Dr. Stephen C. Meyer is an American PhD Professor in the Philosophy of Science (obtained at the University of Cambridge). He is best known for Intelligent Design argument as seen in the complexity in biochemical systems.

Dr. Meyer directs the Seattle-based Discovery Institute’s Center for Science and Culture, and is the leading proponent of Intelligent Design Theory. He has authored two best-selling books on Intelligent Design: ‘Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design’, and ‘Signature in the Cell: DNA and the Evidence for Intelligent Design’, which was named a Book of the Year by the Times of London.

His work in Intelligent Design is introduced in this quote from his website ‘stephencmeyer.org’: “The Origins of Information: Exploring and Explaining Biological Information the 21st century, the information age has finally come to biology. We now know that biology at its root is comprised of information rich systems, such as the complex digital code encoded in DNA. Groundbreaking discoveries of the past decade are revealing the information bearing properties of biological systems.

Philosopher of science Dr. Stephen C. Meyer is examining and explaining the amazing depth of digital technology found in each and every living cell, such as nested coding, digital processing, distributive retrieval and storage systems, and genomic operating systems. Meyer is developing a more fundamental argument for intelligent design that is based not on a single feature like the bacterial flagellum, but rather on a pervasive feature of all living systems. Alongside matter and energy, Dr. Meyer shows that there is a third fundamental entity in the universe needed for life: information.”

In the book’s prologue, Dr. Meyer explains his why his work on the Cambrian Fossil Explosion as evidence for Intelligent Design demands a hearing: “Scientists now know that building a living organism requires information, and building a fundamentally new form of life from a simpler form of life requires an immense amount of new information. Thus, wherever the fossil record testifies to the origin of a completely new form of animal life – a pulse of biological innovation – it also testifies to a significant increase in the information content of the biosphere.”

He then challenges the scientific community with the need to explain how information could possibly originate from an evolutionary process: “Whenever we find functional information – whether embedded in a radio signal, carved in a stone monument, etched on a magnetic disc, or produced by an origin-of-life scientist attempting to engineer a self-replicating – and we trace that information back to its ultimate source, invariably we come to a mind, not merely material process. For this reason, the discovery of digital information in even the simplest living cells indicates the prior activity of a designing intelligence at work in the origin of the first life.”

Throughout the 20 chapters of his book, Dr. Meyer provides the following information, with their page reference, to make it easy for anyone to follow along and learn.

PROLOGUE:

1. The fundamental problem confronting neo-Darwinism, as with chemical evolutionary theory, is the problem of the origin of new biological information (p. IX).
2. As a host of distinguished biologists have explained in recent technical papers, small-scale, or “microevolutionary,” change cannot be extrapolated to explain large-scale, or “macroevolutionary,” innovation. For the most part, microevolutionary changes (such as variation in color or shape) merely utilize or express existing genetic information, while the macroevolutionary change necessary to assemble new organs or whole body plans requires the creation of entirely new information. As an increasing number of evolutionary biologists have noted, natural selection explains “only the survival of the fittest, not the arrival of the fittest” (p. X).
3. The fundamental problem in all of evolutionary biology: the problem of the origin of biological form and information (p. XIII).

CHAPTER 1: DARWIN’S NEMESIS

4. The twin pillars of Darwin’s theory: universal common ancestry, and natural selection (p. 3).
5. The ability of Natural Selection to biological change depends upon the presence of three distinct elements: 1) randomly arising variations, 2) the heritability of those variations, and 3) a competition for survival, resulting in differences in reproductive success among competing organisms (p. 10).
6. Sedgwick: discontinuity in the fossil record is not the exception, but the rule (p. 14).
7. The methods to determine the age between layers of geological strata: 1) superposition, 2) dissimilarity of fossil types, and 3) radiometric dating methods (p. 15).
8. Methodological Naturalism: a late 19th century practice to exclude appeals to divine action or divine ideas as a way of explaining phenomena in the natural world. According to this principle, scientists should accept as a working assumption that all features of the natural world can be explained by material causes without recourse to purposeful intelligence, mind, or conscious agency (p. 19).
9. According to Louis Agassiz: the problem with Darwin’s theory was not just the general incompleteness of the fossil record or even the pervasive absence of ancestral forms of life in the fossil record. The problem was the selective incompleteness of the fossil record (p. 24).

