- A later, more advanced leptomerycid
• Lophiomeryx, Gelocus (late Eocene, early Oligocene) -- The most advanced ruminants yet, called "gelocids" with a more compact and efficient ankle, still smaller side toes, more complex premolars and an almost completely covered mastoid bone, a slightly different lineage split off from this gelocid family in the late Eocene or early Oligocene, eventually giving rise to four families
• Prodremotherium (late Eocene) -- a slightly deer-like ruminant
• Eumeryx (Oligocene) -- a more deer-like ruminant
• Dicrocerus (early Miocene) -- with the first antlers (similar to living muntjacs)
• Acteocemas (Miocene) and several successful Miocene and Pliocene groups that survive today as modern deer -- cervines, white-tails, moose, reindeer
• Climacoceras (very earliest Miocene) -- first giraffids, then Canthumeryx (also very early Miocene), then Paleomeryx (early Miocene), then Palaeotragus (early Miocene) a short-necked giraffid complete with short skin-covered horns
• Samotherium (late Miocene) -- another short-necked giraffe, and then split into Okapia (one species is still alive, the okapi, essentially a living Miocene short-necked giraffe)
• Giraffa (Pliocene) -- the modern long-necked giraffe
• Paracosoryx prodromus (early Miocene, 21 Ma) -- a primitive antilocaprid, probably derived from a North American branch of the bovid lineage
• Merycodus (Miocene) -- with branched permanent horns, led to numerous antilocaprids in the Pliocene, only the pronghorn is still alive

Bovids are known from isolated teeth in the late Oligocene, then from Eotragus, a primitive ancestral mid-Miocene bovid. Protragocerus (Miocene) soon followed. The first sheep (Oioceros) and gazelles (Gazella) are known from the mid-late Miocene (14 Ma), the first cattle (Leptobos, Parabos) from the early Pliocene (5 Ma).

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Cetaceans (whales and dolphins)

Just several years ago, there was still a large gap in the fossil record of the cetaceans. It was thought that they arose from land-dwelling mesonychids (closely related to the artiodactyls) that gradually lost their hind legs and became aquatic. Evolutionary theory predicted that they must have gone through a stage where they were partially aquatic but still had hind legs, but there were no known intermediate fossils. A flurry of recent discoveries from India and Pakistan (the shores of the ancient Tethys Sea) has pretty much filled this gap.

• Eoconodon or similar triisodontine arctocyonids (early Paleocene)
• Microclaenodon (mid-Paleocene)
• Dissacus (mid-Paleocene)
• Hapalodectes or a very similar mesonychid (early Eocene, around 55 Ma)
• Pakicetus (early-mid Eocene, 52 Ma) -- The oldest known whale fossil
• Ambulocetus natans (early-mid Eocene, 50 Ma) -- A recently discovered early whale, with enough of the limbs and vertebrae preserved to see how the early whales moved on land and in the water, this whale had four legs: front legs were stubby, back legs were short but well-developed, with enormous broad feet that stuck out behind like tail flukes, had no true tail flukes, just a long simple tail, size of a sea lion, still had a long snout with no blowhole, probably walked on land like a sea lion, and swam with a seal/otter method of steering with the front feet and propelling with the hind feet -- so, just as predicted, these early whales were much like modern sea lions: they could swim, but they could also still walk on land (Thewissen on whale evolution and Science 1994 below)
• Rodhocetus (mid-Eocene, 46 Ma) -- Another very recent (1993) fossil whale discovery, had hind legs a third smaller than those of A. natans
• Basilosaurus isis, Protocetes, Indocetus ramani -- small-legged whales mid-late Eocene (45-42 Ma)
• Prozeuglodon (late Eocene, 40 Ma) -- another recently discovered whale
• Eocetus, and similar "archeocete whales" of the late Eocene
• Dorudon intermedius -- a late Eocene whale ancestral to modern whales

Picture below is a reconstruction of the skeleton of Ambulocetus natans [ Source: Thewissen J.G.M., Hussain S.T., Arif M. "Fossil evidence for the origin of aquatic locomotion in Archaeocete whales" Science 1994, 263: 210-2 ].

