How old is the earth

The fundamental unity of life

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. Some of the macroscopic properties that characterize all of life are (1) replication, (2) heritability (characteristics of descendents are correlated with those of ancestors), (3) catalysis, and (4) energy utilization (metabolism). At a very minimum, these four functions are required to generate a physical historical process that can be described by a phylogenetic tree.

If every living species descended from an original species that had these four obligate functions, then all living species today should necessarily have these functions (a somewhat trivial conclusion). Most importantly, however, all modern species should have inherited the structures that perform these functions. Thus, 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.

Confirmation:
The structures that all known organisms use to perform these four basic processes are all quite similar, in spite of the odds. All known living things use polymers to perform these four basic functions. Organic chemists have synthesized hundreds of different polymers, yet the only ones used by life, irrespective of species, are polynucleotides, polypeptides, and polysaccharides. Regardless of the species, the DNA, RNA and proteins used in known living systems all have the same chirality, even though there are at least two chemically equivalent choices of chirality for each of these molecules. For example, RNA has four chiral centers in its ribose ring, which means that it has 16 possible stereoisomers—but only one of these stereoisomers is found in the RNA of known living organisms.

Ten years after the publication of The Origin of Species, nucleic acids were first isolated by Friedrich Miescher in 1869. It took another 75 years after this discovery before DNA was identified as the genetic material of life (Avery et al. 1944). It is quite conceivable that we could have found a different genetic material for each species. In fact, it is still possible that newly identified species might have unknown genetic materials. However, 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. The DNA used by living organisms is synthesized using only four nucleosides (deoxyadenosine, deoxythymidine, deoxycytidine, and deoxyguanosine) out of the dozens known (at least 99 occur naturally and many more have been artificially synthesized) (Rozenski et al. 1999; Voet and Voet 1995, p. 969).

In order to perform the functions necessary for life, organisms must catalyze chemical reactions. In all known organisms, enzymatic catalysis is based on the abilities provided by protein molecules (and in relatively rare, yet important, cases by RNA molecules). There are over 320 naturally occurring amino acids known (Voet and Voet 1995, p. 69; Garavelli et al. 2001); however, the protein molecules used by all known living organisms are constructed with the same subset of 22 amino acids.

There must be a mechanism for transmitting information from the genetic material to the catalytic material; all known organisms, with extremely rare exceptions, use the same genetic code for this. The few known exceptions are, nevertheless, simple and minor variations from the "universal" genetic code (see Figure 1.1.1) (Lehman 2001; Voet and Voet 1995, p. 967), exactly as predicted by evolutionary biologists, if common descent were correct, years before the genetic code was solved (Brenner 1957; Crick et al. 1961; Hinegardner and Engelberg 1963; Judson 1996, p. 280-281).

All known organisms use extremely similar, if not the same, metabolic pathways and metabolic enzymes in processing energy-containing molecules. For example, the fundamental metabolic systems in living organisms are glycolysis, the citric acid cycle, and oxidative phosphorylation. In all eukaryotes and in the majority of prokaryotes, glycolysis is performed in the same ten steps, in the same order, using the same ten enzymes (Voet and Voet 1995, p. 445). In addition, the most basic unit of energy storage, the adenosine triphosphate molecule (ATP), is the same in all species that have been studied.

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A nested hierarchy of species
As seen from the phylogeny in Figure 1, the predicted pattern of organisms at any given point in time can be described as "groups within groups," otherwise known as a nested hierarchy. The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes. Common descent is a genetic process in which the state of the present generation/individual is dependent only upon genetic changes that have occurred since the most recent ancestral population/individual. Therefore, gradual evolution from common ancestors must conform to the mathematics of Markov processes and Markov chains. Using Markovian mathematics, it can be rigorously proven that branching Markovian replicating systems produce nested hierarchies (Givnish and Sytsma 1997; Harris 1989; Norris 1997). For these reasons, biologists routinely use branching Markov chains to effectively model evolutionary processes, including complex genetic processes, the temporal distributions of surnames in populations (Galton and Watson 1874), and the behavior of pathogens in epidemics.

The nested hierarchical organization of species contrasts sharply with other possible biological patterns, such as the continuum of "the great chain of being" and the continuums predicted by Lamarck's theory of organic progression (Darwin 1872, pp. 552-553; Futuyma 1998, pp. 88-92). Mere similarity between organisms is not enough to support macroevolution; the nested classification pattern required by a gradual evolutionary process, such as universal common descent, is much more specific than simple similarity. Real world examples that cannot be objectively classified in nested hierarchies are the elementary particles (which are described by quantum chromodynamics), the elements (whose organization is described by quantum mechanics and illustrated by the periodic table), the planets in our Solar System, books in a library, or specially designed objects like buildings, furniture, cars, etc.

Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between "subjective" and "objective" is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically—perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999). Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese.

The difference between classifying cars and classifying languages lies in the fact that, with cars, certain characters (for example, color or manufacturer) must be considered more important than other characters in order for the classification to work. Which types of car characters are more important depends upon the personal preference of the individual who is performing the classification. In other words, certain types of characters must be weighted subjectively in order to classify cars in nested hierarchies; cars do not fall into natural, unique, objective nested hierarchies.