CHAPTER 2: THE BURGESS BESTIARY

10. Phyla = divisions in the biological classification system. They constitute the highest (or widest) categories of biological classification in the animal kingdom (p. 31).
11. Animals within each phylum exhibit distinguishing features that enable taxonomists to further divide and group the animals into smaller divisions: 2) classes, 3) orders, 4) families, 5) genera, 6) species (p. 31).
12. “Phylogenetic Classification” = “rank-free” method, where the groups are treated as equivalent if they emerged at roughly the same time on the tree of life (p. 31).
13. Several features of the Cambrian explosion that are unexpected from a Darwinian point of view: 1) the sudden appearance of Cambrian animal forms; 2) an absence of transitional intermediate fossils connecting the Cambrian animals to simpler Precambrian forms; 3) a startling array of completely novel animal forms with novel body plans; and 4) a pattern in which radical differences in form in the fossil record arise before more minor, small-scale diversification and variations. This pattern turns on its head the Darwinian expectation of small incremental changes only gradually resulting in larger and larger differences in form (p.34).
14. The Cambrian’s sudden appearances and missing intermediates pose difficulties for the Darwinian “branching tree” theory, where Darwinian theory expects changes in morphology should arise only as tiny changes accumulate. This Darwinian commitment to gradual change through microevolutionary variations produces the classic representation of evolutionary history as a branching tree. In Figure 2.7 (The Origin of Animals), Darwinian theory predicts gradual evolutionary change in contrast to the fossil evidence, which shows the abrupt appearance of the major animal groups (p. 35).
15. Darwin deduced that descent with modification required time – and lots of it (p. 37).
16. Theologian William Paley argued that just as complex structures such as watches necessarily issues from intelligent watchmakers, the complex structures in living organisms must likewise owe their origin to a designing intelligence (p. 38)
17. Natural Selection = Darwin’s Counter to Intelligent Design: With natural selection, Darwin proposed a purely natural mechanism for constructing the complex organs and structures (such as eyes) present in many forms of life. His mechanism of natural selection worked by constructing such systems one tiny step at a time, discarding the harmful variations and seizing upon the rare improvement. If evolution progressed by “whole watches” – that is, by entire anatomical systems like the trilobite’s eye – then biology would have fallen back to the old absurdity of imagining that a watch could fall together purely at random and all at once. Thus, unless Darwin’s evolutionary mechanism worked gradually by preserving the tiniest of random changes over millions of years, it didn’t work at all (p. 38).
18. Disparity = the major differences in form that separate the higher-level taxonomic categories such as phyla, classes, and orders. Diversity = The minor differences among organisms classified as different genera or species. Put another way, DISPARITY refers to life’s basic themes; DIVERSITY refers to the variations on those themes. The more body plans in a fossil assembly, the greater the disparity (p. 39-40).
19. On a Darwinian view, small-scale variations and differences should arise first, gradually giving rise to larger-scale differences in form – but just the opposite of the pattern is evident in the Cambrian fossil record (p. 44).

