The Testimony of Numbers

I found this beautiful post. Go read it: here.

Evolution Is A Poor Theory

PROCEEDINGS OF THE BIOLOGICAL SOCIETY OF WASHINGTON
117(2):213-239. 2004

The origin of biological information and the higher taxonomic categories
By: Stephen C. Meyer

Introduction
In a recent volume of the Vienna Series in a Theoretical Biology (2003), Gerd B. Muller and Stuart Newman argue that what they call the “origination of organismal form” remains an unsolved problem. In making this claim, Muller and Newman (2003:3-10) distinguish two distinct issues, namely, (1) the causes of form generation in the individual organism during embryological development and (2) the causes responsible for the production of novel organismal forms in the first place during the history of life. To distinguish the latter case (phylogeny) from the former (ontogeny), Muller and Newman use the term “origination” to designate the causal processes by which biological form first arose during the evolution of life. They insist that “the molecular mechanisms that bring about biological form in modern day embryos should not be confused” with the causes responsible for the origin (or “origination”) of novel biological forms during the history of life (p.3). They further argue that we know more about the causes of ontogenesis, due to advances in molecular biology, molecular genetics and developmental biology, than we do about the causes of phylogenesis--the ultimate origination of new biological forms during the remote past.In making this claim, Muller and Newman are careful to affirm that evolutionary biology has succeeded in explaining how preexisting forms diversify under the twin influences of natural selection and variation of genetic traits. Sophisticated mathematically-based models of population genetics have proven adequate for mapping and understanding quantitative variability and populational changes in organisms. Yet Muller and Newman insist that population genetics, and thus evolutionary biology, has not identified a specifically causal explanation for the origin of true morphological novelty during the history of life. Central to their concern is what they see as the inadequacy of the variation of genetic traits as a source of new form and structure. They note, following Darwin himself, that the sources of new form and structure must precede the action of natural selection (2003:3)--that selection must act on what already exists. Yet, in their view, the “genocentricity” and “incrementalism” of the neo-Darwinian mechanism has meant that an adequate source of new form and structure has yet to be identified by theoretical biologists. Instead, Muller and Newman see the need to identify epigenetic sources of morphological innovation during the evolution of life. In the meantime, however, they insist neo-Darwinism lacks any “theory of the generative” (p. 7).As it happens, Muller and Newman are not alone in this judgment. In the last decade or so a host of scientific essays and books have questioned the efficacy of selection and mutation as a mechanism for generating morphological novelty, as even a brief literature survey will establish. Thomson (1992:107) expressed doubt that large-scale morphological changes could accumulate via minor phenotypic changes at the population genetic level. Miklos (1993:29) argued that neo-Darwinism fails to provide a mechanism that can produce large-scale innovations in form and complexity. Gilbert et al. (1996) attempted to develop a new theory of evolutionary mechanisms to supplement classical neo-Darwinism, which, they argued, could not adequately explain macroevolution. As they put it in a memorable summary of the situation: “starting in the 1970s, many biologists began questioning its (neo-Darwinism's) adequacy in explaining evolution. Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest. As Goodwin (1995) points out, 'the origin of species--Darwin's problem--remains unsolved'“ (p. 361). Though Gilbert et al. (1996) attempted to solve the problem of the origin of form by proposing a greater role for developmental genetics within an otherwise neo-Darwinian framework,1 numerous recent authors have continued to raise questions about the adequacy of that framework itself or about the problem of the origination of form generally (Webster & Goodwin 1996; Shubin & Marshall 2000; Erwin 2000; Conway Morris 2000, 2003b; Carroll 2000; Wagner 2001; Becker & Lonnig 2001; Stadler et al. 2001; Lonnig & Saedler 2002; Wagner & Stadler 2003; Valentine 2004:189-194).What lies behind this skepticism? Is it warranted? Is a new and specifically causal theory needed to explain the origination of biological form?This review will address these questions. It will do so by analyzing the problem of the origination of organismal form (and the corresponding emergence of higher taxa) from a particular theoretical standpoint. Specifically, it will treat the problem of the origination of the higher taxonomic groups as a manifestation of a deeper problem, namely, the problem of the origin of the information (whether genetic or epigenetic) that, as it will be argued, is necessary to generate morphological novelty.In order to perform this analysis, and to make it relevant and tractable to systematists and paleontologists, this paper will examine a paradigmatic example of the origin of biological form and information during the history of life: the Cambrian explosion. During the Cambrian, many novel animal forms and body plans (representing new phyla, subphyla and classes) arose in a geologically brief period of time. The following information-based analysis of the Cambrian explosion will support the claim of recent authors such as Muller and Newman that the mechanism of selection and genetic mutation does not constitute an adequate causal explanation of the origination of biological form in the higher taxonomic groups. It will also suggest the need to explore other possible causal factors for the origin of form and information during the evolution of life and will examine some other possibilities that have been proposed.The Cambrian ExplosionThe “Cambrian explosion” refers to the geologically sudden appearance of many new animal body plans about 530 million years ago. At this time, at least nineteen, and perhaps as many as thirty-five phyla of forty total (Meyer et al. 2003), made their first appearance on earth within a narrow five- to ten-million-year window of geologic time (Bowring et al. 1993, 1998a:1, 1998b:40; Kerr 1993; Monastersky 1993; Aris-Brosou & Yang 2003). Many new subphyla, between 32 and 48 of 56 total (Meyer et al. 2003), and classes of animals also arose at this time with representatives of these new higher taxa manifesting significant morphological innovations. The Cambrian explosion thus marked a major episode of morphogenesis in which many new and disparate organismal forms arose in a geologically brief period of time.To say that the fauna of the Cambrian period appeared in a geologically sudden manner also implies the absence of clear transitional intermediate forms connecting Cambrian animals with simpler pre-Cambrian forms. And, indeed, in almost all cases, the Cambrian animals have no clear morphological antecedents in earlier Vendian or Precambrian fauna (Miklos 1993, Erwin et al. 1997:132, Steiner & Reitner 2001, Conway Morris 2003b:510, Valentine et al. 2003:519-520). Further, several recent discoveries and analyses suggest that these morphological gaps may not be merely an artifact of incomplete sampling of the fossil record (Foote 1997, Foote et al. 1999, Benton & Ayala 2003, Meyer et al. 2003), suggesting that the fossil record is at least approximately reliable (Conway Morris 2003b:505).As a result, debate now exists about the extent to which this pattern of evidence comports with a strictly monophyletic view of evolution (Conway Morris 1998a, 2003a, 2003b:510; Willmer 1990, 2003). Further, among those who accept a monophyletic view of the history of life, debate exists about whether to privilege fossil or molecular data and analyses. Those who think the fossil data provide a more reliable picture of the origin of the Metazoan tend to think these animals arose relatively quickly--that the Cambrian explosion had a “short fuse.” (Conway Morris 2003b:505-506, Valentine & Jablonski 2003). Some (Wray et al. 1996), but not all (Ayala et al. 1998), who think that molecular phylogenies establish reliable divergence times from pre-Cambrian ancestors think that the Cambrian animals evolved over a very long period of time--that the Cambrian explosion had a “long fuse.” This review will not address these questions of historical pattern. Instead, it will analyze whether the neo-Darwinian process of mutation and selection, or other processes of evolutionary change, can generate the form and information necessary to produce the animals that arise in the Cambrian. This analysis will, for the most part, 2 therefore, not depend upon assumptions of either a long or short fuse for the Cambrian explosion, or upon a monophyletic or polyphyletic view of the early history of life.Defining Biological Form and InformationForm, like life itself, is easy to recognize but often hard to define precisely. Yet, a reasonable working definition of form will suffice for our present purposes. Form can be defined as the four-dimensional topological relations of anatomical parts. This means that one can understand form as a unified arrangement of body parts or material components in a distinct shape or pattern (topology)--one that exists in three spatial dimensions and which arises in time during ontogeny.Insofar as any particular biological form constitutes something like a distinct arrangement of constituent body parts, form can be seen as arising from constraints that limit the possible arrangements of matter. Specifically, organismal form arises (both in phylogeny and ontogeny) as possible arrangements of material parts are constrained to establish a specific or particular arrangement with an identifiable three dimensional topography--one that we would recognize as a particular protein, cell type, organ, body plan or organism. A particular “form,” therefore, represents a highly specific and constrained arrangement of material components (among a much larger set of possible arrangements). Understanding form in this way suggests a connection to the notion of information in its most theoretically general sense. When Shannon (1948) first developed a mathematical theory of information he equated the amount of information transmitted with the amount of uncertainty reduced or eliminated in a series of symbols or characters. Information, in Shannon's theory, is thus imparted as some options are excluded and others are actualized. The greater the number of options excluded, the greater the amount of information conveyed. Further, constraining a set of possible material arrangements by whatever process or means involves excluding some options and actualizing others. Thus, to constrain a set of possible material states is to generate information in Shannon's sense. It follows that the constraints that produce biological form also imparted information. Or conversely, one might say that producing organismal form by definition requires the generation of information.In classical Shannon information theory, the amount of information in a system is also inversely related to the probability of the arrangement of constituents in a system or the characters along a communication channel (Shannon 1948). The more improbable (or complex) the arrangement, the more Shannon information, or information-carrying capacity, a string or system possesses.Since the 1960s, mathematical biologists have realized that Shannon's theory could be applied to the analysis of DNA and proteins to measure the information-carrying capacity of these macromolecules. Since DNA contains the assembly instructions for building proteins, the information-processing system in the cell represents a kind of communication channel (Yockey 1992:110). Further, DNA conveys information via specifically arranged sequences of nucleotide bases. Since each of the four bases has a roughly equal chance of occurring at each site along the spine of the DNA molecule, biologists can calculate the probability, and thus the information-carrying capacity, of any particular sequence n bases long.The ease with which information theory applies to molecular biology has created confusion about the type of information that DNA and proteins possess. Sequences of nucleotide bases in DNA, or amino acids in a protein, are highly improbable and thus have large information-carrying capacities. But, like meaningful sentences or lines of computer code, genes and proteins are also specified with respect to function. Just as the meaning of a sentence depends upon the specific arrangement of the letters in a sentence, so too does the function of a gene sequence depend upon the specific arrangement of the nucleotide bases in a gene. Thus, molecular biologists beginning with Crick equated information not only with complexity but also with “specificity,” where “specificity” or “specified” has meant “necessary to function” (Crick 1958:144, 153; Sarkar, 1996:191).3 Molecular biologists such as Monod and Crick understood biological information--the information stored in DNA and proteins--as something more than mere complexity (or improbability). Their notion of information associated both biochemical contingency and combinatorial complexity with DNA sequences (allowing DNA's carrying capacity to be calculated), but it also affirmed that sequences of nucleotides and amino acids in functioning macromolecules possessed a high degree of specificity relative to the maintenance of cellular function.The ease with which information theory applies to molecular biology has also created confusion about the location of information in organisms. Perhaps because the information carrying capacity of the gene could be so easily measured, it has been easy to treat DNA, RNA and proteins as the sole repositories of biological information. Neo-Darwinists in particular have assumed that the origination of biological form could be explained by recourse to processes of genetic variation and mutation alone (Levinton 1988:485). Yet if one understands organismal form as resulting from constraints on the possible arrangements of matter at many levels in the biological hierarchy--from genes and proteins to cell types and tissues to organs and body plans--then clearly biological organisms exhibit many levels of information-rich structure.Thus, we can pose a question, not only about the origin of genetic information, but also about the origin of the information necessary to generate form and structure at levels higher than that present in individual proteins. We must also ask about the origin of the “specified complexity,” as opposed to mere complexity, that characterizes the new genes, proteins, cell types and body plans that arose in the Cambrian explosion. Dembski (2002) has used the term “complex specified information” (CSI) as a synonym for “specified complexity” to help distinguish functional biological information from mere Shannon information--that is, specified complexity from mere complexity. This review will use this term as well.The Cambrian Information ExplosionThe Cambrian explosion represents a remarkable jump in the specified complexity or “complex specified information” (CSI) of the biological world. For over three billions years, the biological realm included little more than bacteria and algae (Brocks et al. 1999). Then, beginning about 570-565 million years ago (mya), the first complex multicellular organisms appeared in the rock strata, including sponges, cnidarians, and the peculiar Ediacaran biota (Grotzinger et al. 1995). Forty million years later, the Cambrian explosion occurred (Bowring et al. 1993). The emergence of the Ediacaran biota (570 mya), and then to a much greater extent the Cambrian explosion (530 mya), represented steep climbs up the biological complexity gradient.One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93). Studies of modern animals suggest that the sponges that appeared in the late Precambrian, for example, would have required five cell types, whereas the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types. Functionally more complex animals require more cell types to perform their more diverse functions. New cell types require many new and specialized proteins. New proteins, in turn, require new genetic information. Thus an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. Molecular biologists have recently estimated that a minimally complex single-celled organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life (Koonin 2000). More complex single cells might require upward of a million base pairs. Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions. The genome size of a modern arthropod, the fruitfly Drosophila melanogaster, is approximately 180 million base pairs (Gerhart & Kirschner 1997:121, Adams et al. 2000). Transitions from a single cell to colonies of cells to complex animals represent significant (and, in principle, measurable) increases in CSI.Building a new animal from a single-celled organism requires a vast amount of new genetic information. It also requires a way of arranging gene products--proteins--into higher levels of organization. New proteins are required to service new cell types. But new proteins must be organized into new systems within the cell; new cell types must be organized into new tissues, organs, and body parts. These, in turn, must be organized to form body plans. New animals, therefore, embody hierarchically organized systems of lower-level parts within a functional whole. Such hierarchical organization itself represents a type of information, since body plans comprise both highly improbable and functionally specified arrangements of lower-level parts. The specified complexity of new body plans requires explanation in any account of the Cambrian explosion.Can neo-Darwinism explain the discontinuous increase in CSI that appears in the Cambrian explosion--either in the form of new genetic information or in the form of hierarchically organized systems of parts? We will now examine the two parts of this question.Novel Genes and ProteinsMany scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins. Such skepticism often derives from consideration of the extreme improbability (and specificity) of functional genes and proteins.A typical gene contains over one thousand precisely arranged bases. For any specific arrangement of four nucleotide bases of length n, there is a corresponding number of possible arrangements of bases, 4n. For any protein, there are 20n possible arrangements of protein-forming amino acids. A gene 999 bases in length represents one of 4999 possible nucleotide sequences; a protein of 333 amino acids is one of 20333 possibilities.Since the 1960s, some biologists have thought functional proteins to be rare among the set of possible amino acid sequences. Some have used an analogy with human language to illustrate why this should be the case. Denton (1986, 309-311), for example, has shown that meaningful words and sentences are extremely rare among the set of possible combinations of English letters, especially as sequence length grows. (The ratio of meaningful 12-letter words to 12-letter sequences is 1/1014, the ratio of 100-letter sentences to possible 100-letter strings is 1/10100.) Further, Denton shows that most meaningful sentences are highly isolated from one another in the space of possible combinations, so that random substitutions of letters will, after a very few changes, inevitably degrade meaning. Apart from a few closely clustered sentences accessible by random substitution, the overwhelming majority of meaningful sentences lie, probabilistically speaking, beyond the reach of random search.Denton (1986:301-324) and others have argued that similar constraints apply to genes and proteins. They have questioned whether an undirected search via mutation and selection would have a reasonable chance of locating new islands of function--representing fundamentally new genes or proteins--within the time available (Eden 1967, Shutzenberger 1967, Lovtrup 1979). Some have also argued that alterations in sequencing would likely result in loss of protein function before fundamentally new function could arise (Eden 1967, Denton 1986). Nevertheless, neither the extent to which genes and proteins are sensitive to functional loss as a result of sequence change, nor the extent to which functional proteins are isolated within sequence space, has been fully known.Recently, experiments in molecular biology have shed light on these questions. A variety of mutagenesis techniques have shown that proteins (and thus the genes that produce them) are indeed highly specified relative to biological function (Bowie & Sauer 1989, Reidhaar-Olson & Sauer 1990, Taylor et al. 2001). Mutagenesis research tests the sensitivity of proteins (and, by implication, DNA) to functional loss as a result of alterations in sequencing. Studies of proteins have long shown that amino acid residues at many active positions cannot vary without functional loss (Perutz & Lehmann 1968). More recent protein studies (often using mutagenesis experiments) have shown that functional requirements place significant constraints on sequencing even at non-active site positions (Bowie & Sauer 1989, Reidhaar-Olson & Sauer 1990, Chothia et al. 1998, Axe 2000, Taylor et al. 2001). In particular, Axe (2000) has shown that multiple as opposed to single position amino acid substitutions inevitably result in loss of protein function, even when these changes occur at sites that allow variation when altered in isolation. Cumulatively, these constraints imply that proteins are highly sensitive to functional loss as a result of alterations in sequencing, and that functional proteins represent highly isolated and improbable arrangements of amino acids -arrangements that are far more improbable, in fact, than would be likely to arise by chance alone in the time available (Reidhaar-Olson & Sauer 1990; Behe 1992; Kauffman 1995:44; Dembski 1998:175-223; Axe 2000, 2004). (See below the discussion of the neutral theory of evolution for a precise quantitative assessment.)Of course, neo-Darwinists do not envision a completely random search through the set of all possible nucleotide sequences--so-called “sequence space.” They envision natural selection acting to preserve small advantageous variations in genetic sequences and their corresponding protein products. Dawkins (1996), for example, likens an organism to a high mountain peak. He compares climbing the sheer precipice up the front side of the mountain to building a new organism by chance. He acknowledges that his approach up “Mount Improbable” will not succeed. Nevertheless, he suggests that there is a gradual slope up the backside of the mountain that could be climbed in small incremental steps. In his analogy, the backside climb up “Mount Improbable” corresponds to the process of natural selection acting on random changes in the genetic text. What chance alone cannot accomplish blindly or in one leap, selection (acting on mutations) can accomplish through the cumulative effect of many slight successive steps.Yet the extreme specificity and complexity of proteins presents a difficulty, not only for the chance origin of specified biological information (i.e., for random mutations acting alone), but also for selection and mutation acting in concert. Indeed, mutagenesis experiments cast doubt on each of the two scenarios by which neo-Darwinists envisioned new information arising from the mutation/selection mechanism (for review, see Lonnig 2001). For neo-Darwinism, new functional genes either arise from non-coding sections in the genome or from preexisting genes. Both scenarios are problematic. In the first scenario, neo-Darwinists envision new genetic information arising from those sections of the genetic text that can presumably vary freely without consequence to the organism. According to this scenario, non-coding sections of the genome, or duplicated sections of coding regions, can experience a protracted period of “neutral evolution” (Kimura 1983) during which alterations in nucleotide sequences have no discernible effect on the function of the organism. Eventually, however, a new gene sequence will arise that can code for a novel protein. At that point, natural selection can favor the new gene and its functional protein product, thus securing the preservation and heritability of both.This scenario has the advantage of allowing the genome to vary through many generations, as mutations “search” the space of possible base sequences. The scenario has an overriding problem, however: the size of the combinatorial space (i.e., the number of possible amino acid sequences) and the extreme rarity and isolation of the functional sequences within that space of possibilities. Since natural selection can do nothing to help generate new functional sequences, but rather can only preserve such sequences once they have arisen, chance alone--random variation--must do the work of information generation--that is, of finding the exceedingly rare functional sequences within the set of combinatorial possibilities. Yet the probability of randomly assembling (or “finding,” in the previous sense) a functional sequence is extremely small.Cassette mutagenesis experiments performed during the early 1990s suggest that the probability of attaining (at random) the correct sequencing for a short protein 100 amino acids long is about 1 in 1065 (Reidhaar-Olson & Sauer 1990, Behe 1992:65-69). This result agreed closely with earlier calculations that Yockey (1978) had performed based upon the known sequence variability of cytochrome c in different species and other theoretical considerations. More recent mutagenesis research has provided additional support for the conclusion that functional proteins are exceedingly rare among possible amino acid sequences (Axe 2000, 2004). Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 1077. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 1077.Other considerations imply additional improbabilities. First, new Cambrian animals would require proteins much longer than 100 residues to perform many necessary specialized functions. Ohno (1996) has noted that Cambrian animals would have required complex proteins such as lysyl oxidase in order to support their stout body structures. Lysyl oxidase molecules in extant organisms comprise over 400 amino acids. These molecules are both highly complex (non-repetitive) and functionally specified. Reasonable extrapolation from mutagenesis experiments done on shorter protein molecules suggests that the probability of producing functionally sequenced proteins of this length at random is so small as to make appeals to chance absurd, even granting the duration of the entire universe. (See Dembski 1998:175-223 for a rigorous calculation of this “Universal Probability Bound”; See also Axe 2004.) Yet, second, fossil data (Bowring et al. 1993, 1998a:1, 1998b:40; Kerr 1993; Monatersky 1993), and even molecular analyses supporting deep divergence (Wray et al. 1996), suggest that the duration of the Cambrian explosion (between 5-10 x 106 and, at most, 7 x 107 years) is far smaller than that of the entire universe (1.3-2 x 1010 years). Third, DNA mutation rates are far too low to generate the novel genes and proteins necessary to building the Cambrian animals, given the most probable duration of the explosion as determined by fossil studies (Conway Morris 1998b). As Ohno (1996:8475) notes, even a mutation rate of 10-9 per base pair per year results in only a 1% change in the sequence of a given section of DNA in 10 million years. Thus, he argues that mutational divergence of preexisting genes cannot explain the origin of the Cambrian forms in that time.4The selection/mutation mechanism faces another probabilistic obstacle. The animals that arise in the Cambrian exhibit structures that would have required many new types of cells, each of which would have required many novel proteins to perform their specialized functions. Further, new cell types require Asystems of proteins that must, as a condition of functioning, act in close coordination with one another. The unit of selection in such systems ascends to the system as a whole. Natural selection selects for functional advantage. But new cell types require whole systems of proteins to perform their distinctive functions. In such cases, natural selection cannot contribute to the process of information generation until after the information necessary to build the requisite system of proteins has arisen. Thus random variations must, again, do the work of information generation--and now not simply for one protein, but for many proteins arising at nearly the same time. Yet the odds of this occurring by chance alone are, of course, far smaller than the odds of the chance origin of a single gene or protein--so small in fact as to render the chance origin of the genetic information necessary to build a new cell type (a necessary but not sufficient condition of building a new body plan) problematic given even the most optimistic estimates for the duration of the Cambrian explosion.Dawkins (1986:139) has noted that scientific theories can rely on only so much “luck” before they cease to be credible. The neutral theory of evolution, which, by its own logic, prevents natural selection from playing a role in generating genetic information until after the fact, relies on entirely too much luck. The sensitivity of proteins to functional loss, the need for long proteins to build new cell types and animals, the need for whole new systems of proteins to service new cell types, the probable brevity of the Cambrian explosion relative to mutation rates--all suggest the immense improbability (and implausibility) of any scenario for the origination of Cambrian genetic information that relies upon random variation alone unassisted by natural selection.Yet the neutral theory requires novel genes and proteins to arise--essentially--by random mutation alone. Adaptive advantage accrues after the generation of new functional genes and proteins. Thus, natural selection cannot play a role until new information-bearing molecules have independently arisen. Thus neutral theorists envisioned the need to scale the steep face of a Dawkins-style precipice of which there is no gradually sloping backside--a situation that, by Dawkins' own logic, is probabilistically untenable.In the second scenario, neo-Darwinists envisioned novel genes and proteins arising by numerous successive mutations in the preexisting genetic text that codes for proteins. To adapt Dawkins's metaphor, this scenario envisions gradually climbing down one functional peak and then ascending another. Yet mutagenesis experiments again suggest a difficulty. Recent experiments show that, even when exploring a region of sequence space populated by proteins of a single fold and function, most multiple-position changes quickly lead to loss of function (Axe 2000). Yet to turn one protein into another with a completely novel structure and function requires specified changes at many sites. Indeed, the number of changes necessary to produce a new protein greatly exceeds the number of changes that will typically produce functional losses. Given this, the probability of escaping total functional loss during a random search for the changes needed to produce a new function is extremely small--and this probability diminishes exponentially with each additional requisite change (Axe 2000). Thus, Axe's results imply that, in all probability, random searches for novel proteins (through sequence space) will result in functional loss long before any novel functional protein will emerge.Blanco et al. have come to a similar conclusion. Using directed mutagenesis, they have determined that residues in both the hydrophobic core and on the surface of the protein play essential roles in determining protein structure. By sampling intermediate sequences between two naturally occurring sequences that adopt different folds, they found that the intermediate sequences “lack a well defined three-dimensional structure.” Thus, they conclude that it is unlikely that a new protein fold via a series of folded intermediates sequences (Blanco et al. 1999:741).Thus, although this second neo-Darwinian scenario has the advantage of starting with functional genes and proteins, it also has a lethal disadvantage: any process of random mutation or rearrangement in the genome would in all probability generate nonfunctional intermediate sequences before fundamentally new functional genes or proteins would arise. Clearly, nonfunctional intermediate sequences confer no survival advantage on their host organisms. Natural selection favors only functional advantage. It cannot select or favor nucleotide sequences or polypeptide chains that do not yet perform biological functions, and still less will it favor sequences that efface or destroy preexisting function.Evolving genes and proteins will range through a series of nonfunctional intermediate sequences that natural selection will not favor or preserve but will, in all probability, eliminate (Blanco et al. 1999, Axe 2000). When this happens, selection-driven evolution will cease. At this point, neutral evolution of the genome (unhinged from selective pressure) may ensue, but, as we have seen, such a process must overcome immense probabilistic hurdles, even granting cosmic time.Thus, whether one envisions the evolutionary process beginning with a noncoding region of the genome or a preexisting functional gene, the functional specificity and complexity of proteins impose very stringent limitations on the efficacy of mutation and selection. In the first case, function must arise first, before natural selection can act to favor a novel variation. In the second case, function must be continuously maintained in order to prevent deleterious (or lethal) consequences to the organism and to allow further evolution. Yet the complexity and functional specificity of proteins implies that both these conditions will be extremely difficult to meet. Therefore, the neo-Darwinian mechanism appears to be inadequate to generate the new information present in the novel genes and proteins that arise with the Cambrian animals.Novel Body PlansThe problems with the neo-Darwinian mechanism run deeper still. In order to explain the origin of the Cambrian animals, one must account not only for new proteins and cell types, but also for the origin of new body plans. Within the past decade, developmental biology has dramatically advanced our understanding of how body plans are built during ontogeny. In the process, it has also uncovered a profound difficulty for neo-Darwinism.Significant morphological change in organisms requires attention to timing. Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21). Thus, events expressed early in the development of organisms have the only realistic chance of producing large-scale macroevolutionary change (Thomson 1992). As John and Miklos (1988:309) explain, macroevolutionary change requires alterations in the very early stages of ontogenesis.Yet recent studies in developmental biology make clear that mutations expressed early in development typically have deleterious effects (Arthur 1997:21). For example, when early-acting body plan molecules, or morphogens such as bicoid (which helps to set up the anterior-posterior head-to-tail axis in Drosophila), are perturbed, development shuts down (Nusslein-Volhard & Wieschaus 1980, Lawrence & Struhl 1996, Muller & Newman 2003).5 The resulting embryos die. Moreover, there is a good reason for this. If an engineer modifies the length of the piston rods in an internal combustion engine without modifying the crankshaft accordingly, the engine won't start. Similarly, processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200).This problem has led to what McDonald (1983) has called “a great Darwinian paradox” (p. 93). McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes--the very stuff of macroevolution--apparently do not vary. In other words, mutations of the kind that macroevolution doesn't need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don't occur.6 According to Darwin (1859:108) natural selection cannot act until favorable variations arise in a population. Yet there is no evidence from developmental genetics that the kind of variations required by neo-Darwinism--namely, favorable body plan mutations--ever occur.Developmental biology has raised another formidable problem for the mutation/selection mechanism. Embryological evidence has long shown that DNA does not wholly determine morphological form (Goodwin 1985, Nijhout 1990, Sapp 1987, Muller & Newman 2003), suggesting that mutations in DNA alone cannot account for the morphological changes required to build a new body plan.DNA helps direct protein synthesis.7 It also helps to regulate the timing and expression of the synthesis of various proteins within cells. Yet, DNA alone does not determine how individual proteins assemble themselves into larger systems of proteins; still less does it solely determine how cell types, tissue types, and organs arrange themselves into body plans (Harold 1995:2774, Moss 2004). Instead, other factors--such as the three-dimensional structure and organization of the cell membrane and cytoskeleton and the spatial architecture of the fertilized egg--play important roles in determining body plan formation during embryogenesis.For example, the structure and location of the cytoskeleton influence the patterning of embryos. Arrays of microtubules help to distribute the essential proteins used during development to their correct locations in the cell. Of course, microtubules themselves are made of many protein subunits. Nevertheless, like bricks that can be used to assemble many different structures, the tubulin subunits in the cell's microtubules are identical to one another. Thus, neither the tubulin subunits nor the genes that produce them account for the different shape of microtubule arrays that distinguish different kinds of embryos and developmental pathways. Instead, the structure of the microtubule array itself is determined by the location and arrangement of its subunits, not the properties of the subunits themselves. For this reason, it is not possible to predict the structure of the cytoskeleton of the cell from the characteristics of the protein constituents that form that structure (Harold 2001:125).Two analogies may help further clarify the point. At a building site, builders will make use of many materials: lumber, wires, nails, drywall, piping, and windows. Yet building materials do not determine the floor plan of the house, or the arrangement of houses in a neighborhood. Similarly, electronic circuits are composed of many components, such as resistors, capacitors, and transistors. But such lower-level components do not determine their own arrangement in an integrated circuit. Biological symptoms also depend on hierarchical arrangements of parts. Genes and proteins are made from simple building blocks--nucleotide bases and amino acids--arranged in specific ways. Cell types are made of, among other things, systems of specialized proteins. Organs are made of specialized arrangements of cell types and tissues. And body plans comprise specific arrangements of specialized organs. Yet, clearly, the properties of individual proteins (or, indeed, the lower-level parts in the hierarchy generally) do not fully determine the organization of the higher-level structures and organizational patterns (Harold 2001:125). It follows that the genetic information that codes for proteins does not determine these higher-level structures either.These considerations pose another challenge to the sufficiency of the neo-Darwinian mechanism. Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, namely, within the genetic text. Yet major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion.Of course, it could be argued that, while many single proteins do not by themselves determine cellular structures and/or body plans, proteins acting in concert with other proteins or suites of proteins could determine such higher-level form. For example, it might be pointed out that the tubulin subunits (cited above) are assembled by other helper proteins--gene products--called Microtubule Associated Proteins (MAPS). This might seem to suggest that genes and gene products alone do suffice to determine the development of the three-dimensional structure of the cytoskeleton.Yet MAPS, and indeed many other necessary proteins, are only part of the story. The location of specified target sites on the interior of the cell membrane also helps to determine the shape of the cytoskeleton. Similarly, so does the position and structure of the centrosome which nucleates the microtubules that form the cytoskeleton. While both the membrane targets and the centrosomes are made of proteins, the location and form of these structures is not wholly determined by the proteins that form them. Indeed, centrosome structure and membrane patterns as a whole convey three-dimensional structural information that helps determine the structure of the cytoskeleton and the location of its subunits (McNiven & Porter 1992:313-329). Moreover, the centrioles that compose the centrosomes replicate independently of DNA replication (Lange et al. 2000:235-249, Marshall & Rosenbaum 2000:187-205). The daughter centriole receives its form from the overall structure of the mother centriole, not from the individual gene products that constitute it (Lange et al. 2000). In ciliates, microsurgery on cell membranes can produce heritable changes in membrane patterns, even though the DNA of the ciliates has not been altered (Sonneborn 1970:1-13, Frankel 1980:607-623; Nanney 1983:163-170). This suggests that membrane patterns (as opposed to membrane constituents) are impressed directly on daughter cells. In both cases, form is transmitted from parent three-dimensional structures to daughter three-dimensional structures directly and is not wholly contained in constituent proteins or genetic information (Moss 2004).Thus, in each new generation, the form and structure of the cell arises as the result of both gene products and preexisting three-dimensional structure and organization. Cellular structures are built from proteins, but proteins find their way to correct locations in part because of preexisting three-dimensional patterns and organization inherent in cellular structures. Preexisting three-dimensional form present in the preceding generation (whether inherent in the cell membrane, the centrosomes, the cytoskeleton or other features of the fertilized egg) contributes to the production of form in the next generation. Neither structural proteins alone, nor the genes that code for them, are sufficient to determine the three-dimensional shape and structure of the entities they form. Gene products provide necessary, but not sufficient conditions, for the development of three-dimensional structure within cells, organs and body plans (Harold 1995:2767). But if this is so, then natural selection acting on genetic variation alone cannot produce the new forms that arise in history of life.Self-Organizational ModelsOf course, neo-Darwinism is not the only evolutionary theory for explaining the origin of novel biological form. Kauffman (1995) doubts the efficacy of the mutation/selection mechanism. Nevertheless, he has advanced a self-organizational theory to account for the emergence of new form, and presumably the information necessary to generate it. Whereas neo-Darwinism attempts to explain new form as the consequence of selection acting on random mutation, Kauffman suggests that selection acts, not mainly on random variations, but on emergent patterns of order that self-organize via the laws of nature.Kauffman (1995:47-92) illustrates how this might work with various model systems in a computer environment. In one, he conceives a system of buttons connected by strings. Buttons represent novel genes or gene products; strings represent the law-like forces of interaction that obtain between gene products-i.e., proteins. Kauffman suggests that when the complexity of the system (as represented by the number of buttons and strings) reaches a critical threshold, new modes of organization can arise in the system “for free”--that is, naturally and spontaneously--after the manner of a phase transition in chemistry.Another model that Kauffman develops is a system of interconnected lights. Each light can flash in a variety of states--on, off, twinkling, etc. Since there is more than one possible state for each light, and many lights, there are a vast number of possible states that the system can adopt. Further, in his system, rules determine how past states will influence future states. Kauffman asserts that, as a result of these rules, the system will, if properly tuned, eventually produce a kind of order in which a few basic patterns of light activity recur with greater-than-random frequency. Since these actual patterns of light activity represent a small portion of the total number of possible states in which the system can reside, Kauffman seems to imply that self-organizational laws might similarly result in highly improbable biological outcomes--perhaps even sequences (of bases or amino acids) within a much larger sequence space of possibilities. Do these simulations of self-organizational processes accurately model the origin of novel genetic information? It is hard to think so.First, in both examples, Kauffman presupposes but does not explain significant sources of preexisting information. In his buttons-and-strings system, the buttons represent proteins, themselves packets of CSI, and the result of preexisting genetic information. Where does this information come from? Kauffman (1995) doesn't say, but the origin of such information is an essential part of what needs to be explained in the history of life. Similarly, in his light system, the order that allegedly arises for “for free” actually arises only if the programmer of the model system “tunes” it in such a way as to keep it from either (a) generating an excessively rigid order or (b) developing into chaos (pp. 86-88). Yet this necessary tuning involves an intelligent programmer selecting certain parameters and excluding others--that is, inputting information.Second, Kauffman's model systems are not constrained by functional considerations and thus are not analogous to biological systems. A system of interconnected lights governed by pre-programmed rules may well settle into a small number of patterns within a much larger space of possibilities. But because these patterns have no function, and need not meet any functional requirements, they have no specificity analogous to that present in actual organisms. Instead, examination of Kauffman's (1995) model systems shows that they do not produce sequences or systems characterized by specified complexity, but instead by large amounts of symmetrical order or internal redundancy interspersed with aperiodicity or (mere) complexity (pp. 53, 89, 102). Getting a law-governed system to generate repetitive patterns of flashing lights, even with a certain amount of variation, is clearly interesting, but not biologically relevant. On the other hand, a system of lights flashing the title of a Broadway play would model a biologically relevant self-organizational process, at least if such a meaningful or functionally specified sequence arose without intelligent agents previously programming the system with equivalent amounts of CSI. In any case, Kauffman's systems do not produce specified complexity, and thus do not offer promising models for explaining the new genes and proteins that arose in the Cambrian.Even so, Kauffman suggests that his self-organizational models can specifically elucidate aspects of the Cambrian explosion. According to Kauffman (1995:199-201), new Cambrian animals emerged as the result of “long jump” mutations that established new body plans in a discrete rather than gradual fashion. He also recognizes that mutations affecting early development are almost inevitably harmful. Thus, he concludes that body plans, once established, will not change, and that any subsequent evolution must occur within an established body plan (Kauffman 1995:201). And indeed, the fossil record does show a curious (from a neo-Darwinian point of view) top-down pattern of appearance, in which higher taxa (and the body plans they represent) appear first, only later to be followed by the multiplication of lower taxa representing variations within those original body designs (Erwin et al. 1987, Lewin 1988, Valentine & Jablonski 2003:518). Further, as Kauffman expects, body plans appear suddenly and persist without significant modification over time.But here, again, Kauffman begs the most important question, which is: what produces the new Cambrian body plans in the first place? Granted, he invokes “long jump mutations” to explain this, but he identifies no specific self-organizational process that can produce such mutations. Moreover, he concedes a principle that undermines the plausibility of his own proposal. Kauffman acknowledges that mutations that occur early in development are almost inevitably deleterious. Yet developmental biologists know that these are the only kind of mutations that have a realistic chance of producing large-scale evolutionary change--i.e., the big jumps that Kauffman invokes. Though Kauffman repudiates the neo-Darwinian reliance upon random mutations in favor of self-organizing order, in the end, he must invoke the most implausible kind of random mutation in order to provide a self-organizational account of the new Cambrian body plans. Clearly, his model is not sufficient.Punctuated EquilibriumOf course, still other causal explanations have been proposed. During the 1970s, the paleontologists Eldredge and Gould (1972) proposed the theory of evolution by punctuated equilibrium in order to account for a pervasive pattern of “sudden appearance” and “stasis” in the fossil record. Though advocates of punctuated equilibrium were mainly seeking to describe the fossil record more accurately than earlier gradualist neo-Darwinian models had done, they did also propose a mechanism--known as species selection--by which the large morphological jumps evident in fossil record might have been produced. According to punctuationalists, natural selection functions more as a mechanism for selecting the fittest species rather than the most-fit individual among a species. Accordingly, on this model, morphological change should occur in larger, more discrete intervals than it would given a traditional neo-Darwinian understanding.Despite its virtues as a descriptive model of the history of life, punctuated equilibrium has been widely criticized for failing to provide a mechanism sufficient to produce the novel form characteristic of higher taxonomic groups. For one thing, critics have noted that the proposed mechanism of punctuated evolutionary change simply lacked the raw material upon which to work. As Valentine and Erwin (1987) note, the fossil record fails to document a large pool of species prior to the Cambrian. Yet the proposed mechanism of species selection requires just such a pool of species upon which to act. Thus, they conclude that the mechanism of species selection probably does not resolve the problem of the origin of the higher taxonomic groups (p. 96).8 Further, punctuated equilibrium has not addressed the more specific and fundamental problem of explaining the origin of the new biological information (whether genetic or epigenetic) necessary to produce novel biological form. Advocates of punctuated equilibrium might assume that the new species (upon which natural selection acts) arise by known microevolutionary processes of speciation (such as founder effect, genetic drift or bottleneck effect) that do not necessarily depend upon mutations to produce adaptive changes. But, in that case, the theory lacks an account of how the specifically higher taxa arise. Species selection will only produce more fit species. On the other hand, if punctuationalists assume that processes of genetic mutation can produce more fundamental morphological changes and variations, then their model becomes subject to the same problems as neo-Darwinism (see above). This dilemma is evident in Gould (2002:710) insofar as his attempts to explain adaptive complexity inevitably employ classical neo-Darwinian modes of explanation.9StructuralismAnother attempt to explain the origin of form has been proposed by the structuralists such as Gerry Webster and Brian Goodwin (1984, 1996). These biologists, drawing on the earlier work of D'Arcy Thompson (1942), view biological form as the result of structural constraints imposed upon matter by morphogenetic rules or laws. For reasons similar to those discussed above, the structuralists have insisted that these generative or morphogenetic rules do not reside in the lower level building materials of organisms, whether in genes or proteins. Webster and Goodwin (1984:510-511) further envisioned morphogenetic rules or laws operating ahistorically, similar to the way in which gravitational or electromagnetic laws operate. For this reason, structuralists see phylogeny as of secondary importance in understanding the origin of the higher taxa, though they think that transformations of form can occur. For structuralists, constraints on the arrangement of matter arise not mainly as the result of historical contingencies--such as environmental changes or genetic mutations--but instead because of the continuous ahistorical operation of fundamental laws of form--laws that organize or inform matter.While this approach avoids many of the difficulties currently afflicting neo-Darwinism (in particular those associated with its “genocentricity”), critics (such as Maynard Smith 1986) of structuralism have argued that the structuralist explanation of form lacks specificity. They note that structuralists have been unable to say just where laws of form reside--whether in the universe, or in every possible world, or in organisms as a whole, or in just some part of organisms. Further, according to structuralists, morphogenetic laws are mathematical in character. Yet, structuralists have yet to specify the mathematical formulae that determine biological forms.Others (Yockey 1992; Polanyi 1967, 1968; Meyer 2003) have questioned whether physical laws could in principle generate the kind of complexity that characterizes biological systems. Structuralists envision the existence of biological laws that produce form in much the same way that physical laws produce form. Yet the forms that physicists regard as manifestations of underlying laws are characterized by large amounts of symmetric or redundant order, by relatively simple patterns such as vortices or gravitational fields or magnetic lines of force. Indeed, physical laws are typically expressed as differential equations (or algorithms) that almost by definition describe recurring phenomena--patterns of compressible “order” not “complexity” as defined by algorithmic information theory (Yockey 1992:77-83). Biological forms, by contrast, manifest greater complexity and derive in ontogeny from highly complex initial conditions--i.e., non-redundant sequences of nucleotide bases in the genome and other forms of information expressed in the complex and irregular three-dimensional topography of the organism or the fertilized egg. Thus, the kind of form that physical laws produce is not analogous to biological form--at least not when compared from the standpoint of (algorithmic) complexity. Further, physical laws lack the information content to specify biology systems. As Polyanyi (1967, 1968) and Yockey (1992:290) have shown, the laws of physics and chemistry allow, but do not determine, distinctively biological modes of organization. In other words, living systems are consistent with, but not deducible, from physical-chemical laws (1992:290).Of course, biological systems do manifest some reoccurring patterns, processes and behaviors. The same type of organism develops repeatedly from similar ontogenetic processes in the same species. Similar processes of cell division reoccur in many organisms. Thus, one might describe certain biological processes as law-governed. Even so, the existence of such biological regularities does not solve the problem of the origin of form and information, since the recurring processes described by such biological laws (if there be such laws) only occur as the result of preexisting stores of (genetic and/or epigenetic) information and these information-rich initial conditions impose the constraints that produce the recurring behavior in biological systems. (For example, processes of cell division recur with great frequency in organisms, but depend upon information-rich DNA and proteins molecules.) In other words, distinctively biological regularities depend upon preexisting biological information. Thus, appeals to higher-level biological laws presuppose, but do not explain, the origination of the information necessary to morphogenesis.Thus, structuralism faces a difficult in principle dilemma. On the one hand, physical laws produce very simple redundant patterns that lack the complexity characteristic of biological systems. On the other hand, distinctively biological laws--if there are such laws--depend upon preexisting information-rich structures. In either case, laws are not good candidates for explaining the origination of biological form or the information necessary