P.D. Gingerich has also done a lot of work on the evolution of whales. See also this Whale Evolution PDF by Gingerich (2004). Some of these whale transitional fossils are recent finds (1980s, 1990s), others have been known for 100 years or more. Here is a list of the "families" of transitionals and when first published or discovered:

• Pakicetidae - include: Pakicetus inachus (1981), Pakicetus attocki (1980), Ichthyolestes pinfoldi (1958), Nalacetus ratimitus (1998)
• Ambulocetidae - include: Ambulocetus natans (1994), Gandakasia potens (1958)
• Remingtoncetidae - include: Remingtoncetus harudiensis (1975), Remingtoncetus sloani (1972), Andrewsiphius kutchensis (1975), Andrewsiphius minor (1975), Dalanistes ahmedi (1995), Attockicetus praecursor (1998)
• Protocetidae - include: Protocetus atavus (1904), Eocetus schweinfurthi (1904), Pappocetus lugardi (1920), Babiacetus mishrai (1998), Rodhocetus kasrani (1994), Takracetus simus (1995), Georgiacetus vogtlensis (1998)
• Basilosaurids - include: Basilosaurus cetoides (1834), Basilosaurus isis (1906), Basilosaurus drazindai (1997), Basiloterus hussaini (1997)
• Dorudontines - include: Dorudon serratus (1845), Dorudon atrox (1906)
• others - Pontogeneus brachyspondylus (1849), Zygorhiza kochii (1847), Saghacetus osiris (1894), Ancalacetus simonsi (1996)

From Thewissen's book The Emergence of Whales: Evolutionary Patterns in the Origin of Cetacea (Springer / Plenum Press, 1998), a quote from the beginning of chapter 14: "Isotopic Approaches to Understanding the Terrestrial-to-Marine Transition of the Earliest Cetaceans" :

"The fossil record is replete with examples of evolutionary transitions between marine and freshwater environments, in both directions. Perhaps the most striking and best documented example of such a transition is the evolution of cetaceans (whales, dolphins, and porpoises) from the extinct group of terrestrial mammals called mesonychians." (J.G.M. Thewissen, editor, The Emergence of Whales, chapter 14)

There are now about 30-40 whale intermediates, and according to the most modern research the common ancestor is seen to be derived from the artiodactyls (Even-Toed ungulates) rather than mesonychids. [ Source: "Whales originated from aquatic artiodactyls in the Eocene epoch of India" by J.G.M. Thewissen, L.N. Cooper, M.T. Clementz, S. Bajpai & B.N. Tiwari in Nature 450, 1190-1194 (20 December 2007) ]. Wikipedia has a good overview of cetacean evolution:

"The traditional theory of cetacean evolution was that whales were related to the mesonychids, an extinct order of carnivorous ungulates (hoofed animals), which looked rather like wolves with hooves and were a sister group of artiodactyls. These animals possessed unusual triangular teeth that are similar to those of whales. For this reason, scientists had long believed that whales evolved from a form of mesonychid." (from the Wikipedia article on "Evolution of Cetaceans")

In the Oligocene (between 34 and 24 Ma), whales split into two lineages:

• Toothed: Agorophius (late Oligocene), Prosqualodon (late Oligocene), Kentriodon (mid-Miocene)
• Baleen (Toothless): Aetiocetus (late Oligocene), Mesocetus (mid-Miocene) lost its teeth, modern baleen whales first appeared in the late Miocene

Video of Nature article Dec 2007 with JGM Thewissen
Video of Whale evolution with Phil Gingerich from PBS Evolution series (2001)

Sirenians (dugongs and manatees)

• Early Eocene -- fragmentary sirenian fossils known from Hungary
• Prorastomus (mid-Eocene) -- A very primitive sirenian with an extremely primitive dental formula (including the ancient fifth premolar that all other mammals lost in the Cretaceous), this could mean sirenians split off from all other mammals very early on, skull is somewhat condylarth-like, had distinctive sirenian ribs
• Protosiren (late Eocene) -- A sirenian with an essentially modern skeleton, though it still had the very primitive dental formula, probably split into the two surviving lineages
• Dugongs: Eotheroides (late Eocene), with a slightly curved snout and small tusks, still with the primitive dental formula
• Halitherium (Oligocene) -- a dugong-ish sirenian with a more curved snout and longer tusks, and then to living dugongs, very curved snout and big tusks
• Manatees: Sirenotherium (early Miocene)
• Potamosiren (late Miocene) -- a manatee-like sirenian with loss of some cheek teeth
• Ribodon (early Pliocene) -- a manatee with continuous tooth replacement, and then the living manatees