CHAPTER 3: SOFT BODIES AND HARD FACTS

20. Renowned Chinese paleontologist J.Y. Chen’s visit to University of Washington, after his work in the excavation of fossils at the Maotianshan Shale in China (1995 Time article), brought even a greater variety of Cambrian body forms from an even older layer of Cambrian rock than those of the Burgess. These Chinese fossils helped to establish that the Cambrian animals appeared even more explosively than previously realized (p. 50-51).
21. In J.Y. Chen’s presentation to the University of Washington faculty, he highlighted the apparent contradiction between the Chinese fossil evidence and Darwinian orthodoxy. One professor in the audience asked Chen if he wasn’t nervous about expressing his doubts about Darwinism so freely – especially given China’s reputation for suppressing dissenting opinion. “In China”, he said, “we can criticize Darwin, but not the government. In America, you can criticize the government, but not Darwin.” (p. 52).
22. Since the discovery of the Burgess Shale, Precambrian and Cambrian discoveries have repeatedly uncovered fossil forms that either establish radically disparate new forms of life or, increasingly, forms that fall into existing higher taxonomic groups. As a result, the fossil record amply documents organisms corresponding to the TERMINAL BRANCHES on the Darwinian tree of life, but it fails to preserve those organisms representing the INTERNAL BRANCHES OR NODES leading to these terminal branches (i.e., representatives of novel phyla and classes of Cambrian-era animals) (p. 69).
23. Yet these intermediates are the very forms required to connect the terminal branches to form a coherent evolutionary tree and establish that the representatives of the Cambrian animals did arise by means of a gradual evolutionary process from simpler Precambrian ancestors (p. 69).
24. Statistical Paleontology = Paleontologist Michael Foote at the University of Chicago has shown, using statistical sampling analysis, that as more and more fossil discoveries fall within existing higher taxonomic groups (i.e., phyla, subphyla and classes), and as they fail to document the rainbow of intermediate forms expected in the Darwinian view of the history of life, it grows ever more improbable that the absence of intermediate forms reflects a sampling bias – that is, an “artifact” of either sampling or preservation. This kind of analysis merely QUANTIFIES what, in other circumstances, we would sense INTUITIVELY (p. 69-70).
25. Paleontologist Donald Prothero, from Occidental College, redefined the “Cambrian explosion” as occurring over 80 million years, but by using the term to describe several explosions (of different kinds), he had done nothing to diminish the difficulty of explaining the origin of the first explosive appearance of the Cambrian animals with their unique body plans and complex anatomical features (p. 73).
26. Expanding the definition of the Cambrian explosion only obscures the real challenge posed by the event, a challenge underscored by the discoveries at Chengjiang. An analysis by MIT geochronologist Samuel Bowring has shown that the main pulse of Cambrian morphological innovation occurred in a sedimentary sequence spanning no more than 6 million years… so the problem of explaining how so many new forms and structures arose so rapidly in the first explosive period of the Cambrian remains, whether or not one decides to include within the designated “Cambrian explosion” other distinct events (p. 73-74).
27. Discoveries at Chengjiang contradict the bottom-up pattern that neo-Darwinian expects. The site does not show the gradual emergence of unique species followed slowly but surely by the emergence of representatives of ever higher and more disparate taxa, leading to novel phyla. Instead, like the Burgess Shale, it shows body plan-level disparity arising first and suddenly, with no evidence of a gradual unfolding and ranging through the lower taxonomic groups (p. 74).
28. Prior to the discovery of the Chengjiang biota, chordates were unknown in the Cambrian period and were thought to have first appeared only much later, during the Ordovician period. Now, following the discoveries at Chengjiang, the first appearance of chordates in the Cambrian period has been amply documented (p. 74).
29. Simon Conway Morris, with D.G. Shu and several Chinese colleagues, has reported an even more dramatic find. They discovered the fossilized remains of 2 small Cambrian fish, Myllokunmingia fengjiaoa and Haikouichthys ercaicunenesis, suggesting a much earlier appearance of both fishes and vertebrates (a class of chordates), both of which were first thought to have originated in the Ordovician period, about 475 million years ago (p. 75).

CHAPTER 4: THE NOT MISSING FOSSILS?

30. The Cambrian explosion attests to the first appearance of organisms representing at least 20 phyla and many more subphyla and classes, each manifesting distinctive body plans (p. 85).
31. Although the Ediacaran biota look simple beside most of the Cambrian animals, they represent an enormous leap in functional complexity over the single-celled organisms and colonial algae that preceded them (p. 86).
32. NEO-DARWINISM = the modern version of Darwin’s theory that invokes random genetic changes called mutations as the source of much of the new variation upon which natural selection acts. Like classical Darwinism, the neo-Darwinian mechanism requires great stretches of time to produce novel biological form and structure (p. 87).
33. The fossil record, given its otherwise pervasive pattern of discontinuity, does not establish the gradual evolution of numerous anatomical and morphological novelties (p. 95-96).

CHAPTER 5: THE GENES TELL THE STORY?

34. In reconstructing the evolutionary history of life, most evolutionary biologists today emphasize the importance of homology. They assume that similarities in anatomy and in the sequences of information-bearing biomacromolecules such as DNA, RNA, and protein point strongly to a common ancestor. They also assume that the degree of difference in such cases is on average proportional to the time elapsed since the divergence from a common ancestor. The greater the difference in the common feature or molecular sequence, the farther back the ancestor from which the feature or sequence arose (p. 100).
35. The 1990 Wray Study (evolutionary biologists Gregory Wray, Jeffrey S. Levinton, Leo H. Shapiro) concluded that the common ancestor of the animal forms lived 1.2 billion years ago, implying that the Cambrian animals took some 700 million years to evolve from this “deep-divergence” point before first appearing in the fossil record (p. 103).
36. But a survey of recent deep-divergence studies, by molecular evolutionists Dan Graur and William Martin, notes one study in which the authors claim to be 95% certain that their divergence date for certain animal groups falls within a 14.2-billion-year range – more than 3X the age of the earth and clearly a meaningless result (p. 107)!
37. Evolutionary biologists typically exclude histones from consideration, because those times do not conform preconceived ideas about what the Precambrian tree of life ought to look like. But that raises obvious questions. If we don’t have fossils documenting a common animal ancestor, and if genetic studies produce such different and contradictory divergent times, how do we know what the tree of life should look like and when the first animals began to diverge from a common ancestor (p. 107-108)?