Because of these facts, a cladistic analysis of cars will not produce a unique, consistent, well-supported tree that displays nested hierarchies. A cladistic analysis of cars (or, alternatively, a cladistic analysis of imaginary organisms with randomly assigned characters) will of course result in a phylogeny, but there will be a very large number of other phylogenies, many of them with very different topologies, that are as well-supported by the same data. In contrast, a cladistic analysis of organisms or languages will generally result in a well-supported nested hierarchy, without arbitrarily weighting certain characters (Ringe 1999). Cladistic analysis of a true genealogical process produces one or relatively few phylogenetic trees that are much more well-supported by the data than the other possible trees.

The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).

There is one caveat to consider with this prediction: if rates of evolution are fast, then cladistic information can be lost over time since it would be essentially randomized. The faster the rate, the less time needed to obliterate information about the historical branching pattern of evolution. Slowly evolving characters let us see farther back into time; faster evolving characters restrict that view to more recent events. If the rate of evolution for a certain character is extremely slow, a nested hierarchy will be observed for that character only for very distantly related taxa. However, "rate of evolution" vs. "time since divergence" is relative; if common descent is true, then in some time frame we will always be able to observe a nested hierarchy for any given character. Furthermore, we know empirically that different characters evolve at different rates (e.g. some genes have higher background mutation rates than others). Thus, if common descent is true, we should observe nested hierarchies over a broad range of time at various biological levels.

Therefore, since common descent is a genealogical process, common descent should produce organisms that can be organized into objective nested hierarchies. Equivalently, we predict that, in general, cladistic analyses of organisms should produce phylogenies that have large, statistically significant values of hierarchical structure (in standard scientific practice, a result with "high statistical significance" is a result that has a 1% probability or less of occurring by chance [P < 0.01]). As a representation of universal common descent, the universal tree of life should have very high, very significant hierarchical structure and phylogenetic signal.

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Convergence of independent phylogenies
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 (Penny et al. 1982; Penny et al. 1991). Independently derived phylogenetic trees of all organisms should match each other with a high degree of statistical significance.

Confirmation:
Well-determined phylogenetic trees inferred from the independent evidence of morphology and molecular sequences match with an extremely high degree of statistical significance. Many genes with very basic cellular functions are ubiquitous—they occur in the genomes of most or all organisms. An oft-cited example is the cytochrome c gene. Since all eukaryotes contain the gene for this essential protein, neither its presence nor its function correlates with organismal morphology. Additionally, because of the fact of DNA coding redundancy, parts of certain DNA sequences have absolutely no correlation with phenotype (e.g. certain introns or the four-fold degenerate third-base position of most DNA codons). Due to these two aspects of certain DNA sequences, ubiquity and redundancy, DNA sequences can be carefully chosen that constitute completely independent data from morphology. (See point 17 and 18 for more background about the molecular sequence evidence and for more detail about how it is independent of morphology.) The degree of phylogenetic congruence between these independent data sets is nothing short of incredible.

In science, independent measurements of theoretical values are never exact. When inferring any value (such as a physical constant like the charge of the electron, the mass of the proton, or the speed of light) some error always exists in the measurement, and all independent measurements are incongruent to some extent. Of course, the true value of something is never known for certain in science—all we have are measurements that we hope approximate the true value. Scientifically, then, the important relevant questions are "When comparing two measurements, how much of a discrepancy does it take to be a problem?" and "How close must the measurements be in order to give a strong confirmation?" Scientists answer these questions quantitatively with probability and statistics (Box 1978; Fisher 1990; Wadsworth 1997). To be scientifically rigorous we require statistical significance. Some measurements of a given value match with statistical significance (good), and some do not (bad), even though no measurements match exactly (reality).

So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 1038 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree (see Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies (for consensus phylogenies from pre-molecular studies see Carter 1954, Figure 1, p. 13; Dodson 1960, Figures 43, p. 125, and Figure 50, p. 150; Osborn 1918, Figure 42, p. 161; Haeckel 1898, p. 55; Gregory 1951, Fig. opposite title page; for phylogenies from the early cytochrome c studies see McLaughlin and Dayhoff 1973; Dickerson and Timkovich 1975, pp. 438-439). Speaking quantitatively, independent morphological and molecular measurements such as these have determined the standard phylogenetic tree, as shown in Figure 1, to better than 38 decimal places. This phenomenal corroboration of universal common descent is referred to as the "twin nested hierarchy." This term is something of a misnomer, however, since there are in reality multiple nested hierarchies, independently determined from many sources of data.

When two independently determined trees mismatch by some branches, they are called "incongruent." In general, phylogenetic trees may be very incongruent and still match with an extremely high degree of statistical significance (Hendy et al. 1984; Penny et al. 1982; Penny and Hendy 1986; Steel and Penny 1993). Even for a phylogeny with a small number of organisms, the total number of possible trees is extremely large. For example, there are about a thousand different possible phylogenies for only six organisms; for nine organisms, there are millions of possible phylogenies; for 12 organisms, there are nearly 14 trillion different possible phylogenies (Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). Thus, the probability of finding two similar trees by chance via two independent methods is extremely small in most cases. In fact, two different trees of 16 organisms that mismatch by as many as 10 branches still match with high statistical significance (Hendy et al. 1984, Table 4; Steel and Penny 1993). For more information on the statistical significance of trees that do not match exactly, see "Statistics of Incongruent Phylogenetic Trees".