to produce it.Cladism: An Artifact of Classification?Some cladists have advanced another approach to the problem of the origin of form, specifically as it arises in the Cambrian. They have argued that the problem of the origin of the phyla is an artifact of the classification system, and therefore, does not require explanation. Budd and Jensen (2000), for example, argue that the problem of the Cambrian explosion resolves itself if one keeps in mind the cladistic distinction between “stem” and “crown” groups. Since crown groups arise whenever new characters are added to simpler more ancestral stem groups during the evolutionary process, new phyla will inevitably arise once a new stem group has arisen. Thus, for Budd and Jensen what requires explanation is not the crown groups corresponding to the new Cambrian phyla, but the earlier more primitive stem groups that presumably arose deep in the Proterozoic. Yet since these earlier stem groups are by definition less derived, explaining them will be considerably easier than explaining the origin of the Cambrian animals de novo. In any case, for Budd and Jensen the explosion of new phyla in the Cambrian does not require explanation. As they put it, “given that the early branching points of major clades is an inevitable result of clade diversification, the alleged phenomenon of the phyla appearing early and remaining morphologically static is not seen to require particular explanation” (Budd & Jensen 2000:253).While superficially plausible, perhaps, Budd and Jensen's attempt to explain away the Cambrian explosion begs crucial questions. Granted, as new characters are added to existing forms, novels morphology and greater morphological disparity will likely result. But what causes new characters to arise? And how does the information necessary to produce new characters originate? Budd and Jensen do not specify. Nor can they say how derived the ancestral forms are likely to have been, and what processes, might have been sufficient to produce them. Instead, they simply assume the sufficiency of known neo-Darwinian mechanisms (Budd & Jensen 2000:288). Yet, as shown above, this assumption is now problematic. In any case, Budd and Jensen do not explain what causes the origination of biological form and information.Convergence and Teleological EvolutionMore recently, Conway Morris (2000, 2003c) has suggested another possible explanation based on the tendency for evolution to converge on the same structural forms during the history of life. Conway Morris cites numerous examples of organisms that possess very similar forms and structures, even though such structures are often built from different material substrates and arise (in ontogeny) by the expression of very different genes. Given the extreme improbability of the same structures arising by random mutation and selection in disparate phylogenies, Conway Morris argues that the pervasiveness of convergent structures suggests that evolution may be in some way “channeled” toward similar functional and/or structural endpoints. Such an end-directed understanding of evolution, he admits, raises the controversial prospect of a teleological or purposive element in the history of life. For this reason, he argues that the phenomenon of convergence has received less attention than it might have otherwise. Nevertheless, he argues that just as physicists have reopened the question of design in their discussions of anthropic fine-tuning, the ubiquity of convergent structures in the history of life has led some biologists (Denton 1998) to consider extending teleological thinking to biology. And, indeed, Conway Morris himself intimates that the evolutionary process might be “underpinned by a purpose” (2000:8, 2003b:511).Conway Morris, of course, considers this possibility in relation to a very specific aspect of the problem of organismal form, namely, the problem of explaining why the same forms arise repeatedly in so many disparate lines of decent. But this raises a question. Could a similar approach shed explanatory light on the more general causal question that has been addressed in this review? Could the notion of purposive design help provide a more adequate explanation for the origin of organismal form generally? Are there reasons to consider design as an explanation for the origin of the biological information necessary to produce the higher taxa and their corresponding morphological novelty?The remainder of this review will suggest that there are such reasons. In so doing, it may also help explain why the issue of teleology or design has reemerged within the scientific discussion of biological origins (Denton 1986, 1998; Thaxton et al. 1992; Kenyon & Mills 1996: Behe 1996, 2004; Dembski 1998, 2002, 2004; Conway Morris 2000, 2003a, 2003b, Lonnig 2001; Lonnig & Saedler 2002; Nelson & Wells 2003; Meyer 2003, 2004; Bradley 2004) and why some scientists and philosophers of science have considered teleological explanations for the origin of form and information despite strong methodological prohibitions against design as a scientific hypothesis (Gillespie 1979, Lenior 1982:4).First, the possibility of design as an explanation follows logically from a consideration of the deficiencies of neo-Darwinism and other current theories as explanations for some of the more striking “appearances of design” in biological systems. Neo-Darwinists such as Ayala (1994:5), Dawkins (1986:1), Mayr (1982:xi-xii) and Lewontin (1978) have long acknowledged that organisms appear to have been designed. Of course, neo-Darwinists assert that what Ayala (1994:5) calls the “obvious design” of living things is only apparent since the selection/mutation mechanism can explain the origin of complex form and organization in living systems without an appeal to a designing agent. Indeed, neo-Darwinists affirm that mutation and selection--and perhaps other similarly undirected mechanisms--are fully sufficient to explain the appearance of design in biology. Self-organizational theorists and punctuationalists modify this claim, but affirm its essential tenet. Self-organization theorists argue that natural selection acting on self organizing order can explain the complexity of living things--again, without any appeal to design. Punctuationalists similarly envision natural selection acting on newly arising species with no actual design involved.And clearly, the neo-Darwinian mechanism does explain many appearances of design, such as the adaptation of organisms to specialized environments that attracted the interest of 19th century biologists. More specifically, known microevolutionary processes appear quite sufficient to account for changes in the size of Galapagos finch beaks that have occurred in response to variations in annual rainfall and available food supplies (Weiner 1994, Grant 1999).But does neo-Darwinism, or any other fully materialistic model, explain all appearances of design in biology, including the body plans and information that characterize living systems? Arguably, biological forms--such as the structure of a chambered nautilus, the organization of a trilobite, the functional integration of parts in an eye or molecular machine--attract our attention in part because the organized complexity of such systems seems reminiscent of our own designs. Yet, this review has argued that neo-Darwinism does not adequately account for the origin of all appearances of design, especially if one considers animal body plans, and the information necessary to construct them, as especially striking examples of the appearance of design in living systems. Indeed, Dawkins (1995:11) and Gates (1996:228) have noted that genetic information bears an uncanny resemblance to computer software or machine code. For this reason, the presence of CSI in living organisms, and the discontinuous increases of CSI that occurred during events such as the Cambrian explosion, appears at least suggestive of design.Does neo-Darwinism or any other purely materialistic model of morphogenesis account for the origin of the genetic and other forms of CSI necessary to produce novel organismal form? If not, as this review has argued, could the emergence of novel information-rich genes, proteins, cell types and body plans have resulted from actual design, rather than a purposeless process that merely mimics the powers of a designing intelligence? The logic of neo-Darwinism, with its specific claim to have accounted for the appearance of design, would itself seem to open the door to this possibility. Indeed, the historical formulation of Darwinism in dialectical opposition to the design hypothesis (Gillespie 1979), coupled with the neo-Darwinism's inability to account for many salient appearances of design including the emergence of form and information, would seem logically to reopen the possibility of actual (as opposed to apparent) design in the history of life.A second reason for considering design as an explanation for these phenomena follows from the importance of explanatory power to scientific theory evaluation and from a consideration of the potential explanatory power of the design hypothesis. Studies in the methodology and philosophy of science have shown that many scientific theories, particularly in the historical sciences, are formulated and justified as inferences to the best explanation (Lipton 1991:32-88, Brush 1989:1124-1129, Sober 2000:44). Historical scientists, in particular, assess or test competing hypotheses by evaluating which hypothesis would, if true, provide the best explanation for some set of relevant data (Meyer 1991, 2002; Cleland 2001:987-989, 2002:474-496).10 Those with greater explanatory power are typically judged to be better, more probably true, theories. Darwin (1896:437) used this method of reasoning in defending his theory of universal common descent. Moreover, contemporary studies on the method of “inference to the best explanation” have shown that determining which among a set of competing possible explanations constitutes the best depends upon judgments about the causal adequacy, or “causal powers,” of competing explanatory entities (Lipton 1991:32-88). In the historical sciences, uniformitarian and/or actualistic (Gould 1965, Simpson 1970, Rutten 1971, Hooykaas 1975) canons of method suggest that judgments about causal adequacy should derive from our present knowledge of cause and effect relationships. For historical scientists, “the present is the key to the past” means that present experience-based knowledge of cause and effect relationships typically guides the assessment of the plausibility of proposed causes of past events.Yet it is precisely for this reason that current advocates of the design hypothesis want to reconsider design as an explanation for the origin of biological form and information. This review, and much of the literature it has surveyed, suggests that four of the most prominent models for explaining the origin of biological form fail to provide adequate causal explanations for the discontinuous increases of CSI that are required to produce novel morphologies. Yet, we have repeated experience of rational and conscious agents--in particular ourselves--generating or causing increases in complex specified information, both in the form of sequence-specific lines of code and in the form of hierarchically arranged systems of parts.In the first place, intelligent human agents--in virtue of their rationality and consciousness--have demonstrated the power to produce information in the form of linear sequence-specific arrangements of characters. Indeed, experience affirms that information of this type routinely arises from the activity of intelligent agents. A computer user who traces the information on a screen back to its source invariably comes to a mind--that of a software engineer or programmer. The information in a book or inscriptions ultimately derives from a writer or scribe--from a mental, rather than a strictly material, cause. Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source from a mind or personal agent. As Quastler (1964) put it, the “creation of new information is habitually associated with conscious activity” (p. 16). Experience teaches this obvious truth.Further, the highly specified hierarchical arrangements of parts in animal body plans also suggest design, again because of our experience of the kinds of features and systems that designers can and do produce. At every level of the biological hierarchy, organisms require specified and highly improbable arrangements of lower-level constituents in order to maintain their form and function. Genes require specified arrangements of nucleotide bases; proteins require specified arrangements of amino acids; new cell types require specified arrangements of systems of proteins; body plans require specialized arrangements of cell types and organs. Organisms not only contain information-rich components (such as proteins and genes), but they comprise information-rich arrangements of those components and the systems that comprise them. Yet we know, based on our present experience of cause and effect relationships, that design engineers--possessing purposive intelligence and rationality--have the ability to produce information-rich hierarchies in which both individual modules and the arrangements of those modules exhibit complexity and specificity--information so defined. Individual transistors, resistors, and capacitors exhibit considerable complexity and specificity of design; at a higher level of organization, their specific arrangement within an integrated circuit represents additional information and reflects further design. Conscious and rational agents have, as part of their powers of purposive intelligence, the capacity to design information-rich parts and to organize those parts into functional information-rich systems and hierarchies. Further, we know of no other causal entity or process that has this capacity. Clearly, we have good reason to doubt that mutation and selection, self-organizational processes or laws of nature, can produce the information-rich components, systems, and body plans necessary to explain the origination of morphological novelty such as that which arises in the Cambrian period.There is a third reason to consider purpose or design as an explanation for the origin of biological form and information: purposive agents have just those necessary powers that natural selection lacks as a condition of its causal adequacy. At several points in the previous analysis, we saw that natural selection lacked the ability to generate novel information precisely because it can only act after new functional CSI has arisen. Natural selection can favor new proteins, and genes, but only after they perform some function. The job of generating new functional genes, proteins and systems of proteins therefore falls entirely to random mutations. Yet without functional criteria to guide a search through the space of possible sequences, random variation is probabilistically doomed. What is needed is not just a source of variation (i.e., the freedom to search a space of possibilities) or a mode of selection that can operate after the fact of a successful search, but instead a means of selection that (a) operates during a search--before success--and that (b) is guided by information about, or knowledge of, a functional target.Demonstration of this requirement has come from an unlikely quarter: genetic algorithms. Genetic algorithms are programs that allegedly simulate the creative power of mutation and selection. Dawkins and Kuppers, for example, have developed computer programs that putatively simulate the production of genetic information by mutation and natural selection (Dawkins 1986:47-49, Kuppers 1987:355-369). Nevertheless, as shown elsewhere (Meyer 1998:127-128, 2003:247-248), these programs only succeed by the illicit expedient of providing the computer with a “target sequence” and then treating relatively greater proximity to future function (i.e., the target sequence), not actual present function, as a selection criterion. As Berlinski (2000) has argued, genetic algorithms need something akin to a “forward looking memory” in order to succeed. Yet such foresighted selection has no analogue in nature. In biology, where differential survival depends upon maintaining function, selection cannot occur before new functional sequences arise. Natural selection lacks foresight.What natural selection lacks, intelligent selection--purposive or goal-directed design--provides. Rational agents can arrange both matter and symbols with distant goals in mind. In using language, the human mind routinely “finds” or generates highly improbable linguistic sequences to convey an intended or preconceived idea. In the process of thought, functional objectives precede and constrain the selection of words, sounds and symbols to generate functional (and indeed meaningful) sequences from among a vast ensemble of meaningless alternative combinations of sound or symbol (Denton 1986:309-311). Similarly, the construction of complex technological objects and products, such as bridges, circuit boards, engines and software, result from the application of goal-directed constraints (Polanyi 1967, 1968). Indeed, in all functionally integrated complex systems where the cause is known by experience or observation, design engineers or other intelligent agents applied boundary constraints to limit possibilities in order to produce improbable forms, sequences or structures. Rational agents have repeatedly demonstrated the capacity to constrain the possible to actualize improbable but initially unrealized future functions. Repeated experience affirms that intelligent agents (minds) uniquely possess such causal powers.Analysis of the problem of the origin of biological information, therefore, exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess. Intelligent agents have foresight. Such agents can select functional goals before they exist. They can devise or select material means to accomplish those ends from among an array of possibilities and then actualize those goals in accord with a preconceived design plan or set of functional requirements. Rational agents can constrain combinatorial space with distant outcomes in mind. The causal powers that natural selection lacks--almost by definition--are associated with the attributes of consciousness and rationality--with purposive intelligence. Thus, by invoking design to explain the origin of new biological information, contemporary design theorists are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence. Instead, they are positing an entity possessing precisely the attributes and causal powers that the phenomenon in question requires as a condition of its production and explanation.ConclusionAn experience-based analysis of the causal powers of various explanatory hypotheses suggests purposive or intelligent design as a causally adequate--and perhaps the most causally adequate--explanation for the origin of the complex specified information required to build the Cambrian animals and the novel forms they represent. For this reason, recent scientific interest in the design hypothesis is unlikely to abate as biologists continue to wrestle with the problem of the origination of biological form and the higher taxa.