CHAPTER 6: THE ANIMAL TREE OF LIFE

38. Studies of molecular homologies often fail to confirm evolutionary trees depicting the history of animal phyla derived from studies of comparative anatomy. Instead, during the 1990’s, early into the revolution in molecular genetics, many studies began to show that phylogenetic trees derived from anatomy and those derived from molecules often contradicted each other (p. 122).
39. Molecular Sequences Do Not Match: After completing a survey of many such difficulties, University of St. Andrews zoologist Pat Willmer and Oxford University zoologist Peter Holland, experts on invertebrate anatomy, draw this conclusion: “Taken together, modern re-evaluations of traditional evidence support different and mutually exclusive subsets of phylogenetic relations… Patterns of symmetry, the number of germ layers in the body, the nature of the body cavity, and the presence or type of serial repetition (segmentation) have all been used to infer common ancestry.” But, they explain, the phylogenetic story these characteristics tell is “now either unacceptable or at least controversial” because the data are, at best, inconsistent (p. 132).
40. The Problem with Phylogenetic Reconstruction: All these problems underscore several fundamental difficulties with the methods of phylogenetic reconstruction. When biologists analyze multiple anatomical traits or genes, the animal phyla consistently defy attempts to arrange them into the pattern of a single tree (p. 132).
41. Theory of Universal Common Descent: assumes that, generally, the more similar 2 organisms are, the more closely related they must be. The presence of nearly identical individual traits or structures within organisms exemplifying otherwise different body plans cannot, therefore, be attributed to evolution form a common ancestor (p. 133).
42. Convergent Evolution: the separate or independent origin of similar characters emerging on separate lines of descent after the point at which those lines diverged from their last common ancestor. Convergent evolution demonstrates that similarity does not always imply homology, or inheritance from a common ancestor (p. 133).
43. Three Classes of Evidence for Cambrian: 1) the fossil record, 2) evidence of genetics, 3) comparative anatomy. These three classes of evidence either provide no compelling evidence for Precambrian animal ancestors (in the case of fossils), or they provide question-begging and conflicting evidence (in the case of genes and anatomy) (p. 135).

CHAPTER 7: PUNK EEK!

44. Punctuated Equilibrium: neither Steven J. Gould nor Niles Eldridge expected to find a wealth of transitional intermediate forms in the fossil record. In their view, the main periods of biological innovation simply occurred too rapidly to leave many fossil intermediates behind (p. 137).
45. Allopatric Speciation: Processes that generate new species from separate parent (or father) populations. Allopatric speciation typically occurs when part of a population of organisms becomes geographically isolated – perhaps by the emergence of a mountain range or the shifting of a river’s course – from a larger parent population and then a daughter population changes in response to differing environmental pressures. Gould and Eldridge use this to explain how new species might arise quickly (p. 139).
46. Genetic Drift: Occurs when genetic changes spread or disappear randomly through a population, without regard for their effect on survival and reproduction (p. 140).
47. Species Selection: Steven J. Gould calls this the process of interspecies or interpopulation competition (as opposed to intraspecies competition) (p.141).

CHAPTER 8: THE CAMBRIAN INFORMATION EXPLOSION

48. Information: “When I was a college professor, I used to ask my students a question: ‘If you want your computer to acquire a new function or capability, what do you have to give it?’ Typically, I would hear a smattering of similar answers from the class: ‘code, instructions, software, information.’ All these are correct. And thanks to discoveries in modern biology, we now know that something similar is true of life: to build a new form of life from a similar preexisting form requires new information.” (p. 155)
49. The cause of the Cambrian Explosion: By what means or process or mechanism could something as complex as a trilobite have arisen? Could natural selection have accomplished such a feat (p. 155)?
50. This scenario still leaves open the question of who designed the designer – how did life originally originate? Is a philosophical naturalist now trapped? Again, no (p. 249).
51. Gregor Mendel: In the 1860’s, this Austrian monk, widely regarded as the founder of modern genetics, showed in his work on garden peas that Darwin’s assumptions about blending inheritance were incorrect. The results of his studies created, at least initially, more problems for Darwinism. Mendel showed that the genetic traits of organisms typically have an integrity that resists blending (p. 156).
52. Gregor Mendel: The classical Mendelian genetics that replaced Darwin’s blending theory of inheritance also suggested limitations on the amount of genetic variability available to natural selection. If plant reproduction produced either green or yellow peas but never some intermediate form, and if the signals for producing the green traits and yellow traits persisted unchanged from generation to generation, it was difficult to see how sexual reproduction and genetic recombination could produce anything more than unique combinations of already existing traits (p. 157).
53. Biological Information: Scientists recognize at least 2 basic types of information: (1) functional (or meaningful) information, and (2) Shannon information, which is not necessarily meaningful or functional. The distinction has arisen in part because of developments in a branch of applied mathematics known as information theory. During the late 1940’s, mathematician Claude Shannon, working at Bell Labs, developed a mathematical theory of information. Shannon equated the amount of information transmitted by a sequence of symbols or characters with the amount of uncertainty reduced or eliminated by the transmission of that sequence (p. 164).
54. Challenge to Neo-Darwinism = Cambrian Explosion: Is it plausible to think that natural selection working on random mutations in DNA could produce the highly specific arrangements of bases necessary to generate the protein building blocks of new cell types and novel forms of life? Perhaps nowhere do such questions pose more of a challenge to neo-Darwinian theory than in discussions of the Cambrian explosion (p. 168).

