the evidence for evolution

Discussion in 'The Sanctuary' started by reggie_jax, Jan 25, 2011.

Thread Status:
Not open for further replies.
  1. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    this is a thread for those who doubt the theory of evolution. it is not only for thebigpayback, though it is in response to him specifically that i am posting this. i was originally going to make this post in the other evolution thread but in my attempt to cut down this text to size its still a pretty lengthy read so i figure, might as well make a new thread of it.

    i realize there are many of you who share this doubt of the theory's credibility. i would only suggest that you owe it to yourself to openly and intently review the facts and draw your own conclusions. if you want a good idea of what evolution is and how scientists interpret it in nature, you must look not to your respected religions but to the science itself.

    many people dislike the idea that these are our closest relatives:
    [​IMG]
    but i'm here to tell you that it's all going to be ok. all life forms are related, and we are derived from a shared communal gene pool.

    here is an abbreviated version of the text, '29+ evidences for macroevolution', off the talk origins website. i cut it short just to give a basic foundation on which to build an understanding of common descent and how it relates to the taxonomy of all life on earth.

    if this sparks any fruitful discussion that can or should be expanded on, then maybe i'll post the rest of the arguments from the text or arguments from other works in this thread at a later time. if you have any questions about what you read in this thread specifically, it might be because i cut certain parts out to make it a less extensive read. you can either visit the link below to see if your question is answered there, or ask it here and i'll look for an explanation.


    29+ Evidences for Macroevolution: the Scientific Case for Common Descent
    test
  2. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    What is Universal Common Descent?

    Universal common descent is the hypothesis that all living, terrestrial organisms are genealogically related. All existing species originated gradually by biological, reproductive processes on a geological timescale. Modern organisms are the genetic descendants of one original species or communal gene pool.

    What is Meant by "Scientific Evidence" for Common Descent?

    Scientific theories are validated by empirical testing against physical observations. Theories are not judged simply by their logical compatibility with the available data. Independent empirical testability is the hallmark of science—in science, an explanation must not only be compatible with the observed data, it must also be testable.

    By "testable" we mean that the hypothesis makes predictions about what observable evidence would be consistent and what would be incompatible with the hypothesis. Simple compatibility, in itself, is insufficient as scientific evidence, because all physical observations are consistent with an infinite number of unscientific conjectures. Furthermore, a scientific explanation must make risky predictions— the predictions should be necessary if the theory is correct, and few other theories should make the same necessary predictions.

    Are There Other Scientifically Valid Explanations?

    The worldwide scientific research community from over the past 140 years has discovered that no known hypothesis other than universal common descent can account scientifically for the unity, diversity, and patterns of terrestrial life. This hypothesis has been verified and corroborated so extensively that it is currently accepted as fact by the overwhelming majority of professional researchers in the biological and geological sciences (AAAS 1990; NAS 2003; NCSE 2003; Working Group 2001).

    No alternate explanations compete scientifically with common descent, primarily for four main reasons: (1) so many of the predictions of common descent have been confirmed from independent areas of science, (2) no significant contradictory evidence has yet been found, (3) competing possibilities have been contradicted by enormous amounts of scientific data, and (4) many other explanations are untestable, though they may be trivially consistent with biological data.

    When evaluating the scientific evidence provided in the following pages, please consider alternate explanations. Most importantly, for each piece of evidence, critically consider what potential observations, if found, would be incompatible with a given alternate explanation. If none exist, that alternate explanation is not scientific. As explained above, a hypothesis that is simply compatible with certain empirical observations cannot use those observations as supporting scientific evidence.

    Introduction to Phylogenetics

    Descent from a common ancestor entails a process of branching and divergence of species, in common with any genealogical process. Genealogies can be graphically illustrated by tree-like diagrams, and this is why you will hear biologists refer to the genealogy of species as the "tree of life". Diagrams such as these are known as phylogenetic trees or phylogenies. The consensus model which evolutionary biologists use to represent the well-supported branches of the universal tree of life I will refer to as the "standard phylogenetic tree".

    Figure 1 shows a simplified example of some of the more familiar branches of the universal phylogenetic tree. The macroevolutionary prediction of a unique, historical universal phylogenetic tree is the most important, powerful, and basic conclusion from the hypothesis of universal common descent. A thorough grasp of this concept is necessary for understanding macroevolutionary deductions.