Picture to the left is an intermediate Sirenian fossil: a seacow with legs. Reconstructed skeleton of Pezosiren portelli. Length is approximately 7 feet. Gray coloring represents extant fossils, white elements are partly conjectural. [ Source: Domning, D. P. (2001) "The earliest known fully quadrupedal sirenian" Nature 413: 625-627 ]

Elephants Picture to the right is a graphic representation of the elephant (proboscidean) evolutionary lineage. The fossil record of their ancestors goes back 50 million years. [ Source: Miller, Finding Darwin's God, page 96 ] Minchenella or a similar condylarth (late Paleocene) -- Known only from lower jaws Phenacolophus (late Paleocene or early Eocene) Pilgrimella (early Eocene) Moeritherium, Numidotherium, Barytherium (early-mid Eocene) -- A group of three similar very early elephants, pig-sized with stout legs, broad spreading feet and flat hooves, no trunk Paleomastodon, Phiomia (early Oligocene) -- The first "mastodonts," medium-sized animals with a trunk Gomphotherium (early Miocene) -- Basically a large edition of Phiomia Stegotetrabelodon (late Miocene) -- One of the first of the "true" elephants, but still had two long rows of cross-crests, functional premolars, and lower tusks Primelephas (latest Miocene) -- Short lower jaw makes it look like an elephant now Primelephas gomphotheroides (mid-Pliocene) -- A later species that split into three lineages, Loxodonta, Elephas, and Mammuthus In general, after the earliest forms of the three modern genera appeared, they show very smooth, continuous evolution with almost half of the speciation events preserved in fossils. For instance, Carroll (1988) says: "Within the genus Elephas, species demonstrate continuous change over a period of 4.5 million years....the elephants provide excellent evidence of significant morphological change within species, through species within genera, and through genera within a family." (page 575)

Primates (and Hominids)

A little more controversial, here is the outline of the lineage that led to humans (homo sapiens sapiens). For more detailed information see the TalkOrigins Fossil Hominids FAQ.

• Palaechthon, Purgatorius (middle Paleocene) -- Very primitive plesiadapids, to modern eyes they look nothing like primates, being simply pointy-faced, small early mammals with mostly primitive teeth, and claws instead of nails, but they show the first signs of primate-like teeth, lost an incisor and a premolar, and had relatively blunt-cusped, squarish molars
• Cantius (early Eocene) -- One of the first true primates (or "primates of modern aspect"), more advanced than the plesiadapids (more teeth lost, bar behind the eye, grasping hand and foot) and beginning to show some lemur-like arboreal adaptations
• Pelycodus and related species (early Eocene) -- Primitive lemur-like primates
• Amphipithecus, Pondaungia (late Eocene, Burma) -- Very early Old World primates known only from fragments, larger brain, shorter nose, more forward-facing eyes (halfway between plesiadapid eyes and modern ape eyes)
• Parapithecus (early Oligocene) -- The OW monkeys split from the apes around now, this was probably at the start of the OW monkey line, from here the OW monkeys go through Oreopithecus (early Miocene, Kenya) to modern monkey groups of the Miocene and Pliocene
• Propliopithecus, Aegyptopithecus (early Oligocene, Egypt) -- From the same time as Parapithecus, but probably at the beginning of the ape lineage, first ape characters (deep jaw, 2 premolars, 5-cusped teeth)
• Aegyptopithecus (early-mid Oligocene, Egypt) -- Slightly later anthropoid (ape/hominid) with more ape features, was a fruit-eating runner/climber, larger, with a rounder brain and shorter face
• Proconsul africanus (early Miocene, Kenya) -- A sexually dimorphic, fruit-eating, arboreal quadruped probably ancestral to all the later apes and humans, mosaic of ape-like and primitive features, ape-like elbow, shoulder and feet, monkey-like wrist, gibbon-like lumbar vertebrae
• Limnopithecus (early Miocene, Africa) -- A later ape probably ancestral to gibbons
• Dryopithecus (mid-Miocene) -- A later ape probably ancestral to the great apes and humans, at this point Africa and Asia connected via Arabia, and the non-gibbon apes divided into two lines
• Sivapithecus (e.g. "Gigantopithecus" and "Ramapithecus" mid-Miocene) -- moved to Asia and gave rise to the orangutan
• Kenyapithecus (mid-Miocene, about 16 Ma) -- stayed in Africa and gave rise to the African great apes and humans
• Australopithecus ramidus (mid-Pliocene, 4.4 Ma) -- A recently discovered very early hominid (or early chimp), from just after the split with the apes, possibly bipedal (only the skull was found), teeth both apelike and humanlike
• Australopithecus afarensis (late Pliocene, 3.9 Ma) -- some excellent fossils ("Lucy") make clear that this was fully bipedal and definitely a hominid, an extremely ape-like hominid, only four feet tall, still had an ape-sized brain of just 375-500 cc (finally answering the question of which came first, large brain or bipedality) and ape-like teeth
• Australopithecus africanus (later Pliocene, 3.0 Ma) -- the more slender lineage, up to five feet tall, with slightly larger brain (430-550 cc) and smaller incisors, teeth gradually became more and more like Homo teeth, these hominids are almost perfect ape-human intermediates, now pretty clear that the slender australopithecines led to the first Homo species
• Homo habilis (latest Pliocene/earliest Pleistocene, 2.5 Ma) -- Straddles the boundary between australopithecines and humans, sometimes lumped with the australopithecines, about five feet tall, face still primitive but projects less, molars smaller, brain 500-800 cc, overlapping australopithecines at the low end and early Homo erectus at the high end, perhaps capable of rudimentary speech, first clumsy stone tools
• Homo erectus (e.g. "Java Man," "Peking Man," "Heidelberg Man," Pleist, 1.8 Ma) -- Looking much more human now with a brain of 775-1225 cc, but still has thick brow ridges and no chin, spread out of Africa and across Europe and Asia, good tools, first fire
• Archaic Homo sapiens (Pleist, 500,000 years ago) -- These first primitive humans were perfectly intermediate between H. erectus and modern humans, with a brain of 1200 cc and less robust skeleton and teeth, over the next 300,000 years brain gradually increased, molars got still smaller, skeleton less muscular, clearly arose from H. erectus but there are continuing arguments about where this happened
• Homo sapiens sapiens (e.g. "Cro-magnons" late Pleist, 40,000 years ago) -- All modern humans, average brain size 1350 cc, in Europe gradually supplanted the Neandertals