CHAPTER 9: COMBINATIONAL INFLATION

55. “Sequence affects function”: Murray Eden, professor of engineering and computer science at MIT, knew that in all computer codes or written texts in which the specificity of sequence determines function, random changes in sequence consistently degrade function or meaning. As he explained, ‘No current existing formal language can tolerate random changes in the symbol sequences which express its sentences. Meaning is almost invariably destroyed’ (p. 170).
56. Wistar Institute Conference: In 1966, a distinguished group of mathematicians, engineers and scientists convened this conference at the Wistar Institute in Philadelphia, called “Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution.” Sir Peter Medawar, a Nobel Laureate and the Director of the North London Medical Research Council’s labs, chaired the meeting. In his opening remarks, he said, “The immediate cause of this conference is a pretty widespread sense of dissatisfaction about what has come to be thought of as the accepted evolutionary theory in the English-speaking world, the so-called neo-Darwinian theory” (p. 171).
57. NEO-DARWINISM = It envisions new genetic information arising from random mutations in the DNA. If at any time from birth to reproduction the right mutations or combinations of mutations accumulate in the DNA of cells involved in reproduction (whether sexual or asexual), then information for building a new protein or proteins will pass to the next generation. When that new protein happens to confer a survival advantage on an organism, the genetic change responsible for the new protein will tend to be passed on to subsequent generations. As favorable mutations accumulate, the features of a population will gradually change over time. Clearly, natural selection plays a crucial role in this process. Favorable mutations are passed on; unfavorable mutations are weeded out. Nevertheless, the process can only select variations in the genetic text that mutations have first produced. For this reason, evolutionary biologists typically recognize that mutation, not natural selection, provide the source of variation and innovation in the evolutionary process (p. 173).
58. Murray Eden’s Argument: Eden challenged, in his Wistar presentation, whether the mutation and selection mechanism had enough time – since the beginning of the universe itself – to generate even a small fraction of the total number of possible amino-acid sequences corresponding to a single functional protein of that length? For Eden, the answer was clearly no. For this reason, Eden thought mutations had virtually no chance of producing new genetic information (p. 176).

CHAPTER 10: THE ORIGIN OF GENES AND PROTEINS

59. Process Control: Like his fellow engineer Murray Eden, Axe’s tendency to view biology as an engineer led him to ask whether selection and mutation could actually build new organisms. Axe’s own research explored the connection between PROCESS CONTROL (a field of study in engineering) and GENETIC REGULATION (a sophisticated version of automated process control at work on a molecular scale inside living cells) (p.186).
60. Mutation and Natural Selection Cannot Produce a Protein Fold: Doug Axe’s experiments confirmed what most evolutionary biologists suspected – that protein-to-protein evolution is a no-go where the mutation and selection mechanism must produce a new protein fold (p. 196).
61. Four reasons why Neo-Darwinism cannot account for Cambrian Explosion: (1) Cambrian explosion as dated by fossil evidence took far less time than has elapsed since the origin of life on earth until the present (about 3.8 billion years); (2) Bacteria are by far the most common type of organisms included in Axe’s estimate of the total number of organisms that have lived on earth. Yet no one thinks that Cambrian animals evolved directly from bacteria; (3) Building new animal forms requires generating far more than just in protein of modest length; (4) The Cambrian animals exhibit structures that would have required many new types of cells, each requiring many novel proteins to perform their specialized functions. But new cell types require not just one or two new proteins, but coordinated systems of proteins to perform their distinctive cellular functions (p. 206).
62. Our growing knowledge about the rarity and isolation of proteins and functional genes in sequence space implies that neither neo-Darwinian scenario for producing new genes is at al plausible. Thus, neo-Darwinism does not explain the Cambrian information explosion (p. 208).