    [​IMG]

    If modern species have descended from ancestral ones in this tree-like, branching manner, it should be possible to infer the true historical tree that traces their paths of descent. Phylogenies have been inferred by biologists ever since Darwin first proposed that life was united by common descent over 140 years ago. Rigorous algorithmic methodologies for inferring phylogenetic trees have been in use for over the past 50 years.

    In 1950, taxonomist Willi Hennig proposed a method for determining phylogenetic trees based on morphology by classifying organisms according to their shared derived characters, which are called synapomorphies (Hennig 1966). This method, now called cladistics, does not assume genealogical relatedness a priori, since it can be used to classify anything in principle, even things like books, cars, or chairs that are obviously not genealogically related in a biological sense (Kitching et al. 1998, Ch. 1, p. 26; ).

    Using firm evolutionary arguments, however, Hennig justified this method as the most appropriate classification technique for estimating evolutionary relationships generated by lineal descent. In fact, Hennig's cladistic method is nothing more than a formalization of the methods systematic biologists had been using intuitively ever since Linnaeus penned Systema Naturae. Biologists today construct their phylogenetic trees based on Hennig's method, and because of cladistics these phylogenetic trees are reproducible and independently testable (Brooks 1991, Ch. 2; Kitching et al. 1998).

    Cladistic-based phylogenies group taxa into nested hierarchies, and they are determined using only shared derived characters of organisms, not shared primitive characters (Brooks 1991, pp. 35-36; Kitching et al. 1998, Ch. 1; Maddison and Maddison 1992, p. 49). In technical phylogenetic jargon, primitive characters are called plesiomorphies, and derived characters are called apomorphies.

    In cladistics, related species are grouped together because they share derived characters (i.e., apomorphies) that originated in a common ancestor of the group, but were not present in other, earlier ancestors of the group. These shared, derived features are called synapomorphies.
    Primitive and derived are therefore relative terms, depending upon the specific group being considered. For example, backbones are primitive characters of vertebrates, while hair is a derived character particular to mammalian vertebrates. However, when considering mammals only, hair is primitive, whereas an opposable thumb is derived.

    In real-life phylogenetic analyses, shared derived characters may be in conflict with other derived characters. Thus, objective methods are required for resolving this character conflict (Kitching et al. 1998, Ch. 1; Maddison and Maddison 1992, p. 49). For instance, wings are a derived character of birds and of bats. Based upon this character alone, the cladistic method would group bats and birds together, which is how the author of Deuteronomy grouped them in the Biblical quote above (Deuteronomy 14:11-18, KJV). However, other shared derived characters indicate that bats should be grouped with wingless mammals, and that birds should be grouped with wingless dinosaurs.
    test
  3. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    Does Phylogenetic Inference Find Correct Trees?

    In order to establish their validity in reliably determining phylogenies, phylogenetic methods have been empirically tested in cases where the true phylogeny is known with certainty, since the true phylogeny was directly observed.

    * Bacteriophage T7 was propagated and split sequentially in the presence of a mutagen, where each lineage was tracked. Out of 135,135 possible phylogenetic trees, the true tree was correctly determined by phylogenetic methods in a blind analysis. Five different phylogenetic methods were used independently, and each one chose the correct tree (Hillis et al.1992 ).

    * In another study, 24 strains of mice were used in which the genealogical relationships were known. Cladistic analysis reproduced almost perfectly the known phylogeny of the 24 strains (Atchely and Fitch 1991).

    * Bush et al. used phylogenetic analysis to retrospectively predict the correct evolutionary tree of human Influenza A virus 83% of the time for the flu seasons spanning 1983 to 1994.

    * In 1998, researchers used 111 modern HIV-1 (AIDS virus) sequences in a phylogenetic analysis to predict the nucleotide sequence of the viral ancestor of which they were all descendants. The predicted ancestor sequence closely matched, with high statistical probability, an actual ancestral HIV sequence found in an HIV-1 seropositive African plasma sample collected and archived in the Belgian Congo in 1959 (Zhu et al.1998 ).