The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al. 2002; Penny et al. 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:

"Biologists seem to seek the 'The One Tree' and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al. 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 106." (Penny and Hendy 1986, p. 414)


For a more realistic universal phylogenetic tree with dozens of taxa including all known phyla, the accuracy is better by many orders of magnitude. To put the significance of this incredible confirmation in perspective, consider the modern theory of gravity. Both Newton's Theory of Universal Gravitation and Einstein's General Theory of Relativity rely upon a fundamental physical constant, G, the gravitational constant. If these theories of gravity are correct, independent methods should determine similar values for G. However, to date, very precise independent measurements of the gravitational constant G disagree by nearly 1% (Kestenbaum 1998; Quinn 2000). Here is how David Kestenbaum describes the current scientific status of the theory of gravity, as reported in the prestigious journal Science:

"While the charge of the electron is known to seven decimal places, physicists lose track of G after only the third. For some, that's an embarrassment. 'It grates on me like a burr in the saddle,' says Alvin Sanders, a physicist at the University of Virginia in Charlottesville. Over the past few decades, he and a handful of other physicists have dedicated themselves to measuring G more accurately. To their dismay, they've come up with wildly different values. 'You might say we've had negative progress,' says Barry Taylor, a physicist at the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland. ...

'Nobody understands it [the far-out results of the PTB, the German standards lab in Braunschweig],' says Meyer. 'They must have made an unbelievable mistake, but we cannot find it.' ... says Terry Quinn, 'we may just have to throw the PTB result out.'" (Kestenbaum 1998)


Over two years later, the same Terry Quinn (of the International Bureau of Weights and Measures [BIPM] in Sèvres, France) summarized the situation in a review for the journal Nature:

"The current interest in measuring G was stimulated by the publication in 1996 of a value for G that differed by 0.6% from the accepted value given in the previous 1986 CODATA report. To take account of this, the 1998 CODATA report recommends a value for G ... with an uncertainty of 0.15%, some ten times worse than in 1986. Whereas the other fundamental constants were more accurately known in 1998 than in 1986, the uncertainty in G increased dramatically. The G community appeared to be going backwards rather than forwards." (Quinn 2000)


Nevertheless, a precision of just under 1% is still pretty good; it is not enough, at this point, to cause us to cast much doubt upon the validity and usefulness of modern theories of gravity. However, if tests of the theory of common descent performed that poorly, different phylogenetic trees, as shown in Figure 1, would have to differ by 18 of the 30 branches! In their quest for scientific perfection, some biologists are rightly rankled at the obvious discrepancies between some phylogenetic trees (Gura 2000; Patterson et al. 1993; Maley and Marshall 1998). However, as illustrated in Figure 1, the standard phylogenetic tree is known to 38 decimal places, which is a much greater precision 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.

Furthermore, if common descent is true, we expect that including more data in phylogenetic analyses will increase the correspondence between phylogenetic trees. As explained in the phylogenetic caveats sidebar, gene trees are not equivalent to species trees (Avise and Wollenberg 1997; Fitch 1970; Hudson 1992; Nichols 2001; Wu 1991). Genetics and heredity are stochastic (i.e. probabilistic) processes, and consequently we expect that phylogenies constructed with single genes will be partially incongruent. However, including multiple independent genes in a phylogenetic analysis should circumvent this difficulty; in general more than five independent genes are needed to accurately reconstruct a species phylogeny (Wu 1991). Phylogenetic trees constructed with multiple genes should thus be more accurate than those constructed with single genes, and indeed combined gene trees are more congruent (Baldauf et al. 2000; Hedges 1994; Hedges and Poling 1999; Penny et al. 1982).

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Intermediate and transitional forms: the possible morphologies of predicted common ancestors
Example 1: reptile-birds
Example 2: reptile-mammals
Example 3: ape-humans
Example 4: legged whales
Example 5: legged seacows
All 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. Similarly, 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, both past and present, fit in that phylogeny uniquely. Since the standard phylogenetic tree is the best approximation of the true historical phylogeny, we expect that all fossilized animals should conform to the standard phylogenetic tree within the error of our scientific methods.

Every node shared between two branches in a phylogeny or cladogram represents a predicted common ancestor; thus there are ~29 common ancestors predicted from the tree shown in Figure 1. Our standard tree shows that the bird grouping is most closely related to the reptilian grouping, with a node linking the two (A in Figure 1); thus we predict the possibility of finding fossil intermediates between birds and reptiles. The same reasoning applies to mammals and reptiles (B in Figure 1). However, we predict that we should never find fossil intermediates between birds and mammals.

It should be pointed out that there is no requirement for intermediate organisms to go extinct. In fact, all living organisms can be thought of as intermediate between adjacent taxa in a phylogenetic tree. For instance, modern reptiles are intermediate between amphibians and mammals, and reptiles are also intermediate between amphibians and birds. As far as macroevolutionary predictions of morphology are concerned, this point is trivial, as it is essentially just a restatement of the concept of a nested hierarchy.

However, a phylogenetic tree does make significant predictions about the morphology of intermediates which no longer exist or which have yet to be discovered. Each predicted common ancestor has a set of explicitly specified morphological characteristics, based on each of the most common derived characters of its descendants and based upon the transitions that must have occurred to transform one taxa into another (Cunningham et al. 1998; Futuyma 1998, pp. 107-108). From the knowledge of avian and reptilian morphology, it is possible to predict some of the characteristics that a reptile-bird intermediate should have, if found. Therefore, we expect the possibility of finding reptile-like fossils with feathers, bird-like fossils with teeth, or bird-like fossils with long reptilian tails. However, we do not expect transitional fossils between birds and mammals, like mammalian fossils with feathers or bird-like fossils with mammalian-style middle ear bones.