One famous offshoot group, the Neandertals (other spelling is Neanderthals), developed in Europe about 500,000 years ago. They are considered to be the same species as us, but a different subspecies, Homo sapiens neanderthalensis. They were more muscular, with a slightly larger brain of 1450 cc, a distinctive brow ridge, and differently shaped throat (possibly limiting their language). They are known to have buried their dead.

"The current fossil, molecular, and archeological evidence strongly supports the specific distinction of the Neanderthals from early and modern H. sapiens. The Neanderthal lineage first appeared some 500,000 years ago, according to the molecular clock, and the fossil record suggests that the 'Steinheim group' reflects a basal Neanderthal anatomical condition. This group exploited the colder conditions of an Ice Age Europe, their survival in this region enabled by the increasing development of their 'cold exaptations.' This initial split between these two groups was not based on a greater ability to withstand Ice Age conditions (though ultimately this must have pushed them farther apart over time), but occurred for some other reason, perhaps cultural....The molecular evidence shows that Neanderthal mtDNA [mitochondrial DNA] is significantly different not only from modern humans, but also from homo sapiens dating back to 40,000 years ago....By 30,000 years ago, increased competition, increased mortality rates, and a declining birthrate sent the Neanderthals in a downward spiral to extinction. There is no need to appeal to an argument of 'prehistoric genocide' to explain their final disappearance from the earth some 27,000 years ago." (from Bones, Stones, and Molecules by Cameron / Groves [Elsevier Academic Press, 2004], page 283-284)

Adapted from the detailed TalkOrigins "Transitional Vertebrate Fossils FAQ" (1994, 1997) by Kathleen Hunt, and updated from the book Evolution: What the Fossils Say and Why It Matters by paleontologist / geologist Donald R. Prothero (Columbia Univ Press, 2007).

Reply to a Catholic Creationist (updated December 2008)

See also Catholic Views on Evolution and Creation

Picture: classic Christian Fish symbol for Jesus Christ, Son of God, Savior (in Greek), and Darwin Fish mockery: Darwin, Son of Satan, Send us to hell?