Evolution's Shortcomings

Source Article

Standard Evolutionary Theory
Has Shortcomings
By: Henry Schaefer
Atlanta Journal-Constitution
September 28, 2002
See at: Atlanta Journal-Constitution

As a theorist who uses quantum mechanics to solve problems ranging from biochemistry to astrophysics, the subject of this essay is of great interest to me. It is a question that is discussed in depth in my University of Georgia freshman seminar entitled “Science and Christianity: Conflict or Coherence?” This autumn 18 gifted UGA students and I are spending six weeks examining Stephen Hawking’s best-selling book “A Brief History of Time.” Therein Hawking states, “A theory is a good theory if it satisfies two requirements. It must accurately describe a large class of observations on the basis of a model that contains only a few arbitrary elements. And it must make definite predictions about the results of future observations.”I consider Hawking’s statement to be an excellent definition of a good theory. How does evolution stack up to the two demands of a good theory? By the term “evolution,” I mean the claim that random mutations and natural selection can fully account for the complexity of life, and particularly macroscopic living things.I think that the standard evolutionary model does a good job of categorizing and systematizing the fossil record. It serves as an effective umbrella or big tent under which to collect a large number of observations. If evolution has a weakness in this regard, it is that the tent is too big. Thus the 20th century witnessed a series of hoaxes, beginning in 1908 with Piltdown Man and continuing to recent fabricated fossil “discoveries” in China, that have been embraced as missing links by distinguished paleontologists.Nevertheless, I give evolution a B grade with respect to Hawking’s first category.The second requirement for a good theory is far more problematical for the standard evolutionary model, sometimes called the modern synthesis. Over the past 150 years evolutionary theorists have made countless predictions about fossil specimens to be observed in the future.Unfortunately for these seers, many new fossils have been discovered, and the interesting ones almost always seem to be contrary to the “best” predictions. This is sometimes true even when the predictions are rather vague, as seen by the continuing controversies associated with the purported relationships between dinosaurs and birds.Is the expectation that a good theory be predictive unrealistic? Let us consider two theories to which evolution is often favorably compared. The theory of gravity precisely predicted the appearances of Halley’s comet in 1910 and 1986. On the latter occasion I was on sabbatical from Berkeley at the University of Canterbury in Christchurch, New Zealand. The newspaper (informed by classical mechanics and the law of gravity) told me exactly when I had to wake up in the middle of the night to enjoy the wonder of Halley’s Comet. And in fact, the theory of gravity never fails for the macroscopic objects to which it is applicable.A second successful theory, the atomic theory, is grounded in Schroedinger’s Equation and the Dirac Equation. Atomic theory is able to make many predictions of the spectra of the hydrogen molecule and the helium atom to more significant figures that may be currently measured in the laboratory. We are utterly confident that these predictions will be confirmed by future experiments.By any reasonable standard the theory of gravity and the atomic theory are good theories, well deserving of A grades. In comparison with these quantitative theories of the physical sciences, when it comes to Hawking’s second requirement for a good theory, the standard evolutionary model fails, and should be given a D grade at best. Might I be more detailed in stating my reservations concerning the standard evolutionary model? Sure. Let me preface these brief remarks by noting that I think the scientific evidence that God created the universe 13-15 billion years ago is good.My first concern is that, with the collapse of the Miller-Urey model, there is no plausible scientific mechanism for the origin of life, i.e., the appearance of the first self-replicating biochemical system. The staggeringly high information content of the simplest living thing is not readily explained by evolutionists.Second, the time frame for speciation events seems all wrong to me. The major feature of the fossil record is stasis, long periods in which new species do not appear. When new developments occur, they come rapidly, not gradually.My third area of reservation is that I find no satisfactory mechanism for macroevolutionary changes. Analogies between a few inches of change in the beaks of a Galapagos finch species and a purported transition from dinosaur to bird (or vice versa) appear to me inappropriate.