Confirmation:
Example 1: bird-reptiles
In the case just mentioned, we have found a quite complete set of dinosaur-to-bird transitional fossils with no morphological "gaps" (Sereno 1999), 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 (Carroll 1997, pp. 306-323; Norell and Clarke 2001; Sereno 1999; Xu et al. 1999; Xu et al. 2000; Xu et al. 2002). All have the expected possible morphologies (see Figure 3.1.1 from Prediction 3.1 for a few examples), including organisms such as Protarchaeopteryx, Caudipteryx, and the famous "BPM 1 3-13" (an unnamed dromaeosaur from China) which are flightless bipedal dinosaurs with modern-style feathers (Chen et al.1998 ; Qiang et al. 1998; Norell et al. 2002). Additionally, several similar flightless dinosaurs have been found covered with nascent evolutionary precursors to modern feathers (branched feather-like integument indistinguishable from the contour feathers of true birds), including Sinornithosaurus ("Bambiraptor"), Sinosauropteryx, Beipiaosaurus, Microraptor, and an unnamed dromaeosaur specimen, NGMC 91, informally called "Dave" (Ji et al. 2001). The All About Archaeopteryx FAQ gives a detailed listing of the various characters of Archaeopteryx which are intermediate between reptiles and modern birds.

Example 2: reptile-mammals

We also have an exquisitely complete series of fossils for the reptile-mammal intermediates, ranging from the pelycosauria, therapsida, cynodonta, up to primitive mammalia (Carroll 1988, pp. 392-396; Futuyma 1998, pp. 146-151; Gould 1990; Kardong 2002, pp. 255-275). As mentioned above, the standard phylogenetic tree indicates that mammals gradually evolved from a reptile-like ancestor, and that transitional species must have existed which were morphologically intermediate between reptiles and mammals—even though none are found living today. However, there are significant morphological differences between modern reptiles and modern mammals. Bones, of course, are what fossilize most readily, and that is where we look for transitional species from the past. Osteologically, two major striking differences exist between reptiles and mammals: (1) reptiles have at least four bones in the lower jaw (e.g. the dentary, articular, angular, surangular, and coronoid), while mammals have only one (the dentary), and (2) reptiles have only one middle ear bone (the stapes), while mammals have three (the hammer, anvil, and stapes) (see Figure 1.4.1).

Early in the 20th century, developmental biologists discovered something that further complicates the picture. In the reptilian fetus, two developing bones from the head eventually form two bones in the reptilian lower jaw, the quadrate and the articular (see the Pelycosaur in Figure 1.4.1). Surprisingly, the corresponding developing bones in the mammalian fetus eventually form the anvil and hammer of the unique mammalian middle ear (also known more formally as the incus and malleus, respectively; see Figure 1.4.2) (Gilbert 1997, pp. 894-896). These facts strongly indicated that the hammer and anvil had evolved from these reptilian jawbones—that is, if common descent was in fact true. This result was so striking, and the required intermediates so outlandish, that many anatomists had extreme trouble imagining how transitional forms bridging these morphologies could have existed while retaining function. Young-earth creationist Duane Gish stated the problem this way:

"All mammals, living or fossil, have a single bone, the dentary, on each side of the lower jaw, and all mammals, living or fossil, have three auditory ossicles or ear bones, the malleus, incus and stapes. ... Every reptile, living or fossil, however, has at least four bones in the lower jaw and only one auditory ossicle, the stapes. ... There are no transitional fossil forms showing, for instance, three or two jawbones, or two ear bones. No one has explained yet, for that matter, how the transitional form would have managed to chew while his jaw was being unhinged and rearticulated, or how he would hear while dragging two of his jaw bones up into his ear." (Gish 1978, p. 80)

Gish was incorrect in stating that there were no transitional fossil forms, and he has been corrected on this gaff numerous times since he wrote these words. However, Gish's statements nicely delineate the morphological conundrum at hand. Let's review the required evolutionary conclusion. During their evolution, two mammalian middle ear bones (the hammer and anvil, aka malleus and incus) were derived from two reptilian jawbones. Thus there was a major evolutionary transition in which several reptilian jawbones (the quadrate, articular, and angular) were extensively reduced and modified gradually to form the modern mammalian middle ear. At the same time, the dentary bone, a part of the reptilian jaw, was expanded to form the major mammalian lower jawbone. During the course of this change, the bones that form the hinge joint of the jaw changed identity. Importantly, the reptilian jaw joint is formed at the intersection of the quadrate and articular whereas the mammalian jaw joint is formed at the intersection of the squamosal and dentary (see Figure 1.4.1).

How could hearing and jaw articulation be preserved during this transition? As clearly shown from the many transitional fossils that have been found (see Figure 1.4.3), the bones that transfer sound in the reptilian and mammalian ear were in contact with each other throughout the evolution of this transition. In reptiles, the stapes contacts the quadrate, which in turn contacts the articular. In mammals, the stapes contacts the incus, which in turn contacts the malleus (see Figure 1.4.2). Since the quadrate evolved into the incus, and the articular evolved into the malleus, these three bones were in constant contact during this impressive evolutionary change. Furthermore, a functional jaw joint was maintained by redundancy—several of the intermediate fossils have both a reptilian jaw joint (from the quadrate and articular) and a mammalian jaw joint (from the dentary and squamosal). Several late cynodonts and Morganucodon clearly have a double-jointed jaw. In this way, the reptilian-style jaw joint was freed to evolve a new specialized function in the middle ear. It is worthy of note that some modern species of snakes have a double-jointed jaw involving different bones, so such a mechanical arrangement is certainly possible and functional.