    * In the past decade, phylogenetic analyses have played a significant role in successful convictions in several criminal court cases (Albert et al. 1994; Arnold et al. 1995; Birch et al. 2000; Blanchard et al. 1998; Goujon et al. 2000; Holmes et al. 1993; Machuca et al. 2001; Ou et al. 1992; Veenstra et al. 1995; Vogel 1997; Yirrell et al. 1997), and phylogenetic reconstructions have now been admitted as expert legal testimony in the United States (97-KK- 2220 State of Louisiana v. Richard J. Schmidt [PDF]). The legal test in the U. S. for admissibility of expert testimony is the Daubert guidelines (U. S. Supreme Court Case Daubert v. Merrell Dow Pharmaceuticals, Inc., 509 U.S. 579, 587-89, 113 S. Ct. 2786, 2794, 125 L. Ed. 2d 469, 1993). The Daubert guidelines state that a trial court should consider five factors in determining "whether the testimony's underlying reasoning or methodology is scientifically valid": (1) whether the theory or technique in question can be and has been tested; (2) whether it has been subjected to peer review and publication; (3) its known or potential error rate; (4) the existence and maintenance of standards controlling its operation; and (5) whether it has attracted widespread acceptance within the relevant scientific community (quoted nearly verbatim). Phylogenetic analysis has officially met these legal requirements.
    test
  4. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    Prediction 1.1: 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 common polymers of life


    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.

    Nucleic acids are the genetic material of life

    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 102 occur naturally and many more have been artificially synthesized) (Rozenski et al. 1999; Voet and Voet 1995, p. 969).

    Protein catalysis

    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 390 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.

    The universal genetic code

    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 based on the theory of common descent, years before the genetic code was finally solved (Brenner 1957; Crick et al. 1961; Hinegardner and Engelberg 1963; Judson 1996, p. 280-281).
    The scientists who cracked the genetic code in the 1950's and 1960's worked under the assumption that the code was universal or nearly so (Judson 1996, p. 280-281).

    These scientists (which included Francis Crick, Sydney Brenner, George Gamow, and several others) all made this assumption and justified it based upon evolutionary reasoning, even in the complete absence of any direct experimental evidence for a universal code.

    "Crick urged on his companions two other simplifying assumptions of great audacity. ... they assumed, with some apprehension, that the genetic code would be the same for all living things. There was no evidence whatever for this; .... Yet universality seemed inevitable for an obvious reason: since a mutation that changed even one word or letter of the code would alter most of a creature's proteins, it looked sure to be lethal."
    (Judson 1996, p. 280-281)

    [​IMG]

    In fact, the assumption of a universal genetic code was instrumental in their success in solving the code. For instance, in 1957, nearly ten years before the genetic code was finally solved, Sydney Brenner published an influential paper in which he concluded that all overlapping triplet codes were impossible if the code was universal (Brenner 1957). This paper was widely considered a landmark work, since many researchers were leaning towards an overlapping code. Of course, it turned out that Brenner was correct about the nature of the true code.

    In 1961, five years before the code was deciphered, Crick referenced Brenner's work in his landmark report in the journal Nature, "General nature of the genetic code for proteins" (Crick et al. 1961). Although the organism used in the paper was the bacterium E. coli, Crick titled the paper "the genetic code for proteins", not "a genetic code" or "the genetic code of E. coli". In this paper, Crick and others concluded that the code was (1) a triplet code, (2) non-overlapping, and (3) that the code is read from a fixed starting point (i.e. the "start" codon). These conclusions were explicitly based on the assumption that the code was essentially the same in tobacco, humans, and bacteria, though there was no direct empirical support for this assumption. These conclusions, when applied to organisms from bacteria to humans, turned out to be correct. Thus, experimental work also assumed a universal code due to common descent.