CHAPTER 11: ASSUME A GENE

63. ORFAN (“Open Reading Frames of Unknown Origin”) GENES = Genes tend to be explained through descent with modification (via mutation) from common ancestral genes. Yet genomic studies are now turning up hundreds of thousands of genes in many diverse organisms that exhibit no significant similarity in sequence to any other known gene… As scientists have explored and sequenced more genomes, they have discovered more and more ORFan genes without finding anything like a corresponding number of homologs. These number of “unpaired” ORFan genes continues to grow.

CHAPTER 12: COMPLEX ADAPTATIONS AND THE NEO-DARWINIAN MATH

64. Bolyerine Snakes: Boa-like snakes that have an anatomical specialization found in no other vertebrate. Their maxilla, the tooth-bearing bone of the upper jaw, is divided into TWO SEGMENTS, linked by a flexible joint and serviced by many specialized nerves, extra bones, tissues, and differently arranged ligaments. This unique trait allows the snakes to bend the front half of their upper jaw backwards when they attack prey. Could this complex system of bones, joints, tissues, and ligaments have evolved gradually? (p. 230)
65. Bolyerine Snakes and Irreducible Complexity: As Stephen Jay Gould asked: “How can a jawbone be half broken?” As University of Illinois biologist Tom Frazzetta observed, “I find it difficult to envision a smooth transition from a single maxilla to the divided condition seen in bolyerine snakes.” Yet because the intermediate forms would not be viable, building a bolyerine jaw would require all the necessary parts – the jointed maxilla, the adjoining ligaments, and the necessary muscles and tissues – arising together (p. 231).
66. Tom Frazzetta, “Complex Adaptations in Evolving Populations”: He explains his problem in examining the jaw of bolyerine snakes: “When modifying the design of a machine, an engineer is not bound by the need to maintain a real continuity between the first machine and the modification… But in evolution, transitions from one type to the next presumably involve a greater continuity by means of a vast number of intermediate types. Not only must the end product – the final machine – be feasible, but so must be all the intermediates. The evolutionary problem is, in a real sense, the gradual improvement of a machine while it is running!” (p. 232).
67. Michael Behe (“Edge of Evolution”): Neo-Darwinian mechanism does not have the capacity to generate even 2 coordinated mutations in the time available for human evolution – and thus does not explain how humans arose.