Since Figure 1.4.3 was made, several important intermediate fossils have been discovered that fit between Morganucodon and the earliest mammals. These new discoveries include a complete skull of Hadrocodium wui (Luo et al. 2001) and cranial and jaw material from Repenomamus and Gobiconodon (Wang et al. 2001). These new fossil finds clarify exactly when and how the malleus, incus, and angular completely detached from the lower jaw and became solely auditory ear ossicles.

Recall that Gish stated: "There are no transitional fossil forms showing, for instance, three or two jawbones, or two ear bones" (Gish 1978, p. 80). Gish simply does not understand how gradual transitions happen (something he should understand, obviously, if he intends to criticize evolutionary theory). These fossil intermediates illustrate why Gish's statement is a gross mischaracterization of how a transitional form should look. In several of the known intermediates, the bones have overlapping functions, and one bone can be called both an ear bone and a jaw bone; these bones serve two functions. Thus, there is no reason to expect transitional forms with intermediate numbers of jaw bones or ear bones. For example, in Morganucodon, the quadrate (anvil) and the articular (hammer) serve as mammalian-style ear bones and reptilian jaw bones simultaneously. In fact, even in modern reptiles the quadrate and articular serve to transmit sound to the stapes and the inner ear (see Figure 1.4.2). The relevant transition, then, is a process where the ear bones, initially located in the lower jaw, become specialized in function by eventually detaching from the lower jaw and moving closer to the inner ear.

Example 3: human-apes
"All advances by degrees in Nature, and nothing by leaps, and this law as applied to each, is part of my doctrine of Continuity. Although there may exist in some other world species intermediate between Man and the Apes, Nature has thought it best to remove them from us, in order to establish our superiority beyond question. I speak of intermediate species, and by no means limit myself to those leading to Man."

Gottfried Wilhelm Leibniz
Protogaea 1749


One of the most celebrated examples of transitional fossils is our collection of fossil hominids (see Figure 1.4.4 below). 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.

Example 4: legged fossil whales
"Finally, and most glaringly obvious, if random evolution is true there must have been a large number of transitional forms between the mesonychid and the ancient whale: Where are they? It seems like quite a coincidence that of all the intermediate species that must have existed between the mesonychid and whale, only species that are very similar to the end species have been found. (Behe 1994)"

- Michael J. Behe

Anti-Darwinian, Intelligent Design conjecturist,
writing against the validity of evolution less than a year before three transitional species between whales and land-dwelling Eocene Mesonychids were found.


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, lacking external hindlimbs. 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 (Bajpai and Gingerich 1998; Gingerich et al. 1983; Gingerich et al. 1990; Gingerich et al. 1994; Gingerich et al. 2001; Thewissen et al. 2001).

Example 5: legged seacows
Seacows (manatees and dugongs) are fully aquatic mammals with flippers for forelimbs and no hindlimbs. Evolutionary theory predicts that seacows evolved from terrestrial ancestors with legs, and that thus we could find seacow intermediates with legs. Recently, a new transitional fossil has been found in Jamaica, a seacow with four legs (Domning 2001).

There are many other examples such as these

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Anatomical vestiges
"The wing of the ostrich resembles those of the gyrfalcon and the hawk. Who does not know how the speed of the gyrfalcon and hawk in flight exceeds that of other birds? The ostrich certainly has wings like theirs but not their speed of flight. Truly, it has not the capacity to be lifted from the ground and gives only the impression of spreading its wings as if to fly; however, it never supports itself above the earth in flight.

It is exactly the same with all those hypocrites who pretend to live a life of piety, giving the impression of holiness without the reality of holy behaviour."

The Aberdeen Bestiary
Folio 41v , c. AD 1200
— on the ostrich, its vestiges a symbol of hypocricy since the 2nd century A.D.


Some of the most renowned evidence for evolution are the various nonfunctional or rudimentary vestigial characters, both anatomical and molecular, that are found throughout biology. A vestige is defined, independently of evolutionary theory, as a reduced and rudimentary structure compared to the same complex structure in other organisms. Vestigial characters, if functional, perform relatively simple, minor, or inessential functions using structures that were clearly designed for other complex purposes. Though many vestigial organs have no function, complete non-functionality is not a requirement for vestigiality (Crapo 1985; Culver et al. 1995; Darwin 1872, pp. 601-609; Dodson 1960, p. 44; Griffiths 1992; McCabe 1912, p. 264; Merrell 1962, p. 101; Moody 1962, p. 40; Muller 2002; Naylor 1982; Strickberger 2000; Weismann 1886, pp. 9-10; Wiedersheim 1893, p. 2, p. 200, p. 205).

For example, wings are very complex anatomical structures specifically adapted for powered flight, yet ostriches have flightless wings. The vestigial wings of ostriches may be used for relatively simple functions, such as balance during running and courtship displays—a situation akin to hammering tacks with a computer keyboard. The specific complexity of the ostrich wing indicates a function which it does not perform, and it performs functions incommensurate with its complexity. Ostrich wings are not vestigial because they are useless structures per se, nor are they vestigial simply because they have different functions compared to wings in other birds. Rather, what defines ostrich wings as vestigial is that they are rudimentary wings which are useless as wings.