    In fact, in 1963—three years before the code was finally solved—Hinegardner and Engelberg published a paper in Science formally explaining the evolutionary rationale for why the code must be universal (or nearly so) if universal common descent were true, since most mutations in the code would likely be lethal to all living things. Note that, although these early researchers predicted a universal genetic code based on common descent, they also predicted that minor variations could likely be found. Hinegardner and Engelberg allowed for some variation in the genetic code, and predicted how such variation should be distributed if found:
    test
  5. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    "... if different codes do exist they should be associated with major taxonomic groups such as phyla or kingdoms that have their roots far in the past." (Hinegardner and Engelberg 1963)

    Similarly, before alternate codes were found, Francis Crick and Leslie Orgel expressed surprise that minor variants of the code had not been observed yet:

    "It is a little surprising that organisms with somewhat different codes do not coexist."
    (Crick and Orgel 1973, p. 344)

    Crick and Orgel were correct in their surprise, and today we know of about a dozen minor variants of the standard, universal genetic code (see the grey, red, and green codons in Figure 1.1.1). As Hinegardner and Engelberg predicted, the minor variations in the standard genetic code are indeed associated with major taxonomic groups (vertebrates vs. plants vs. single-celled ciliates, etc.).

    Common metabolism

    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.

    Potential Falsification:

    Thousands of new species are discovered yearly, and new DNA and protein sequences are determined daily from previously unexamined species (Wilson 1992, Ch. 8). At the current rate, which is increasing exponentially, nearly 30,000 new sequences are deposited at GenBank every day, amounting to over 38 million new bases sequenced every day. Each and every one is a test of the theory of common descent. When I first wrote these words in 1999, the rate was less than one tenth what it is today (in 2006), and we now have 20 times the amount of DNA sequenced.

    Based solely on the theory of common descent and the genetics of known organisms, we strongly predict that we will never find any modern species from known phyla on this Earth with a foreign, non-nucleic acid genetic material. We also make the strong prediction that all newly discovered species that belong to the known phyla will use the "standard genetic code" or a close derivative thereof.

    For example, according to the theory, none of the thousands of new and previously unknown insects that are constantly being discovered in the Brazilian rainforest will have non-nucleic acid genomes. Nor will these yet undiscovered species of insects have genetic codes which are not close derivatives of the standard genetic code. In the absence of the theory of common descent, it is quite possible that every species could have a very different genetic code, specific to it only, since there are 1.4 x 1070 informationally equivalent genetic codes, all of which use the same codons and amino acids as the standard genetic code (Yockey 1992). This possibility could be extremely useful for organisms, as it would preclude interspecific viral infections. However, this has not been observed, and the theory of common descent effectively prohibits such an observation.

    As another example, nine new lemur and two marmoset species (all primates) were discovered in the forests of Madagascar and Brazil in 2000 (Groves 2000; Rasoloarison et al. 2000; Thalmann and Geissmann 2000). Ten new monkey species have been discovered in Brazil alone since 1990 (Van Roosmalen et al. 2000). Nothing in biology prevents these various species from having a hitherto unknown genetic material or a previously unused genetic code—nothing, that is, except for the theory of common descent. However, we now know definitively that the new lemurs use DNA with the standard genetic code (Yoder et al. 2000); the marmosets have yet to be tested.

    Furthermore, each species could use a different polymer for catalysis. The polymers that are used could still be chemically identical yet have different chiralities in different species. There are thousands of thermodynamically equivalent glycolysis pathways (even using the same ten reaction steps but in different orders), so it is possible that every species could have its own specific glycolysis pathway, tailored to its own unique needs. The same reasoning applies to other core metabolic pathways, such as the citric acid cycle and oxidative phosphorylation.

    Finally, many molecules besides ATP could serve equally well as the common currency for energy in various species (CTP, TTP, UTP, ITP, or any ATP-like molecule with one of the 293 known amino acids or one of the dozens of other bases replacing the adenosine moiety immediately come to mind). Discovering any new animals or plants that contained any of the anomalous examples proffered above would be potential falsifications of common ancestry, but they have not been found.
    test
  6. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    Prediction 1.2: 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 produced by a branching evolutionary process, such as 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.

    Interestingly, Linnaeus, who originally discovered the objective hierarchical classification of living organisms, also tried to classify rocks and minerals hierarchically. However, his classification for non-living objects eventually failed, as it was found to be very subjective. Hierarchical classifications for inanimate objects don't work for the very reason that unlike organisms, rocks and minerals do not evolve by descent with modification from common ancestors.

    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.
    test
  7. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    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.

    Confirmation:

    Most existing species can be organized rather easily in a nested hierarchical classification. This is evident in the use of the Linnaean classification scheme. Based on shared derived characters, closely related organisms can be placed in one group (such as a genus), several genera can be grouped together into one family, several families can be grouped together into an order, etc.