Now I would like to answer a few objections from a Catholic creationist I received in Email. The creationist states:

<< I am no scientist, nor do I wish to argue "science" with you. I am a Christian and I believe Revelation over science. Truth cannot contradict truth. Therefore, if science contradicts the Holy Writ, I do not believe science. My only point in referring you to Dr. Humphries was that there are alternate theories. When most of the bishops were Arians, Athanasius was still right. If you wish to deform the Text of which God Himself is the Author in order to accomodate man-made theories, that is your perogative. Only, such a conviction on your part demands a greater conviction than my own. >>

This shows an appalling lack of appreciation for modern science. It's not a matter of "deforming" the Bible, it's a matter how we understand the first chapters of Genesis. There are many plausible views held by Christian scholars. The modern Popes (i.e. Pius XII, JPII, Benedict XVI) have argued a theistic evolutionary framework is compatible with the Catholic faith (along with other scientists who are Catholic -- physicist Fr. Stanley Jaki, astronomer Fr. George Coyne, other members of the Pontifical Academy of Sciences, etc). I find most creationists who reject evolution wholesale really know nothing of the science that's behind the theory. It seems your typical creationist has read a few creationist books or culled objections from a few creationist web sites, but rarely if ever do they read a modern book of science (biology, paleontology, geology, etc) by an evolutionist (which are basically all professional scientists). That's as fair as reading anti-Catholic fundamentalist literature to arrive at an accurate understanding of the Catholic faith. What one needs to do is examine the real science and what the evolutionists have to say for themselves. What is the evidence they present? I have done that (summarized above), and find it very convincing. Truth cannot contradict truth, and if the evidence points in the direction of an old earth and evolution, we should be committed to that truth wherever its found. Science is not about "proof" or absolutes, but a scientific theory advances and becomes more carefully understood as new evidence and research is found.

Pope John Paul II in his 1996 address to the Pontifical Academy of Sciences declared evolution to be "more than a hypothesis" and that a significant argument in favor of the theory is that it has been progressively accepted by researchers following independently conducted scientific work in various fields. As the Catechism states:

"...the origins of the world and of man has been the object of many scientific studies which have splendidly enriched our knowledge of the age and dimensions of the cosmos, the development of life-forms and the appearance of man. These discoveries invite us to even greater admiration for the greatness of the Creator..." (paragraph 283)

Neither the Catechism nor the Pope suggest we should abandon modern science and turn to fundamentalist "creation scientists" who have no credibility in the scientific world. Humphreys is a Protestant young-earther who is not taken seriously by anyone in conventional science. Why a Catholic would refer to him I do not know. 

<< My unsolicited advice to you: Do not throw caution to the wind, and show some moderation. These are only theories -- theories which contradict divine revelation. Listen, then, to the words of Saint Augustine...Augustine does not say that we should reconcile our Scriptures with their theories, but that we must reconcile their theories to our Scriptures. If their theories are unreconcilable with our Scriptures, then believe the theories to be false, not the Scriptures! Stop deforming the Sacred Writ to conform to "scientific" theories, and start making scientific theories conform to the Holy Scriptures. That is what Dr. Humphries the Fundamentalist has done. It is time we Catholics did the same. >>

This shows a misunderstanding of what a theory is -- macroevolution is considered both a fact and a theory, just as gravity. Macroevolution happened (fact) and we know that from the lines of evidence presented above, but how it precisely happened (theory) and does happen are debated among scientists. A scientific theory is defined as above a mere hypothesis (i.e. evolution is "more than a hypothesis") and includes, incorporates, unites, and explains observable facts and laws. Since Genesis can be plausibly interpreted a number of ways, theistic evolution does not contradict divine revelation.

<< If the First Adam is a myth, so is the Second Adam. Think about that long and hard....If a scientist were to commit sacrilege and examine a consecrated Host, what do you think he would tell you about it? Yet you know he is absolutely, irrefutably wrong. Why, then, is he so infallibly right when it comes to the creation of the Universe and of man? Has not God told you just as plainly -- just as literally! -- of how He miraculously created the Universe and man, as He has told you of the miracle of Transubstantiation? Science refutes them both. Why, then, do you believe Him on the one and doubt Him on the other? Because of science? What kind of faith is that? And where is the consistency? >>

A couple of objections are made here. First of all, Adam would not be a "myth" since evolutionary theory would seem to trace our ancestors back to an original man and woman (let's call them "Adam" and "Eve" as Genesis does^* [see note below]). Whether Adam received his body through an evolutionary development is a matter for science to determine (see the large TalkOrigins Fossil Hominids site by Jim Foley). God would create the soul in that first man and woman. So I don't deny there was an original "Adam" or first man who had his soul created by God nor a Fall of those first human parents as the Catholic faith defines and explains (see my long article on Original Sin). I simply do not interpret all of Genesis literally (e.g. the talking snake or serpent in Genesis 3). Though I'll admit there are seemingly good theological objections to the evolution of man that need to be answered, there are no good scientific ones.