The High Cost of Ignorance

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Watching a well-known television news—commentary program recently, I was quite surprised at an exchange between the host and his guest. Although the host openly professes to be Christian and belongs to a major mainline denomination, he utterly rejected his guest's reference to the Old Testament to support his point. "That's all just allegorical," the host snorted. "It doesn't mean anything for us today." When the guest then tried to quote from one of Paul's epistles, the host interrupted again. "That's not the gospel," he snapped.
How sad, I thought, that such a nationally known and respected figure can so casually dismiss the Old Testament—about three quarters of the entire Bible—as "just allegorical" and irrelevant and then turn around and dismiss more than half of what's left over with "that's not the gospel."
It's this kind of thinking that prompted the theme of this issue—that the Bible is always relevant and a book for all mankind, for all ages.
Few people have ever considered the Bible a reliable guide for proper diet and good physical and mental health. Yet scattered throughout its pages are priceless laws and principles that would literally save millions of lives every year—if people would only pay attention to them.
Consider, for a moment, one of today's deadliest killers, AIDS. Probably a week doesn't go by that you don't see the disease mentioned in the headlines or referred to on the evening news. It is the fourth-leading cause of death worldwide. Yet AIDS is entirely preventable and wouldn't even exist if people only lived according to the laws revealed in the Bible.
How did the AIDS epidemic begin? No one knows for sure, but now we know that African green monkeys carry a related virus naturally in their blood. Several decades ago the virus jumped to human beings, apparently when hunters killed and butchered infected monkeys for food. Once it entered the human bloodstream, the virus proved deadly and unstoppable.
But it need not have started there, and wouldn't have, if people obeyed God's laws that forbid eating the flesh of apes—a biblically designated "unclean" animal. God's Word clearly states that the flesh of some animals should never be eaten (Leviticus 11; Deuteronomy 14).
So AIDS could have ended there. But it didn't. Those who were initially infected had sexual relations with their spouses—but also with others. In violating God's laws forbidding adultery (Exodus 20:14), those who were infected unknowingly passed on a death sentence to their unsuspecting sexual partners. Some of them, in turn, passed it on to others.
In the Western world the disease—still unnamed and unidentified—was first noticed in homosexual men, among whom it was spreading like wildfire. Researchers soon discovered that common homosexual practices were highly effective ways to spread the deadly virus. Such behavior is condemned in the Bible (Leviticus 20:13; 1 Corinthians 6:9-10).
In most other countries AIDS spread as a heterosexual disease (between men and women). Prostitution, extramarital and premarital sex—all violations of God's commands—saw to it that the epidemic would continue its grim march around the globe. Another factor—sharing syringes to inject illegal drugs—also played a significant role.
Now, because of all of these factors, AIDS is firmly entrenched throughout the world. At any of these stages along the way, the disease could have been confined so that it would have died out within a generation—had not people persisted in disobeying God's laws. The sins of others have affected many innocent people as well, including babies, spouses, and hemophiliacs who received tainted blood transfusions.
The world spends some $60 billion a year treating AIDS, educating people about it and trying to slow its advance. It has already taken some 20 million lives; another 36 million live under its death sentence.
That's a terribly costly price to pay for ignorance. Isn't it about time we paid attention to what God says?
—Scott Ashley

Did God Create Evil People?

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Viewing the suffering around the globe caused by evil leaders is discouraging. Some countries are run by outright drug lords. Others are ruled by leaders who abuse their own people. Saddam Hussein has become a poster boy of the evil tyrant in the 21st century just as Hitler and Stalin were in the 20th. Why would a good God create such evil people?
by Gary Petty
Just over a century ago the Wright brothers got the first airplane off the ground. Could they have ever imagined that someday men would stand on the moon?
Medical science has made enormous strides in dealing with human diseases and injuries. In economically advanced nations we take for granted the automobile, television, electricity, air travel and computers.
In spite of all this scientific wonder, the last century witnessed the evil of Auschwitz, communist totalitarianism, the rise of terrorism in the name of religion and the use of technology as a tool of despotism.
Christianity rightly claims that each person has value and is a special creation of the Creator. Then why do people commit heinous crimes? Did God create people evil?
Over the millennia many thinking people have struggled with this dilemma. There's a wonder and beauty to human life, but there is also a terrible evil that plagues mankind.
When we look at what makes us different from animals, the gulf is enormous. Prairie dogs burrow, human beings construct skyscrapers. Sparrows chirp simple musical notes, human beings compose symphonies. Horses learn to answer what is two plus two by pounding a hoof four times, human beings calculate the distance between galaxies in light years.
At the same time, prairie dogs, sparrows and horses don't manufacture nerve gas and use it to murder their own kind. The irony is that our uniqueness of consciousness, creativity and ability to think in abstracts are the same abilities that give us the capability for unimaginable evil.
Did God plan to make people evil?
The biblical account of creation shows that the first human beings originally displayed no evil thoughts or actions. They lived in harmony with their Creator and with each other.
The Bible reveals that human beings were made in the image and likeness of God. This is why we have the ability to love, to reason and to feel and express complex emotions.
God also gave us something else. Along with reasoning—and the capacity to look at facts and come to conclusions—comes the power to choose. We make hundreds of reasoned choices each day. We decide what to wear and pick what we'll have for lunch. We determine which projects get priority. We also choose which thoughts we'll consider and which ones we'll discard, how we'll deal with our emotions and what actions we'll take in treating others.
In this way human beings have the capacity to choose between good and evil. We can choose to control our anger or we can choose to burn down our neighbor's house in revenge. The issue of choice is a complex human activity, but freedom of choice explains why human beings can be both good and evil.
Why would anyone choose evil?
We are born with a few inherent instincts. One is self-preservation. If we didn't have a will to survive, the entire race would've died off millennia ago. We also want to avoid unpleasant experiences. No one wants to feel physical pain or the discomfort of being cold or hungry. No one wants to feel emotionally rejected or made to feel worthless by others. We also want to feel good. We desire to please our five senses.
The instinct for self-preservation, need for food and shelter, and desire to please the senses aren't evil. But how we choose to fulfill those desires can be good or evil.
It really comes down to how much we're motivated by selfishness. It's hard to accept that all the evil in the world comes down to something so simple. Selfishness is the root of evil.
Because of the intensity of our instinct for self-preservation and our desire for fulfillment of the senses, each person tends to see himself or herself as the center of the universe. Yet the more a person is motivated by unbridled selfishness, the more hurtful his or her choices will be.
It's easy to see evil in people like Saddam Hussein, who on a national scale exerted selfishness on others through force and violence. It's much more difficult to come to grips with the selfishness that lies within each of us.
The more we focus on our selfish desires, the less we are able to recognize or understand our own faults and to experience concern for the welfare of others. The more a person is controlled by selfishness, the more that person shifts responsibility for his or her actions to others.
The introduction of evil
In our supposedly enlightened society we've relegated Satan to the status of myth. According to the Bible, however, Satan the devil most assuredly is a real being. He is a created angel who rebelled against God and became His—and mankind's—adversary.
When Satan chose to reject God, his character became the opposite of the Creator's. Where God's focus is love and peace, Satan's is hate and violence. Where God is outward in His concern for others, the devil is inward and selfish in every thought and action.
In the Genesis account, Satan tempts Eve with the forbidden fruit. Genesis 3:6 says that Eve "saw that the tree was good for food, that it was pleasant to the eyes, and a tree desirable to make one wise . . ." Eve was motivated by three human drives that have the capacity to produce evil.
She was motivated by the fact that the fruit was "good for food"—appealing to her need for self-preservation. It "was pleasant to the eyes"—pleasing to the senses. And it was "desirable to make one wise." Human beings are designed with a wonderful sense of curiosity—a desire to know and acquire understanding.
Eve knew God had forbidden them to eat of the fruit of this particular tree. Satan lied and told her that God was holding back something good. Her natural, morally neutral tendencies were now twisted into selfishness. Eve now wanted to satisfy her self-centered need for pleasure and intellectual superiority. Adam was motivated by the same selfishness. Once they disobeyed God, they immediately began to experience life on Satan's level.
Their human nature became a mixture of good and evil. The evil in them, and in all of us, is a reflection of the devil's evil nature and is the opposite of what God intended for us.
Biblical clarification of human nature
The apostle John, writing near the end of the first century, writes about three human motivations—"the lust of the flesh, the lust of the eyes, and the pride of life" (1 John 2:16). John sees the evil in human beings as rooted in the motivations of self-preservation, fulfillment of the five senses and this need to feel superior to others. This is just another way of stating Eve's motivations as recorded in Genesis.
We find another revealing passage in chapter 2 of Paul's letter to the Ephesians. There he describes Satan as "the prince of the power of the air" (verse 2).
Paul recognized Satan's ability to "broadcast" attitudes of anger, hatred, greed and lust—influencing human beings with all the negative, destructive aspects of his nature. Human minds are like radios that are tuned into his thoughts and emotions. Satan appeals to our desire for self-preservation and self-fulfillment, and every person takes on some of his nature.
Can a person change?
Much of human history is bleak. Sadly, all too often it is a chronicle of man's inhumanity to man, war, crime, racism and waste of human life.
Many people spend their lives making money and never have enough. Others have countless sexual encounters only to end up feeling empty and dying from a sexually transmitted disease. The world is dotted with grand cathedrals and megachurches where people go to be entertained and feel good about themselves, but their nature of lust and greed stays the same. Unless human nature is changed, religion is nothing more than a show.
People can undergo behavioral modification, but changing their essential nature requires an added spiritual dimension. Only God can change the core of our being. The central message of Jesus Christ is that wayward human beings can be forgiven of their sins and can have their nature changed.
The apostle Paul writes to members of the Church in Ephesians 2:1-3: "And you He made alive, who were dead in trespasses and sins, in which you once walked according to the course of this world, according to the prince of the power of the air, the spirit who now works in the sons of disobedience, among whom also we all once conducted ourselves in the lusts of our flesh, fulfilling the desires of the flesh and of the mind, and were by nature children of wrath, just as the others."
Paul says that these Christians were going through a dramatic change of life and were no longer "by nature children of wrath." In verse 10 Paul explains that "we are His workmanship, created in Christ Jesus for good works, which God prepared beforehand that we should walk in them."
Human beings are the only physical creatures still unfinished. Dogs are dogs. Birds are birds. They are complete creations that can only adapt to a new environment in limited ways. On the other hand, human beings are searching for meaning. We can and do grow emotionally, mentally and socially.
One of the most incredible concepts revealed in the Bible is that salvation is creation. Although it is the foundational first step in our salvation, the Messiah didn't come to earth just to die for the forgiveness of sins. God's forgiveness opens the door for human beings to have a relationship with their Creator and begin the growth process to become what God intended us to be.
The world of violence, poverty, alcoholism, drug abuse, drive-by shootings and broken marriages isn't the world God created for us. We've done this to ourselves, with Satan's help. It will never get better until each of us is willing to recognize the evil of our own selfishness.
Remember that self-preservation, desire to fulfill the senses and curiosity to acquire knowledge aren't evil. But these aspects of our nature have been twisted into self-centeredness. The driving force in so much of what people say and do is in the pursuit of things, feeling good and claiming superiority to others.
What we're missing
The great irony is that selfishness is amazingly self-destructive. The more we obsess on satisfying self through possessions, status, sex or any other purely physical means, the more unsatisfied we become. Human beings can never experience real happiness without dealing with the spiritual side of our nature.
Once Satan awakens selfishness in us, we are unable to fully control our own desires and emotions. We need help from outside ourselves. We can never come into a close relationship with the Creator until we recognize our moral helplessness.
There's a fascinating passage in 1 Corinthians 2 where the apostle Paul writes about the uniqueness of the human spirit. Today we would call this spirit the mind, which is the capacity for conscious thought and emotions. Paul then makes a remarkable statement in verse 11: "For what man knows the things of a man except [by] the spirit of the man which is in him? Even so no one knows the things of God except [by] the Spirit of God."
God wants to transform our corrupted nature into divine nature. When we repent and sincerely want to change, God takes a "piece" of Himself, His Spirit—His unselfish nature, His mind, His pure love—and places that inside our minds to change how we think and feel.
Baptism symbolizes major change
It is a travesty that in so much of Christianity today baptism has become an unimportant and often-ignored doctrine. Yet Jesus clearly commanded His followers to be baptized as a symbol of God's washing away of their sins. Paul also explained that baptism represented putting to death the old man and being raised to a new life, empowered to become like Christ through the help of God's Spirit (Romans 6, 8).
Another New Testament symbol that has been all but forgotten is the laying on of hands. In the early Church a person was baptized and then the elders of the Church laid hands on him or her so that through them God would then place His Holy Spirit within the newly baptized persons (Acts 8:17). The New Testament is filled with instructions about how a Spirit-led Christian then becomes a "new man" (Ephesians 4:22-24; Colossians 3:9-10).
Many people profess Christ, but afterwards remain the same person. The "come to Jesus just as you are" message may have appeal, but if a person truly accepts Christ then he knows he must make changes to become a "new man." Corrupted human nature is unfit to spend eternity in God's Kingdom. This physical life is the preparation ground for eternity.
All of us experience good and evil, and in the process we become a mixture of good and evil. We can be saved from the evil only by what God is doing through Jesus Christ as a sacrifice for our sins and as the model for our character. We Christians struggle with selfishness as long as we possess elements of human nature, but if we submit to God's creative process then we can literally be His children forever in His Kingdom.
The hardest thing to admit
The notorious gangster Al Capone once said: "I have spent the best years of my life giving people the lighter pleasures, helping them have a good time, and all I get is abuse, the existence of a hunted man."
People who are totally controlled by their own selfishness don't realize that their actions are morally wrong. They believe they deserve to please their senses no matter what the cost is to others. The reality is that all have sinned and have fallen short of the glory of God (Romans 3:23).
But God didn't create the evil world we live in. Nor did He create the devil, the unrealized and unseen evil influence that affects us all. God is the only solution to our problems. The sickness of selfishness lies within mankind and can only be solved through a miraculous change in human nature.
But that change can begin with you! If you're tired of the struggle for meaning and purpose, then it's time you asked God to start His creative process of salvation within you.
Jesus Christ promised His disciples that He was leaving to prepare a place for them, but that He would return to establish His Father's Kingdom on earth. This is a call to those who wish to be citizens of that Kingdom. God wants you to be His child. Are you willing to come to Him as your Father? GN