CHAPTER 13: THE ORIGIN OF BODY PLANS

68. Fruit Fly Experiments (Eric Wieschaus): At 1982 meeting of American Assoc. for the Advancement of Science, one questioner asked Wieschaus about his experiments on fruit fly mutations as related to demonstrating the processes of macroevolution: “Without exception, the mutants he studied perished as deformed larvae long before achieving reproductive age (p. 256).
69. Fruit Fly Experiments (Eric Wieschaus): At 1982 meeting of American Assoc. for the Advancement of Science, another questioner then asked Wiechaus about the implications of his findings on evolutionary theory. Here Wiechaus responded more soberly, wondering aloud about whether his collection of mutants offered any insights into how the evolutionary process could have constructed novel body plans: “The problem is, we think we’ve hit all the genes required to specify the body plan of Drosophila, and yet these results are obviously not promising as raw materials for macroevolution. The next question then is what are – or what would be – the right mutations for major evolutionary change? 30 years later, developmental and evolutionary biologists still don’t know the answer to that question (p. 256-257)
70. If mutating the genes that regulate body-plan construction destroy animal forms as they develop from an embryonic state, then how do mutations and selection build animal body plans in the first place (p. 257)?
71. The neo-Darwinian mechanism has failed to explain the generation of new genes and proteins needed for building the new animal forms that arose in the Cambrian explosion (p. 257).
72. Genetic Research Results – Key Embryonic Regulatory Genes: Painstaking genetic research – performed by Nusslein-Volhard and Wieschaus and many other developmental biologists – has uncovered many of the key embryonic regulatory genes that help switch cells into their differential adult types. This research has also uncovered a profound difficulty cutting to the very core of the neo-Darwinian view of life: early-acting body-plan mutations and embryonic lethals (p. 259).
73. Mutation Timing: to create significant changes in the forms of animals requires attention to timing. Mutations in genes expressed late in the development of an animal will affect relatively few cells and architectural features, because by late in development the basic outlines of the body plan have already been established. Late-acting mutations therefore cannot cause any significant or heritable changes in the form or body plan of the whole animal (p. 259).
74. Mutation Timing: Mutations that are expressed early in the development of animals have probably the only realistic chance of producing large-scale macroevolutionary change. As evolutionary geneticists Bernard John and George Mikos explain, “macroevolutionary change” requires changes in “very early embryogenesis” (p. 259).
75. Georgia Tech Geneticist John F. McDonald – The “Great Darwinian Paradox”: Genes that are variable within natural populations seem to affect only minor aspects of form and function – while those genes that govern major changes, the very stuff of macroevolution, apparently do not vary or vary only to the detriment of the organism.So, the kind of mutations the evolutionary process would need to produce new animal body plans – namely, beneficial regulatory changes expressed early in development – don’t occur. Whereas, the kind that it doesn’t need – viable genetic mutations in DNA generally expressed late in development – do occur. THE KIND OF MUTATIONS WE NEED FOR MAJOR EVOLUTIONARY CHANGE WE DON’T GET; THE KIND WE GET WE DON’T NEED (p. 262).
76. Paul Nelson (Philosophy of Biology, Specialty in Evolutionary Theory and Developmental Biology) – Three Premises that summarize the challenge to neo-Darwinism posed by animal development:
    1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determines what follows.
    2. Thus, to evolve any body plan, mutations expressed early in development must occur, must be viable, and must be stably transmitted to offspring.
    3. Such early-acting mutations of global effect on animal development, however, are those least likely to be tolerated by the embryo and, in fact, never have been tolerated in any animals that developmental biologists have studied (p. 263).
77. Swedish evolutionary biologist Soren Lovtrup: “Without variation, no selection; without selection, no evolution”. This echoes Darwin’s theory from the beginning: “nothing can be effected by natural selection unless favorable variations occur” (p. 264).

CHAPTER 14: THE EPIGENETIC REVOLUTION

78. EPIGENETICS = refers to a source of information that lies beyond the genes. As Muller and Newman explain in their introduction to their 2003 essays “Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology”, “Detailed information at the level of the gene does not serve to explain form.” So, “epigenetic” or “contextual information” plays a crucial role in the formation of animal body assemblies during embryological development (p. 272).
79. In their (Gerd Muller and Stuart Newman) view, neo-Darwinism “completely avoids the question of the origination of phenotypic traits and organismal form.” As they and others in their volume maintain, neo-Darwinism lacks an explanation for the origin of organismal form precisely because it cannot explain the origin of epigenetic information” (p. 273).
80. DEVELOPMENTAL BIOLOGY: I (Stephen Meyer) asked Professor Jonathan Wells why developmental biology was so important to evolutionary theory and to assessing neo-Darwinism. I’ll never forget his reply: “Because that’s where the whole theory is going to unravel” (p. 273).
81. DNA Isn’t Enough for Information Needed to Build Complex Biological Systems = DNA does help direct protein synthesis. But once proteins are synthesized, they must be arranged into higher-level systems of proteins and structures. Genes and proteins are made from simple building blocks – nucleotide bases and amino acids, respectively – arranged in specific ways. Yet the properties of individual proteins do not fully determine the organization of these higher-level structures and patterns. Other sources of information must help arrange individual proteins into systems of proteins, systems of proteins into distinctive cell types, cell types into tissues, and different tissues into organs. And different organs and tissues must be arranged to form body plans (p.276-277).
82. Building a new body plan requires more than just genetic information. It requires both genetic and epigenetic information – information by definition that is not stored in DNA and thus cannot be generated by mutations to the DNA. It follows that the mechanism of natural selection acting on random mutations in DNA cannot by itself generate novel body plans, such as those that first arose in the Cambrian explosion (p. 282).
83. Neo-Darwinism’s Inadequacy to Explain Evolution – MICRO vs MACRO Evolution: Biologists Scott Gilbert, John Opitz and Rudolf Raff have attempted to develop a new theory of evolution to supplement classical neo-Darwinism, which, they argue, cannot adequately explain large-scale macroevolutionary change. As they note, “Starting in the 1970’s, many biologists began questioning its (Neo-Darwinism’s) adequacy in explaining evolution. Genetics might be adequate to explain microevolution, but macroevolutionary 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. 287).
84. Cambrian Explosion and Darwin’s Enigma: The Cambrian explosion now looks less like the minor anomaly that Darwin perceived it to be, and more like a profound enigma, one that exemplifies a fundamental and as yet unsolved problem – the ORIGINATION OF ANIMAL FORM (p. 287).