    As a specific example (see Figure 1), plants can be classified as vascular and nonvascular (i.e. they have or lack xylem and phloem). Nested within the vascular group, there are two divisions, seed and non-seed plants. Further nested within the seed plants are two more groups, the angiosperms (which have enclosed, protected seeds) and the gymnosperms (having non-enclosed seeds). Within the angiosperm group are the monocotyledons and the dicotyledons.

    Most importantly, the standard phylogenetic tree and nearly all less inclusive evolutionary phylogenies have statistically significant, high values of hierarchical structure (Baldauf et al. 2000; Brown et al. 2001; Hillis 1991; Hillis and Huelsenbeck 1992; Klassen et al. 1991).

    Potential Falsification:


    It would be very problematic if many species were found that combined characteristics of different nested groupings. Proceeding with the previous example, some nonvascular plants could have seeds or flowers, like vascular plants, but they do not. Gymnosperms (e.g. conifers or pines) occasionally could be found with flowers, but they never are. Non-seed plants, like ferns, could be found with woody stems; however, only some angiosperms have woody stems.

    Conceivably, some birds could have mammary glands or hair; some mammals could have feathers (they are an excellent means of insulation). Certain fish or amphibians could have differentiated or cusped teeth, but these are only characteristics of mammals. A mix and match of characters like this would make it extremely difficult to objectively organize species into nested hierarchies. Unlike organisms, cars do have a mix and match of characters, and this is precisely why a nested hierarchy does not flow naturally from classification of cars.

    If it were impossible, or very problematic, to place species in an objective nested classification scheme (as it is for the car, chair, book, atomic element, and elementary particle examples mentioned above), macroevolution would be effectively disproven. More precisely, if the phylogenetic tree of all life gave statistically significant low values of phylogenetic signal (hierarchical structure), common descent would be resolutely falsified.

    In fact, it is possible to have a "reciprocal" pattern from nested hierarchies. Mathematically, a nested hierarchy is the result of specific correlations between certain characters of organisms. When evolutionary rates are fast, characters become randomly distributed with respect to one another, and the correlations are weakened. However, the characters can also be anti-correlated—it is possible for them to be correlated in the opposite direction from what produces nested hierarchies (Archie 1989; Faith and Cranston 1991; Hillis 1991; Hillis and Huelsenbeck 1992; Klassen et al. 1991). The observation of such an anti-correlated pattern would be a strong falsification of common descent, regardless of evolutionary rates.

    One widely used measure of cladistic hierarchical structure is the consistency index (CI). The statistical properties of the CI measure were investigated in a frequently cited paper by Klassen et al. (Klassen et al. 1991; see Figure 1.2.1). The exact CI value is dependent upon the number of taxa in the phylogenetic tree under consideration. In this paper, the authors calculated what values of CI were statistically significant for various numbers of taxa. Higher values of CI indicate a greater degree of hierarchical structure.

    [​IMG]

    As an example, a CI of 0.2 is expected from random data for 20 taxa. A value of 0.3 is, however, highly statistically significant. Most interesting for the present point is the fact that a CI of 0.1 for 20 taxa is also highly statistically significant, but it is too low—it is indicative of anti-cladistic structure. Klassen et al. took 75 CI values from published cladograms in 1989 (combined from three papers) and noted how they fared in terms of statistical significance. The cladograms used from 5 to 49 different taxa (i.e. different species). Three of the 75 cladograms fell within the 95% confidence limits for random data, which means that they were indistinguishable from random data. All the rest exhibited highly statistically significant values of CI. None exhibited significant low values; none displayed an anti-correlated, anti-hierarchical pattern.

    Note, this study was performed before there were measures of statistical significance which would allow researchers to "weed out" the bad cladograms. Predictably, the three "bad" data sets considered under ten taxa—it is of course more difficult to determine statistical significance with very little data. Seventy-five independent studies from different researchers, on different organisms and genes, with high values of CI (P < 0.01) is an incredible confirmation with an astronomical degree of combined statistical significance (P << 10-300, Bailey and Gribskov 1998; Fisher 1990). If the reverse were true—if studies such as this gave statistically significant values of CI (i.e. cladistic hierarchical structure) which were lower than that expected from random data—common descent would have been firmly falsified.