....and if we should fail?

Dhimmitude is the ultimate fate of any people who fall to the terrorists. It is the reason we need to take this war seriously. Apparently 51% of Americans do understand. Do you?

Rich Terrorists or Poor Terrorists?

So do these guys become Jihadists because of poverty or is it something else?

Many left-liberal critics postulate that Islamist terror is a backlash against economic inequality and social injustice.

In other words, if Osama and al-Zarqawi had had a dream mansion in their youth, with a large screen TV, a remote control, a play station and an indoor swimming pool, then neither of them would have become very interested in a holy jihad against the West. Right?

The only problem with this picture is that, as the empirical evidence suggests, when it comes to a significant number of the Islamist jihadists, poverty is something that eluded them all of their lives. These terrorists come from wealthy, educated, and privileged backgrounds. They have been the beneficiaries of all the luxuries of modernization and Westernization. . .which they ultimately despise and reject.

What do you make of this phenomenon? Prof. Mansur why don’t we begin with you?

Go read the rest here.

Gospels tell of true Jesus, says Canadian scholar

Mainstream academics are increasingly confident about the historical portrait of Jesus in the gospels, says a prominent Canadian scholar -- despite the skeptical headlines generated by a few celebrity theologians. "If you bracket off the Jesus Seminar -- and they grab all the headlines -- the work of the last 30 years has given us much greater confidence that the gospels can yield a coherent, historically accurate portrait of Jesus," said Craig Evans, Payzant Distinguished Professor of New Testament at Acadia University in Wolfville, N.S. "The half-dozen leaders and three-dozen members of the Jesus Seminar create the impression the scholarship is seriously divided. But I've been at annual meetings of the Institute for Biblical Research, with hundreds of scholars, and no one can take their outrageous claims seriously any more. "The trend -- from archeology, new literary discoveries and reassessing the cultural context -- is to see the gospel as essentially reliable. Our understanding of Jesus is more nuanced, more Jewish and more unpredictable." Evans, the author of 14 books (including the Dictionary of New Testament Background), was delivering the University of Calgary's annual Bental Lecture on Education and Theology, Monday, at Northmount Baptist Church. Before a packed house of over 250 academics, students and laymen, he addressed on the topic, "What Are They Saying About the Historical Jesus?" -- the "They" being scholars. Evans began his lecture with a slap at Dan Brown's blockbuster The Da Vinci Code; for all Brown purports to use modern scholarship, "some of his facts are at best dubious and some are demonstrably mistaken," Evans said. However, Brown can be credited with stirring up renewed interest in the historical Jesus -- including the 10 new books refuting him. Scholars' new confidence in the historical accuracy of the gospels has resulted largely from a new appreciation of Jesus' Jewishness, said Evans. This came initially from Jewish scholars like Geza Vermes, with his trilogy, Jesus the Jew. Jesus' Jewishness discredits the theory of celebrity academics John Dominic Crossan and Burton Mack, that he was a cynic philosopher. Though few of the Dead Sea Scrolls are devoted to First century Jewish messianic hopes, the scrolls have clarified those expectations, said Evans, who helped found Trinity Western University's Dead Sea Scrolls Institute in the mid-1990s. And Jesus clearly expressed those hopes. Scroll 4Q521 (fourth Qumran cave, fragment 521), from 100 BC, prophesizes, "when the messiah comes, the good news will be preached to the poor, the eyes of the blind will be opened, and the dead will be raised" -- exactly the message the gospel says Jesus sent to John the Baptist in prison to confirm his messianic identity (Matt 11:3-5). Seeing Jesus as the Jewish messiah must influence how Christians see their saviour, Evans said in a later interview with the Herald: "He wasn't saying, 'Come on, fellows, it's time to go to heaven.' He was saying, 'God's reign is breaking into the world. And God can't abide sin, so it's time to return to the ways of righteousness.' " Both archeology and an appreciation of Jewish culture also discredit Crossan's theory that a crucified criminal would never have been buried -- that Jesus' body would have been thrown to the dogs. The preserved remains of a crucified Jew proves Jewish burial laws applied to criminals. There is cultural credibility in the gospel stories of Jesus' use of Passover imagery for his impending execution, the interaction of Roman and Jewish officials, the Jewish council taking charge of the body, and the women finding the empty tomb -- "careful attention to the tomb would have been exactly what we expected." Addressing the controversy over Mel Gibson's The Passion of the Christ -- particularly the issue, who killed Jesus? -- Evans said the consensus is, "Roman and Jewish authorities working together" in standard imperial procedure. Gibson, however, was "too soft on Pilate," whose hesitation to condemn the troublemaker was simply cynical political caution. The full text of Evan's lecture will be available by mid-November at the website of the Chair of Christian Thought, www.christchair.ucalgary.ca

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Eroding Evolution's Believability

Once again, evolutionists strike when the iron is hot in an attempt to affirm the same bogus evolutionary dogma they have crammed down our throats for 150 years. Once again, they've got it wrong. The recent discovery of a dwarf skeleton on the remote Indonesian island of Flores has scientists anxious to create another sub-class of humans. This one is called Homo floresiensis, which implies that they belong to a different species of people than those living today, we Homo sapiens. Researchers found the skull and part of the skeleton of an adult female, plus bones and teeth from seven other individuals. These remains have many features similar to Homo erectus, another so-called human species claimed to be the ape-man of Africa and our subhuman ancestor. Now researchers suggest the Flores bones are dwarfed descendants of Homo erectus. At least with this much I would be willing to agree. According to many experts, "there is so little evidence in Homo erectus specimens outside the range of human variation that they are likely just another type of human resulting from genetic diversification." But the showstopper in the recent discovery of Homo flores came when the 3-foot-tall adult female skeleton was dated as only 18,000 years old. That means this hobbit-like dwarf of a human shatters the long-held scientific belief that Homo sapiens systematically crowded out other upright walking human cousins some 160,000 years ago and took over the human population tens of thousands of years ago. But wait, there's more. This "would-be missing link" between us and the original missing link also happens to have the brain size of a grapefruit, which is 2/3 smaller than ours. It is actually closer to the brain size of a modern day monkey and other pre-human ancestors who purportedly became extinct 2 million years ago. According to authorities, this is what makes the dwarf skeleton the most extreme figure to be included in the extended human family. Chris Stringer, the director of human origins studies at the Natural History Museum in London, said this finding "rewrites our knowledge of human history." In other words, this finding suggests recent evolution was (just had to be) more complex than previously thought. (Now that's an understatement.) Think about the rather recent results from mapping the human genome. They revealed the instructions for creating human life are packed into roughly 35,000 genes, only 15,000 more genes than certain worms and about twice as many as a fruit fly. This discovery alone dramatically increased the complexity of function in DNA necessary to sustain increasingly complex life forms and account for the spontaneous creation and diversification of all species according to traditional notions of evolution. Now add the recent finding of Flores man. He contains a jumble of features that appear borrowed from extinct primitive man. Yet he lived crossing timelines with both Homo erectus and Homo sapiens. If previous timelines are to be believed, this indicates dramatic changes in DNA and creation of a new species rather recently – not millions of years ago. It also suggests a lengthy coexistence of two different species of man based on geologic evidence that a massive volcano caused the extinction of Homo flores as recently as 12,000 years ago. None of these possibilities are consistent with traditional evolutionary theory. Confounding evolutionists further, the Flores man had to migrate to the Indonesian island by boat. Yet building a boat to sail on the open sea is traditionally thought to be beyond the intellectual abilities of Homo erectus. Remember, Homo flores has a brain size smaller than even Homo erectus. Additionally, the site of the find gives evidence of controlled use of fire and sophisticated stone tools. All together, these new findings shatter another long-held belief by evolutionists: that you need a particular brain size to do anything intelligent. As for their small body size of the recently found species, it adds no support to evolutionary theory. Nature is full of examples such as deer, elephants and pigs living in marginal, isolated environments that gradually dwarf when food and resources are limited. Dwarfism also exists in the current human population worldwide. According to the Guinness Book of World Records, some of the more famous modern-day dwarfs include actress Tamara de Treaux, who at 2 feet 7 inches tall played ET in Steven Spielberg's blockbuster film. There is also Filipino paratrooper and black-belt martial arts exponent Weng Wang, who measures just 2 feet 9 inches tall. And the shortest married couple was the Brazilian pair Douglas da Silva and Claudia Rocha. When they married in 1998, they were 35 inches and 36 inches, respectively. All contradictions of the traditional theory ignored, evolutionary dogma continues to be shoveled with the dirt that uncovered Homo flores. Yet there is good news. The bones of Homo flores found are apparently not fossilized. That means scientists are hopeful they might yield DNA that could shed the truth on evolutionary theory and the absurdity of human descent from apes by proving Homo flores is genetically human. Just don't look for the retraction of their present claims on the evening news.