The above also confuses science with faith. We don't learn from science that the Eucharist is the body and blood of Christ (i.e. transubstantiation), we take that on faith based on revelation (Scripture and Tradition) and the authority of the Catholic Church who interprets that revelation. Science would have nothing to say about that, nor about miracles in general. So here we're confusing faith and divinely revealed doctrine with science. Also, science is not about "absolutes" or "proof" but improves as we move forward in research, discoveries, and technology. Scientists themselves are certainly not infallible, they have made many mistakes. But it is once again science and other scientists using the "scientific method" that corrects them.

The theory of evolution is the best we have from modern science today that explains the development of plants, animals, and man. If one rejects evolution wholesale, what comprehensive scientific theory of "creationism" would one substitute in its place that explains the evidence and data we find from the natural history of our world?

see also Part 1: The Scientific Evidence for an Old Earth

^*note: So I don't misrepresent the science, here is what the latest genetics evidence tells us about the real "Adam" and "Eve":

"....the fact that a single ancestor gave rise to all of the diversity present today does not mean that this was the only person alive at the time -- only that descendent lineages of the other people alive at the same time died out.....we are all the recent descendents of a single woman who lived in Africa less than 150,000 years ago. This result begs the question of where Eve actually lived -- where in Africa was the Garden of Eden? In one sense this is a red herring, since we know that there were many women alive all over Africa at this time.....the root of the male family tree was placed in Africa -- exactly the same answer that mtDNA had given us for women. The shocker came when a date was estimated for the age of the oldest common ancestor. This man, from whom all men alive today ultimately derive their Y-chromosomes, lived 59,000 years ago. More than 80,000 years after that estimated for Eve! Did Adam and Eve never meet? No they didn't, but the reason is fairly complicated....." (The Journey of Man: A Genetic Odyssey by Spencer Wells [Random House Paperback, 2003], pages 32, 40, 54)

Author Spencer Wells also comments in an interview for Princeton University Press:

How does the genetic Adam relate to the Adam of the Bible?

"It's interesting that both genetics and the Bible show that there is a common origin of humanity. According to genetic data we come from a single male ancestor. In the Bible too it is mentioned that there is a single male Adam and single female, Eve. I don't equate our results one-to-one with the biblical story, of course, because if you count back through the generations described in the Bible, Adam should have existed in 4004 BC, and our Adam existed 60,000 years ago. Also, our Adam and Eve weren't the only people alive at the time, just the lucky ones who left descendants down to the present day. But it is nice to know that we arrive at the same general conclusion: we're all related." (from an interview with geneticist Spencer Wells)

Possible Scenario (updated December 2008)

The following is a possible scenario how Adam/Eve could be reconciled with a population of early hominids/humans.

<< I just quoted decrees from the Council of Trent which are binding on all Catholics, which clearly state that Adam was "the first man", and "the whole human race" is descended from him. >>

So, how can we combine the evidence present in the world that God created with the given interpretation of God's word?

I start from the assumption that a "human" has a human soul, whereas a non-human does not. I also assume that a human soul is immaterial and its presence has no visible material effect, such as a change in DNA.

Here is one possibility. Start with a population of unsouled upright apes, call then "huma" because they are not quite human yet. God puts human souls into two of them, Adam and Eve (or puts a soul into one male, Adam, and clones a female, Eve, from him e.g. Genesis 2:21-23 "Eve from Adam"). Adding a soul does not change the original huma DNA at all. We now have a pair of humans, Adam and Eve, in a population of huma. Adam and Eve only mate with each other and have human children with souls. In order to avoid incest the children need to find mates outside their immediate family so they mate with some of the huma. This is possible because their DNA is compatible with huma DNA; the mating is open to the possibility of creating life.

God gives a soul to all hybrid human/huma offspring so all the children with at least one human parent are also human, i.e. they have a soul. Because only the descendants of the initial pair mate with huma, all the children from such matings are descended from both Adam and Eve since they will have both as grandparents, great-grandparents etc.