Vestigial structures have perplexed naturalists throughout history and were noted long before Darwin first proposed universal common descent. Many eighteenth and nineteenth century naturalists identified and discussed vestigial structures, including Johann Wolfgang von Goethe (1749-1832), Georges-Louis Leclerc, Compte de Buffon (1707-1788), and Georges Cuvier (1769-1832). Over sixty years before Darwin's publication of On the Origin of Species, the eminent French anatomist Geoffroy St. Hilaire (1772-1844) discussed his observations of the vestigial wings of the cassowary and ostrich during his travels with Napoleon to Egypt:

"There is another species that, like the ostrich, never leaves the ground, the Cassowary, in which the shortening [of the wing] is so considerable, that it appears little more than a vestige of a wing. Its arm is not, however, entirely eliminated. All of the parts are found under the skin. ...

Whereas useless in this circumstance, these rudiments of the furcula have not been eliminated, because Nature never works by rapid jumps, and She always leaves vestiges of an organ, even though it is completely superfluous, if that organ plays an important role in the other species of the same family. Thus, under the skin of the Cassowary's flanks are the vestiges of the wings ..." (Geoffroy 1798)


Geoffroy was at a loss for why exactly nature "always leaves vestiges of an organ," yet he could not deny his empirical observations. Ten years later, Jean-Baptiste Lamarck (1744-1829) identified several vestigial structures in his Zoological Philosophy (Lamarck 1809, pp. 115-116):

"Eyes in the head are characteristic of a great number of different animals, and essentially constitute a part of the plan of organisation of the vertebrates. Yet the mole, whose habits require a very small use of sight, has only minute and hardly visible eyes ...

Olivier's Spalax, which lives underground like the mole, and is apparently exposed to daylight even less than the mole, has altogether lost the use of sight: so that it shows nothing more than vestiges of this organ. Even these vestiges are entirely hidden under the skin and other parts, which cover them up and do not leave the slightest access to light.

The Proteus, an aquatic reptile allied to the salamanders, and living in deep dark caves under water, has, like the Spalax, only vestiges of the organ of sight, vestiges which are covered up and hidden in the same way." (Lamarck 1809, p. 116)


Even Aristotle discussed the peculiar vestigial eyes of moles in the fourth century B.C. in De animalibus historiae (lib. I cap. IX), in which he identified them as "stunted in development" and "eyes not in the full sense."

As these individuals noted, vestiges can be especially puzzling features of organisms, since these "hypocritical" structures profess something that they do not do—they clearly appear designed for a certain function which they do not perform. However, common descent provides a scientific explanation for these peculiar structures. Existing species have different structures and perform different functions. If all living organisms descended from a common ancestor, then both functions and structures necessarily have been gained and lost in each lineage during macroevolutionary history. Therefore, from common descent and the constraint of gradualism, we predict that many organisms should retain vestigial structures as structural remnants of lost functions. Note that the exact evolutionary mechanism which created a vestigial structure is irrelevant as long as the mechanism is a gradual one.

http://www.talkorigins.org/faqs/comdesc/section2.html

 

Bob

You did not seem to like when I would show that all the evidence you proposed was wrong. for some reason I still can not understand, you seemed to think that showing that a supposed evidence for a young earth was fatally flawed was not a good way to argue against it. So I have taken a different tact above. There are a few things for you to chew on and attmpt to falsify if you wish.

It is also getting a litle frustrating to be constantly having to debunk and endless supply of searches for an anomaly. You post one particular anomaly, I refute it, you think there is something wrong with presenting evidence against your claims, you rarely defend something after its been refuted and we move on to something else in a shotgun approach. After I refuted the whole list from AIG, you simply discounted the real facts and reposted the same list. That was amazing! Let's suppose that one of your anomalies is true. At this point, it is still only an anomaly since there are millions of facts to support an old earth. So millions of facts can not be overturned by one anomalous piece of data. You need to find a way to better explain the wealth of data!

But since you seem to have a problem with me falsifying your posts, and since we seem to be getting no where simply posting quotes with alternative points of view, why do we not stay on a particular topic.

If you have not noticed, the topic I have picked out is your dino blood posts. It works so well for our purposes. First, it gives us a topic, of your choosing, that could show one peice of evidence for a young earth. Second, I have been making constant allegations against the honesty of the YEC leaders, you know those people supplying you with your quotes. I still do not know what you think of this type of stuff.

So, we get to kill two birds with one stone. You have alleged dino bloodcells being found indicating fresh bone. You based your post on Wieland who based his statements on the work of Schweitzer. Now, I have accused Wieland of being dishonest in his treatment of Schweitzer's work and that this is symptomatic of general dishonesty on the part of YEC leaders. A_Christian has ben kind enough to post a link to one of Schweitzer's actual papaers on the subject ( http://www.pnas.org/cgi/reprint/94/12/6291.pdf ), so we have the actual work that Wieland based his on to compare.

So, if you believe that the YEC leaders are being honest, then it follows that you think Wieland was being honest. If you think that Wieland was being honest then it logically follows that you should be able to quote from the actual paper listed above to show were it discusses the bloodcells and fresh bone. It also allows us to stay on one topic for a few posts and allows you to make and defend an argument in your own words.

Now, if you fail to respond, I will assume that you do not think that the YEC leaders are honest and you cannot defend their tactics with backing facts. If you respond but do not defend Wieland with material from Schweitzer's actual paper above, then I will assume that you think that YEC leaders are in general honest but that Wieland was not and that you withdraw the claim of dino blood.