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The World Situation

This is an anonymous letter. Not sent to me, but it was sent to Hal Lindsey. I'm copying it off of his site and posting it here. Everyone needs to be aware of this.

Dear Tom, Kevin, Kirby and Ted,
As your father, I believe I owe it to you to share some thoughts on the present world situation. We have over the years discussed a lot of important things, like going to college, jobs and so forth. But this really takes precedence over any of those discussions. I hope this might give you a longer term perspective that fewer and fewer of my generation are left to speak to.
To be sure you understand that this is not politically flavored, I will tell you that since Franklin D. Roosevelt, who led us through pre and WWII (1933 - 1945) up to and including our present President, I have without exception, supported our presidents on all matters of international conflict.
This would include just naming a few in addition to;
President Roosevelt (D) - WWII:
President Truman (D) - Korean War 1950;
President Kennedy (D) - Bay of Pigs (1961);
President Kennedy (D) - Vietnam (1961);
Eight presidents (5 Republican &4 Democrat) during the cold war (1945 - 1991);
President Clinton's (D) strikes on Bosnia (1995) and on Iraq (1998).
So be sure you read this as completely non-political or otherwise you will miss the point.
Our country is now facing the most serious threat to its existence, as we know it, that we have faced in your lifetime and mine (which includes WWII).
The deadly seriousness is greatly compounded by the fact that there are very few of us who think we can possibly lose this war and even fewer who realize what losing really means.
First, let's examine a few basics:
1. When did the threat to us start?
Many will say September 11th, 2001. The answer as far as the United States is concerned is 1979, 22 years prior to September 2001, with the following attacks on us: Iran Embassy Hostages, 1979; Beirut, Lebanon Embassy 1983; Beirut, Lebanon Marine Barracks 1983; Lockerbie, Scotland Pan-Am flight to New York 1988; First New York World Trade Center attack 1993; Dhahran, Saudi Arabia Khobar Towers Military complex 1996; Nairobi, Kenya US Embassy 1998; Dar es Salaam, Tanzania US Embassy 1998; Aden, Yemen USS Cole 2000; New York World Trade Center 2001; Pentagon 2001. (Note that during the period from 1981 to 2001 there were 7,581 terrorist attacks worldwide).
2. Why were we attacked?
Envy of our position, our success and our freedoms. The attacks happened during the administrations of Presidents Carter, Reagan, Bush #1, Clinton and Bush #2. We cannot fault either the Republicans or Democrats as there were no provocations by any of the presidents or their immediate predecessors, Presidents Ford or Carter.
4. Who were the attackers?
In each case, the attacks on the US were carried out by Muslims.
5. What is the Muslim population of the World?
25%
6. Isn't the Muslim Religion peaceful?
Hopefully, but that is really not material. There is no doubt that the predominately Christian population of Germany was peaceful, but under the dictatorial leadership of Hitler (who was also a professed Christian), that made no difference. You either went along with the administration or you were eliminated. There were 5 to 6 million Christians killed by the Nazis for political reasons (including 7,000 Polish priests).
Thus, almost the same number of Christians were killed by the Nazis, as the six million holocaust Jews who were killed by them, and we seldom heard of anything other than the Jewish atrocities. Although Hitler kept the world focused on the Jews, he had no hesitancy about killing anyone who got in his way of exterminating the Jews or of taking over the world – German, Christian or any others. Same with the Muslim terrorists. They focus the world on the US, but kill all in the way – their own people or the Spanish, French or anyone else.5 The point here is that just like the peaceful Germans were of no protection to anyone from the Nazis, no matter how many peaceful Muslims there may be, they are no protection for us from the terrorist Muslim leaders and what they are fanatically bent on doing – by their own pronouncements – killing all of us infidels. I don't blame the peaceful Muslims. What would you do if the choice was shut up or die?
6. So who are we at war with?
There is no way we can honestly respond that it is anyone other than the Muslim terrorists. Trying to be politically correct and avoid verbalizing this conclusion can well be fatal. There is no way to win if you don't clearly recognize and articulate who you are fighting.
So with that background, now to the two major questions;
Can we lose this war?
What does losing really mean?
If we are to win, we must clearly answer these two pivotal questions.
We can definitely lose this war, and as anomalous as it may sound, the major reason we can lose is that so many of us simply do not fathom the answer to the second question – What does losing mean? It would appear that a great many of us think that losing the war means hanging our heads, bringing the troops home and going on about our business, like post Vietnam. This is as far from the truth as one can get. What losing really means is:
We would no longer be the premier country in the world. The attacks will not subside, but rather will steadily increase. Remember, they want us dead, not just quiet. If they had just wanted us quiet, they would not have produced an increasing series of attacks against us over the past 18 years. The plan was clearly to terrorist attack us until we were neutered and submissive to them.
We would of course have no future support from other nations for fear of reprisals. Why? Because if the greatest world-power surrenders to Islamic terrorism, they would realize there is no one else to help them.
They will pick off the other non-Muslim nations, one at a time. It will be increasingly easier for them. They already hold Spain hostage.
It doesn't matter whether it was right or wrong for Spain to withdraw its troops from Iraq. Spain did it because the Muslim terrorists bombed their train and told them to withdraw the troops. Anything else they want Spain to do, will be done. Spain is finished.
The next will probably be France. Our one hope for France is that they might see the light and realize that if we don't win, they are finished too, in that they can't resist the Muslim terrorists without us. However, it may already be too late for France. France is already 20% Muslim and fading fast. See the attached article on the French condition by Tom Segel. 6
If we lose the war, our production, income, exports and way of life will all vanish as we know it. After losing, who would trade or deal with us if they were threatened by the Muslims. If we can't stop the Muslims, how could anyone else? The Muslims fully know what is riding on this war and therefore are completely committed to winning at any cost. We better know it too and be likewise committed to winning at any cost.
Why do I go on at such lengths about the results of losing? Simple. Until we recognize the costs of losing, we cannot unite and really put 100% of our thoughts and efforts into winning. And it is going to take that 100% effort to win.
So, how can we lose the war? Again, the answer is simple. We can lose the war by imploding. That is, defeating ourselves by refusing to recognize the enemy and their purpose and really digging in and lending full support to the war effort. If we are united, there is no way that we can lose. If we continue to be divided, there is no way that we can win.
Let me give you a few examples of how we simply don't comprehend the life and death seriousness of this situation.
President Bush selects Norman Mineta as Secretary of Transportation.
Although all of the terrorist attacks were committed by Muslim men between 17 and 40 years of age, Secretary Mineta refuses to allow profiling. Does that sound like we are taking this thing seriously? This is war. For the duration we are going to have to give up some of the civil rights we have become accustomed to. We had better be prepared to lose some of our civil rights temporarily or we will most certainly lose all of them permanently.
And don't worry that it is a slippery slope. We gave up plenty of civil rights during WWII and immediately restored them after the victory and, in fact, added many more since then. Do I blame President Bush or President Clinton before him? No, I blame us for blithely assuming we can maintain all of our Political Correctness and all of our civil rights during this conflict and have a clean, lawful, honorable war. None of those words apply to war. Get them out of your head.
Some have gone so far in their criticism of the war and/or the Administration that it almost seems they would literally like to see us lose. I hasten to add that this isn't because they are disloyal. It is because they just don't recognize what losing means. Nevertheless, that conduct gives the impression to the enemy that we are divided and weakening, it concerns our friends, and it does great damage to our cause.
Of more recent vintage, the uproar fueled by the politicians and media regarding the treatment of some prisoners of war perhaps exemplifies best what I am saying.
We have recently had an issue involving the treatment of a few Muslim prisoners of war by a small group of our military police. These are the type prisoners who just a few months ago were throwing their own people off buildings, cutting off their hands, cutting out their tongues and otherwise murdering their own people just for disagreeing with Saddam Hussein. And just a few years ago these same type prisoners chemically killed 400,000 of their own people for the same reason.They are also the same type enemy fighters who recently were burning Americans and dragging their charred corpses through the streets of Iraq. And still more recently the same type enemy that was and is providing videos to all news sources internationally, of the beheading of an American prisoner they held.
Compare this with some of our press and politicians who for several days have thought and talked about nothing else but the “humiliating” of some Muslim prisoners – not burning them, not dragging their charred corpses through the streets, not beheading them, but “humiliating” them. Can this be for real?
The politicians and pundits have even talked of impeachment of the Secretary of Defense. If this doesn't show the complete lack of comprehension and understanding of the seriousness of the enemy we are fighting, the life and death struggle we are in and the disastrous results of losing this war, nothing can.
To bring our country to a virtual political standstill over this prisoner issue makes us look like Nero playing his fiddle as Rome burned – totally oblivious to what is going on in the real world. Neither we, nor any other country, can survive this internal strife.
Again I say, this does not mean that some of our politicians or media people are disloyal. It simply means that they absolutely oblivious to the magnitude of the situation we are in and into which the Muslim terrorists have been pushing us for many years. Remember, the Muslim terrorists stated goal is to kill all infidels. That translates into all non-Muslims – not just in the United States, but throughout the world. We are the last bastion of defense.
We have been criticized for many years as being 'arrogant'. That charge is valid in at least one respect. We are arrogant in that we believe that we are so good, powerful and smart, that we can win the hearts and minds of all those who attack us, and that with both hands tied behind our back, we can defeat anything bad in the world.
We can't. If we don't recognize this, our nation as we know it will not survive, and no other free country in the World will survive if we are defeated.
And finally, name any Muslim country throughout the world that allows freedom of speech, freedom of thought, freedom of religion, freedom of the press, equal rights for, let alone allowing everyone to have equal status – especially for women, or that has been productive in one single way that contributes to the good of the World.
This has been a long way of saying that we must be united on this war or we will be equated in the history books to the self-inflicted fall of the Roman Empire. If, that is, the Muslim leaders will allow history books to be written or read.
If we don't win this war right now, keep a close eye on how the Muslims take over France in the next 5 years or less. They will continue to increase the Muslim population of France and continue to encroach little by little on the established French traditions.
The French will be fighting among themselves over what should or should not be done, which will continue to weaken them and keep them from any united resolve. Doesn't that sound eerily familiar?
Democracies don't have their freedoms taken away from them by some external military force. Instead, they give their freedoms away, politically correct piece by politically correct piece. And they are giving those freedoms away to those who have shown, worldwide, that they abhor freedom and will not apply it to you or even to themselves, once they are in power.
They have universally shown that when they have taken over, they then start brutally killing each other over who will be the few who control the masses. Will we ever stop hearing from the politically correct, about the “peaceful Muslims”?
I close on a hopeful note, by repeating what I said above. If we are united, there is no way that we can lose. I believe that after the election, the factions in our country will begin to focus on the critical situation we are in and will unite to save our country. It is your future we are talking about.
Do whatever you can to preserve it.

The Other Side

There is always more than one way to look at things! So to be totally fair and balanced, I decided to present you with a different point of view.

I am a senior citizen. During the Clinton Administration I had an extremely good and well-paying job. I took numerous vacations and had several vacation homes. Since President Bush took office, I have watched my entire life change for the worse. I lost my job. I lost my two sons in that terrible Iraqi War. I lost my homes. I lost my health insurance. As a matter of fact I lost virtually everything and became homeless. Adding insult to injury, when the authorities found me living like an animal, instead of helping me, they arrested me. I will do anything that Senator Kerry wants to insure that a Democrat is back in the White House come next year. Bush has to go.

Sincerely,

Saddam Hussein