Over time the number of humans increases and the number of huma declines until the huma are extinct.

In scientific terms we have a large interbreeding population, as shown by the current level of genetic diversity in humans. Theologically all humans are descended from that first ensouled pair, as required by the Council or Trent.

You may or may not accept this particular scenario, but it shows that there is a way to reconcile revelation and science. It also avoids the problem of incest among Adam and Eve's children.

Rossum (a buddhist from Catholic Answers forums)

For more see also Adam, Eve, and the Hominid Fossil Record

also Hominization: Origin of Mankind, and a Story of the Fall

BIBLIOGRAPHY (updated July 2010)

ORIGIN OF LIFE AND EVOLUTION OF THE "BIG PICTURE"

• Why Evolution is True by Jerry A. Coyne (Penguin Books, 2009)
• The Evolution Revolution: design without intelligence by Ken McNamara & John Long (Melbourne Univ Press, 2007)
• Evolution edited by In-Young Chang and Jennifer Curry (H.W. Wilson, 2006)
• Genesis: The Scientific Quest for Life's Origin by Robert M. Hazen (Joseph Henry Press, 2005)
• Evolution: The Remarkable History of a Scientific Theory by Edward J. Larson (Modern Library, 2004)
• Life's Solution: Inevitable Humans in a Lonely Universe by Simon Conway Morris (Cambridge Univ Press, 2003)
• Aquagenesis: the origin and evolution of life in the sea by Richard Ellis (Viking, 2001)
• Evolution: The Triumph of an Idea by Carl Zimmer (HarperCollins, 2001)
• A Walk Through Time: from stardust to us : the evolution of life on earth by Liebes, Sahtouris, Swimme (Wiley, 1998)
• The Origin of Species by Charles Darwin (Signet Classic, 2003, orig 1859)

EVOLUTION, PHILOSOPHY, AND CHRISTIANITY (CATHOLICISM)

• Creation or Evolution? Do We Have to Choose? by Denis Alexander (Monarch Books, 2008)
• Creation and Evolution: A Conference with Pope Benedict XVI (Ignatius Press, 2008)
• Chance or Purpose? Creation, Evolution and a Rational Faith by Cardinal Christoph Schonborn (Ignatius Press, 2007)
• Intelligent Design: William Dembski and Michael Ruse in Dialogue (Fortress Press, 2007)
• Debating Design: From Darwin to DNA edited by William Dembski and Michael Ruse (Cambridge Univ Press, 2004)
• Perspectives on an Evolving Creation edited by Keith Miller (Eerdmans, 2003)
• Responses to 101 Questions on God and Evolution by John F. Haught (Paulist Press, 2001)
• Intelligent Design: The Bridge Between Science and Theology by William Dembski (Intervarsity Press, 1999)
• Finding Darwin's God: A Scientist's Search for Common Ground Between God and Evolution by Kenneth R. Miller (HarperCollins, 1999)
• Only a Theory: Evolution and the Battle for America's Soul by Kenneth R. Miller (Viking Adult, 2008)
• Darwin's Forgotten Defenders: The Encounter Between Evangelical Theology and Evolutionary Thought by David N. Livingstone (Eerdmans, 1987)
• The Post-Darwinian Controversies by James R. Moore (Cambridge Univ Press, 1981, 1979)

INVERTEBRATE EVOLUTION

• An Introduction to the Invertebrates by Janet Moore (Cambridge Univ Press, 2006)
• On the Origin of Phyla by James W. Valentine (Univ of Chicago Press, 2004)
• Invertebrate Palaeontology and Evolution by E.N.K. Clarkson (Blackwell Science, 1998)

EVOLUTION OF ARTHROPODS (INCLUDING INSECTS)

• Evolution of the Insects by David Grimaldi and Michael S. Engel (Cambridge Univ Press, 2005)
• Crustacea and Arthropod Relationships edited by Stefan Koenemann and Ronald A. Jenner (Taylor & Francis, 2005)
• Arthropod Fossils and Phylogeny edited by Gregory D. Edgecombe (Columbia Univ Press, 1998)
• The Evolution of Insects by Philip S. Callahan (Holiday House, 1972)

VERTEBRATE EVOLUTION

• Vertebrate Paleontology by Michael J. Benton (Wiley-Blackwell, 2004, 3rd edition)
• Patterns and Processes of Vertebrate Evolution by Robert L. Carroll (Cambridge Univ Press, 1997)
• Vertebrate Paleontology and Evolution by Robert L. Carroll (Freeman, 1988)