This allows us to discuss both one particular set of facts and the honesty of the YEC leaders supplying the facts.

 

I'd sure like to see the world as it was a thousand years ago. I want to taste it, touch it, hear it and really 'feel' it. I cannot. I guess that means the world really did not exist then.

Put differently... When a crime scene investigator goes to the scene, he can figure out what happened without ever having seen the actual crime. Is that a problem.

You seem to have an odd look at deep time. If you do not accept an old earth, what about the evidence that shows it to be so. How do you explain that? You just dismiss it? The data got there somehow.

But since you dismiss deep time, let's try biology. Why do humans and the other apes share so many genetic traits? So you cannot fall back on "common designer" let's stick with things that do not code for proteins. Why do we share mutations? Take for example that mutation the humans and the other apes and primates have that disables the production of Vitamin C. All of them have the same exact mutation, right down to the individual base pairs, in the same spot. (There are four enzymes that animals use to make vitamin C. In all the primates, including humans, one enzyme has been disabled by a specific mutation.) Common descent says to expect this. How do you explain it in your worldview? When your finished, we can move on to other mutations.

A retrovirus can insert a part of its DNA into the genome of its host which can then be passed down to the animals descendants. There are quite a few cases of specific sequences of long term repeats of retrovirus DNA inserted at specific spots in the genome of humans and the other apes. Why would we share these LTRs? Common descent would insist that we would share such things. Created kinds would insist that we would not. So why do we?

 

You'll have to explain that one to me. Are you questioning if time itself is real?

 

No, the original assumption was not a billions of year old earth. The data led to the conclusion. You still have not shown the data to be false, only that you deny the data.

Nothing in uniformitarian geology assumes that catastrophes cannot happen. The assumption is that things work today the way they worked in the past. If you want to say all those geologists are wrong, you'll have to demonstrate it rather than assert it.

Do you think water erodes things differently today than in the past? Do you think the effects of a landslide are different today? What about a flood? What about a volcano? What about an earthquake? What about sand dune formation? What about fossilization? What about rock formation? What about fossil fuel formation? What about metamorphosis of rocks? What things do you think happen differently today and why?

Fine, then show me what exactly is circular about geology. I think you are confusing empirical with circular.

 

Amazing that when someone copies and pastes a list from a website, not any kind of argument in his own words, and not even a copy of the support for the list, that is a "GREAT post... ."

But when someone show from a factual basis and in his own words how the "facts" are wrong it is "smoke and hor [sic] air" and of "no substance at all."

It was actually the first post, the list, that was without substance.

 

Paul of Eugene:

"Observing how fast the pacific ocean plate moves today and measuring that against the Hawiian Island chain and finding out a projected age for the creation of the different islands is not circular logic, its just a straightforward calculation. Finding out that the age of the islands as revealed by radiological methods is consistent with the first determination is not circular reasoning; its a valuable check on the other, completely independent line of reasoning."
===================

One still has to speculate and presume (a priori) and postulate, consequently, in both of your examples of mathematical extrapolation, that the entire Universe, as currently and empirically perceived, was even in existence 20,000 BC.

No one was there at the imagined time (except perhaps God) according to BB theory itself so one can calculate all one likes but the fact remains that those calculations are merely sub-atomic processes occurring in the deepest and furthest recesses of our brains.

Didn't you hear the one about the guy sitting on the park bench flailing his arms at 'invisible' flies? When informed that there was no such thing as 'invisible' flies, he confidently responded that his superior arm-flailing techniques kept them away.

 

Paul of Eugene:

"Are you under the impression that relativity and quantum mechanics somehow rule out having ancestors or having descendants? That would be a silly kind of science indeed!"
============

Not entirely, if we throw some Gestalt Psychology and Pre-suppositional Philosophy into the equation.

If one rules out the possibility at the outset of one's investigation (as evolutionists do) of some phenomenon ever having occurred in past time or space, and assumes instead, that some other historical phenomenon occured in replacement thereof, then invariably, those philosophical pre-suppostions must of necessity, contribute to the rational and logical conclusions of the investigations, whether they are scientific or not.

Otherwise known in philosophy as circular reasoning based on a tautological model and ideological represention of the supposed phenomena.

 

Paul of Eugene:

"And they did a very good job of explaining the things they could document about geology by means of the "uniformitarian" principle, and showed how these same structures in the earth were not consistent with a single flood being the cause of all the geological formations."
++++++++++

It seems that geology went astray though ever since geologists started basing the age of sedimentary strata on the evolutionary time-scale imagined by biologists according to the dating scheme which they invented for the presumed evolution of the fossil remains embedded therein.

 

No. What I did not like was that you failed to address the point and merely "assumed" that half-hearted-response would eliminate the data that so refutes evolutionism's mythologies today.

A poster-child example of this was the issue with salts in the sea. Uranium salts are not in equilibrium - they are being added 100x faster than the outflux. You "ignore" the disconfirming data and choose instead to focus on salts like Aluminum that are in a state if equilibrium.

Your response is a "classic rabbit trail" tactic playing a shell game with your responses instead of admiting to the Bible-confirming data - you actually seek "to obfuscate it".

How sad that this should be a Christian response to data that points to a young earth.

Young Earth "data" and no one to refute it.

What is even "more amazing" is that there would be Christians "trying to refute the Bible even when the science data AGREES with the Bible" as can be seen on this thread.

That has to make you stop and think.