    Keep in mind that about 1.5 million species are known currently, and that the majority of these species has been discovered since Darwin first stated his hypothesis of common ancestry. Even so, they all have fit the correct hierarchical pattern within the error of our methods. Furthermore, it is estimated that only 1 to 10% of all living species has even been catalogued, let alone studied in detail. New species discoveries pour in daily, and each one is a test of the theory of common descent (Wilson 1992, Ch. 8).
    test
  8. Shadow

    Shadow Kotaro's Master

    Joined:
    Apr 11, 2004
    Messages:
    60,689
    I was going to come in here and refute your claim but to hell if i'm reading all of that
    test
  9. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    it's not my claim. it's a general scientific consensus. good luck refuting it.
    test
  10. Shadow

    Shadow Kotaro's Master

    Joined:
    Apr 11, 2004
    Messages:
    60,689
    i won't be reading it soooooo yea
    test
  11. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    i have a feeling that most people won't be reading it. i posted it so that anyone who has a genuine doubt of the theory can explore it and reassess their views. in another thread, bigpayback seemed to be under the impression that the theory is based on human fossil records. this is a common mistake. evolution has far reaching biological interpretations, and it's made a lot of sense out of modern biology and the taxonomic structure as we know it.
    test
  12. Shadow

    Shadow Kotaro's Master

    Joined:
    Apr 11, 2004
    Messages:
    60,689
    Well that guy doesn't really know what he's talking about tbh...but coo
    test
  13. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    since you're the only person who has even responded i don't want to be rude to you

    but you seem to be here with the sole intention of telling me that you reject whatever it is that i have posted, yet refuse to even read it. ask yourself if you are truly acting on behalf of free thinking and genuine skepticism, or if you are inclined to reject any theory that doesn't conform to your preconceived notion of reality.
    test
  14. Shadow

    Shadow Kotaro's Master

    Joined:
    Apr 11, 2004
    Messages:
    60,689
    i am a open minded person but i generally i'd rather listen to what that person thinks rather than what other think. If you were to state your own beliefs and why you believe them, i'd listen but doing what spill and whatshisface does leads to to reject it because they are not telling me what they believe but reciting random google things and saying their your own is just retarded.

    I'm a free thinker and i will continue to be one
    test
  15. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    so you want me to restate the evidence in my own words? that i can do, though my arguments will not be nearly as detailed as the article i provided. i assumed you'd be interested not only in my perspective, but the subject in general, and the discoveries of intellectuals and professionals who's understanding of the subject is far more advanced than my own.

    basically, the idea that organisms evolve and species branch off from one another leads to the conclusion that all forms of life share a common ancestor or at the least are derived from a communal gene pool, and that biological diversity is a direct result of adaptions to variations in the environment or any other natural factors that effect survival.

    this conclusion is significant because it leads to predictions that are scientifically testable, such as the nature of taxonomic grouping and what patterns should be observed if the premise is true. the most basic conclusion of common descent has been that the genetic code must be universal or nearly so, since major changes would prove to be lethal. this assumption was made prior to the discovery of an actual universal code. upon further study of genetics, this assumption was found to be correct. the basic structure of DNA is widely universal, across all species of life. it always uses the same 22 amino acids. nucleic acid is always the genetic material of life.

    consider you are composing a family tree, and genetic scientists are able to trace the origins of your genes, and tell you who your ancestors are. do you believe that science has this capability? if you do, then how much of a stretch is it to suggest that we can observe use the genetic code to determine how life is related and in what order it has arisen? we know that all life wasn't created at once in some biblical creation myth, species appear and disappear over the course of millions of years and new species arise. for instance our own appearance as a species is somewhat recent. all of this is consistent with the conclusion that we are descended from a common ancestor or communal gene pool.

    at the same time, we have more than just similarity to other creatures. we are part of a very precisely organized natural structure called a 'nested hierarchy.' nested hierarchies only arise through evolutionary processes. another example of something that can be placed in a nested hierarchy is human language. we can trace the origins of language and which languages branched off of each other through the science of linguistics. this is because over time, the capacity of a spoken language evolved and spread throughout mankind. as it spread, it left evidence of its history. the same is true with the spread of life and consistent evidence through fossil records and genetic research.