EVOLUTION OF TETRAPODS (FOUR-LEGGED "AMPHIBIANS")

• Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body by Neil Shubin (Pantheon, 2008)
• Gaining Ground: the origin and evolution of tetrapods by Jennifer A. Clack (Indiana Univ Press, 2002)
• At the Water's Edge: Fish with Fingers, Whales with Legs, and How Life Came Ashore but Then Went Back to Sea by Carl Zimmer (Free Press, 1999)

EVOLUTION OF MAMMALS (INCLUDING WHALES)

• The Rise of Placental Mammals: origins and relationships of the Major Extant Clades edited by Kenneth D. Rose and J. David Archibald (Johns Hopkins Univ Press, 2005)
• The Origin and Evolution of Mammals by T.S. Kemp (Oxford Univ Press, 2005)
• Morphological Change in Quaternary Mammals of North America edited by Robert A. Martin and Anthony D. Barnosky (Cambridge Univ Press, 2005)
• Beasts of Eden: walking whales, dawn horses, and other enigmas of mammal evolution by David Rains Wallace (Univ of CA Press, 2004)
• Mammals from the Age of Dinosaurs: origins, evolution, and structure by Zofia Kielan-Jaworowska, Richard L. Cifelli, and Zhe-Xi Luo (Columbia Univ Press, 2004)
• Late Cretaceous and Cenozoic Mammals of North America -- Biostratigraphy and Geochronology edited by Michael O. Woodburne (Univ of CA Press, 2004)
• Horns, Tusks, and Flippers: the evolution of hoofed mammals by Donald R. Prothero and Robert M. Schoch (Johns Hopkins Univ Press, 2002)
• The Emergence of Whales: evolutionary patterns in the origin of Cetacea edited by J.G.M. Thewissen (Plenum Press, 1998)
• Fossil Horses: Systematics, Paleobiology, and Evolution of the Family Equidae by Bruce J. MacFadden (Cambridge Univ Press, 1994)
• The Evolution of Perissodactyls by Donald R. Prothero and Robert M. Schoch, ed. (Oxford Univ Press, 1989)

EVOLUTION OF BIRDS

• The Inner Bird: anatomy and evolution by Gary W. Kaiser (Vancouver: UBC Press, 2007)
• Dinosaurs of the Air : the evolution and loss of flight in dinosaurs and birds by Gregory S. Paul (Johns Hopkins Univ Press, 2002) 
• Taking Wing : Archaeopteryx and the evolution of bird flight by Pat Shipman (Simon & Schuster, 1998)
• The Rise of Birds : 225 million years of evolution by Sankar Chatterjee (Johns Hopkins Univ Press, 1997)
• The Origin and Evolution of Birds by Alan Feduccia (Yale Univ Press, 1996)

HUMAN EVOLUTION

• The First Human: The Race to Discover our Earliest Ancestors by Ann Gibbons (Doubleday, 2006)
• Bones, Stones, and Molecules: "Out of Africa" and Human Origins by David W. Cameron and Colin P. Groves (Elsevier, 2004)
• The Journey of Man: A Genetic Odyssey by Spencer Wells (Random House paperback, 2003)
• The Human Fossil Record (volume 1, forthcoming in 4 volumes) by Schwartz / Tattersall (John Wiley and Sons, 2002)
• Extinct Humans by Ian Tattersall and Jeffrey H. Schwartz (Westview Press / Perseus Books, 2000)
• The Cambridge Encyclopedia of Human Evolution edited by Steve Jones, Robert Martin, David Pilbeam (Cambridge Univ Press, 1992)
• The Search for Eve by Michael H. Brown (Harper and Row, 1990)
• Guide to Fossil Man by Michael H. Day (Univ of Chicago Press, 1986, 4th edition)
• Lucy: The Beginnings of Humankind by Donald C. Johanson and Maitland A. Edey (Simon and Schuster, 1981)

see also Part 1: The Scientific Evidence for an Old Earth

International Theological Commission on Creation and Evolution

The Talk Origins Age of the Earth FAQs
http://www.talkorigins.org/origins/faqs-youngearth.html

The Talk Origins Evolution FAQs
http://www.talkorigins.org/origins/faqs-evolution.html

The Full Transcript and Audio of the Firing Line 1997 Creation-Evolution Debate

P