In Christ,

Bob

[ March 21, 2004, 03:26 PM: Message edited by: BobRyan ]

 

No - as stated above - I think the "Shell game" is flawed. Looking at aluminum salts and ignoring uranium salts (because they disconfirm your assumptions) is not "a compelling answer" to the problem of salts in the oceans pointing to a young earth.

This point just is not that hard to get.

Wrong again.

I zeroed in on a few blatant examples showing that you "refuted nothing". You merely posted half-answers (as in the case of the salt data above) in the hope that your shell game would not be exposed.

Intead of "moving on past this salt data" - I continue to "Stick with it" and have shown that 100xoutflux more than compensates for a half-life of 700 million years. Your case is "Dead".

You continue to "conjecture" that you find no data refuting your views - but then are stuck, on point after point.

That was amazing!

Excellent propaganda UTEOTW! When the data is NOT in your favor (data that you CLAIM does not exist) you call it "an anomaly"!!

Outstanding "tactic".

Sadly - some Christians choose to take Bible affirming data and call it "anomally"

Are you interested in a "parade of anomally"?? Is that of interest to you? Or are you just as willing to ignore reams of data?

Does the fact that science AND Bible exegesis refute your views - "mean anything to you"?

In Christ.

Bob

 

Entropy and the problem of genetic wells.

The basic mythological principle upon which the fabrications of the doctrines of evolutionism are built - is the "tale" of spontaneous organization and spontaneous generation - instead of genetic wells and entropy.

For illustration of the genetic well - notice that no amount of breeding beagles will give you a wolf. That is because dominant genetic Data has been lost and you can't climb back up the chain.

However - evolution "needs" the ability to "Self organize" to have "genetic data infused cumulatively so that beagles give birth to wolves on some regular - albeit infrequent - basis". In the evolutionists fairytale - this must happen "so often" that the wolf offspring being to breed "with each other" and form viable communities.

Without this alchemy - that forms the core and fabric of today's doctrines of evolutionism - it just won't work.

Obivously such frank statements only magnify the flaws in the doctrines of evolutionism and would never be "expected" to be utterred by evolutionism's true believers.

But the fact remains.

In Christ,

Bob

 

I'd sure like to see the world as it was a thousand years ago. I want to taste it, touch it, hear it and really 'feel' it. I cannot. I guess that means the world really did not exist then.

Put differently... When a crime scene investigator goes to the scene, he can figure out what happened without ever having seen the actual crime. Is that a problem.

You seem to have an odd look at deep time. If you do not accept an old earth, what about the evidence that shows it to be so. How do you explain that? You just dismiss it? The data got there somehow.

But since you dismiss deep time, let's try biology. Why do humans and the other apes share so many genetic traits? So you cannot fall back on "common designer"

Common descent would insist that we would share such things. Created kinds would insist that we would not. So why do we? [/QUOTE]

Written documents and historical monuments confirm the existence of the world as it was a thousand years ago as do the artifacts found in most archeological excavations.

We can see them and even touch and feel some of them so we may safely assume that the world really did exist 1 - 5000 years ago.

Put differently... When an impartial investigator delves into the human fossil record he can figure out that human evolution never happened without ever having been to Africa.
Is that a problem?

The data and evidence for deep time and an old earth only got into your mind through the world-wide dissemination of evolutionary theories during the last century.

Humans and the other apes share so many genetic traits simply because they have so many genetic traits in common. This alone doesn't prove that any dark and hairy apes ever evolved into dark and hairy humans in 'darkest' Africa at any time.

There is a vast difference between the ideological concepts of "common designer" and common descent. Intelligent Designers may easily postulate that another and greater Intelligent Designer could have easily insisted "that we would share such things with all other creatures on earth."

It is wuite evident that we're all in the great 'boat' of life together and share the whole planet in our common quest and search for food, truth and signs of other life.

 

Ah, but you are contending that it is BASELESS speculation and it is clear the simple math involved is an excellent BASIS for the speculation.

In fact, the speculation that God intended Genesis One to be interpreted literally is clearly comprimised by the physical evidence, which God Himself is reponsible for, as He is every detail of the universe.

 

Well yes, ever since writing appeared about that time, written records do confirm there was a world. And its interesting that carbon 14 dating is confirmed by that writing, and also confirms earlier dates. Why would carbon 14 dating suddenly start being unreliable?

Well, the scientists who drilled ice cores in Antarctica and in Iceland and counted back for 200,000 annual layers felt like they were seeing and touching things that assured them the world existed then, too.

What did you really say there?

So why did you pass when the evidence was rolling in?

I have to admit there are some things I just can't argue against, and this statement has to be one of them.

It's always funny how critics of science talk as if there was only one thing that proved evolution is true. Please be assured that the mere fact that we share a lot of genes with apes does not stand alone in the cataloging of evidence.

So why do we share the defective gene for making vitamin C - with the exact same defect in the exact same place in the genome - with other primates? The logical conclusion for your side would be that the designer just kept making the same mistake in species after species. This does not fit well with my theology. Does it fit with yours?

 

For BobRyan: You earlier suggested the uranium salts in the ocean are insufficient due to all the uranium that would have been pumped in there over the millions of years.

Well, here's a site where some scientists think they have explained what happens to the extra uranium on its way to the ocean:

http://homepage.eircom.net/~radphys/biartz.pdf

Briefly, they claim to have discovered that dissolved uranium in fresh water precipitates out as the fresh water hits salt water. Not all of it - just enough to account for the present observe amount of uranium in the oceans.