    there are many natural observations that could have happened that would contradict the nested hierarchical nature of life. reptiles could have hair and mammory glands, fish could have cusped teeth, ferns could have woody stems. or more basic conclusions like different polymers of life could be assigned to different organisms to fit their unique niche in an environment, such a scenario would place the organisms with a distinct evolutionary advantage, yet it is impossible when you consider the assumption that we all evolved as different branches of the same process, and related extensions of a common ancestor.

    all life has a conceivable order than can be broken down through the observations of evolution. for instance:

    As a specific example (see Figure 1), plants can be classified as vascular and nonvascular (i.e. they have or lack xylem and phloem). Nested within the vascular group, there are two divisions, seed and non-seed plants. Further nested within the seed plants are two more groups, the angiosperms (which have enclosed, protected seeds) and the gymnosperms (having non-enclosed seeds). Within the angiosperm group are the monocotyledons and the dicotyledons.

    the structure of the different forms of life and their relation puzzled mankind for ages before the discovery of evolution. the theory puts into perspective many apparent facts about the science of taxonomy. in many ways it has become intertwined and inseparable from our understanding of biology and genetics in general.
    test
  16. zyclon B gas

    zyclon B gas sososerious

    Joined:
    Apr 23, 2002
    Messages:
    16,218
    i'll still believe that "evolution" and creationism go hand in hand.
    test
  17. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    well.. i'm not sure how 'creationism' is technically defined, i've always taken it to mean a literal interpretation of the biblical creation myth. if that is the case, then it is not at all compatible with science. if you mean that the biblical stories were metaphorical in nature and that god is responsible for the first life and the ensuing process of adaption of that life through natural selection, then i essentially see no problem with this. i encourage this type of thinking.

    religious thinkers should not shy away from science, nor should scientists explicitly rebel against religious dogma for the mere sake of being counter-culture. all of humanity should unite in the art of interpreting the laws of existence. if god exists, these laws and processes can be viewed as god directly communicating his will to the entire universe. if god doesn't exist, well then the info is still extremely useful and applicable in real-life scenarios.
    test
  18. zyclon B gas

    zyclon B gas sososerious

    Joined:
    Apr 23, 2002
    Messages:
    16,218
    this is all i ever say.

    just think of it like this:

    "let there be light" - big bang theory

    why can't they be one in the same thing. if god is eternal, who's to say that his 7 days were 7 days to us and not 7 billion years, which may be 7 days to him?

    remember, humans can't think in terms of eternity. we have to limit time. in fact, we created time that we're accustom to - shit, we have daylight savings in which we literally adjust time for our satisfaction - humans used to think the earth was flat, you don't think they could be off on their timing?

    i swear everyone's arguing two theories when they're one in the same.
    test
  19. reggie_jax

    reggie_jax rapper noyd

    Joined:
    Feb 2, 2007
    Messages:
    2,437
    it funny.. the big bang theory is largely rejected by creationists despite the fact that it seems to agree with the premise of creation. this is something i've always found perplexing.

    you know one of the earliest proponents of the theory was actually a catholic priest named george lemaitre.. his work supported the theory of a 'big bang' prior to einstein himself even accepting the theory, even though it was einstein's work that lead him to these conclusions.

    'A Day Without Yesterday': Georges Lemaitre & the Big Bang

    this is a testimony for the validity of the scientific method, and a rebuttal against certain apologists who suggest that 'atheists have faith in scientists.' if einstein, one of the most influential and most proficient scientific minds known to date, could be wrong about such a fundamental aspect of the universe then it stands to reason that no scientific idea can or should be accepted unless it stands up to the empirical testing and peer reviewed process of the scientific method.
    test
  20. zyclon B gas

    zyclon B gas sososerious

    Joined:
    Apr 23, 2002
    Messages:
    16,218
    see, why can't we just have a discussion like that instead of "evolution disproves creation" and vice versa?

    i believe humans try to rationalize what they don't understand in order to comfort themselves.
    test
Thread Status:
Not open for further replies.

Share This Page

Users Viewing Thread (Users: 0, Guests: 0)