CHAPTER 15: THE POST-DARWINIAN WORLD AND SELF-ORGANIZATION

85. The 3 Pillars of Neo-Darwinism (Biologists Marc Kirschner, John Gerhart):
    1. VARIATION = Evolutionary change occurs as the result of random, minute variations (or mutations)
    2. NATURAL SELECTION = The process of natural selection sifts among those variations and mutations, such that some organisms leave more offspring than others (differential reproduction) based on the presence or absence of certain variations
    3. HER ITABILITY = Favored variations must be inherited faithfully in subsequent generations of organisms, thus causing the population in which they reside to change or evolve over time
86. Order vs. Information = Self-organizational theorists seek to explain the origin of “order” in living systems by reference to purely physical or chemical processes (or laws describing those processes). But what needs to be explained in living systems is not mainly order in the sense of simple repetitive or geometric patterns. Instead, what requires explanation is the adaptive complexity and the information, genetic and epigenetic, necessary to build it (p. 305).
87. Proponents of self-organization fail to offer examples of either biological information or complex anatomical structures arising from physics and chemistry alone (p. 305).
88. SPECIFIED COMPLEXITY – CRYSTALS vs. PROTEINS = information-rich sequences in DNA, RNA, and proteins are characterized by “specified complexity”, where the irregular and unpredictable arrangement of characters (or constituents) is critical to the function that the sequence performs.
    What does all this have to do with self-organization? Simply this: the law-like, self-organizing processes that generate the kind of order present in a crystal or a vortex do not also generate complex sequences or structures.
    Laws of nature by definition describe REPETITIVE PHENOMENA – order in that sense – that can be described with differential equations or universal “if-then” statements. In nature, repetition provides grist for lawful description.
    The information-bearing sequences in protein-coding DNA and RNA molecules do not exhibit such repetitive “order”, however. The kind of non-repetitive “order” on display in DNA and RNA – a precise sequential “order” necessary to ensure function – is not the kind that laws of nature or law-like self-organizational processes can – in principle – generate or explain (p. 307).

CHAPTER 16: OTHER POST-DARWINIAN MODELS

89. NEO-DARWINISM = emphasizes large-scale macroevolutionary change occurs as the inevitable by-product of the accumulation of small-scale “microevolutionary” changes within populations (p. 314).
90. Most evolutionary biologists today recognize the origin of the eukaryotic cell as a COMPLETELY UNSOLVED PROBLEM – unexplained by either neutral or adaptive theories of evolution (p. 324).
91. Where does the programming come from that accounts for the “pre-programmed adaptive capacity” of living organisms? If, as James Shaprio argues, natural selection and exclusively random mutations don’t produce this information-rich pre-programming, then what did (p. 335)?

CHAPTER 17: THE POSSIBILITY OF INTELLIGENT DESIGN

92. All Evolutionary Theories have 2 Things in Common:
    1. They rely on strictly material processes
    2. They have failed to identify a cause capable of generating the information necessary to produce new forms of life.
93. Is it possible that INTELLIGENT DESIGN – the purposeful action of a conscious and rational agent – might have played a role in the Cambrian explosion (p. 337)?
94. INTELLIGENT DESIGN (ID) = not a biblically based idea, but instead an evidence-based theory about life’s origins – one that challenges some, but not all, meanings of the term “evolution”.
    Intelligent design challenges the idea that natural selection and random mutation (and other similarly undirected materialistic processes) can explain the most striking appearances of design in living organisms.
    Instead, ID affirms that there are certain features of living systems that are best explained by the design of an actual intelligence – a conscious and rational agent, a mind – as opposed to a mindless, materialistic process (p. 338-339).
95. Darwin’s Theory of Evolution by Natural Selection has 3 Assertions:
    1. Change over Time
    2. Universal Common Descent
    3. Creative power of natural selection acting on random variations
96. Today’s Evolutionary Argument (Richard Dawkins) = The mechanism of natural selection acting on random genetic variations (and mutations) can produce not just new biological form and structure, but also the APPEARANCE of design in living organisms (p. 338).
97. How an Evolutionist sees Design = Appearance of design as entirely illusory because they think that purely mindless, materialistic processes such as natural selection and random mutations can produce the intricate designed-like structures in living organisms. In this view, natural selection and random mutation mimic the powers of a DESIGNING INTELLIGENCE without themselves being intelligently directed or guided in any way (p. 339).
98. Difference between Neo-Darwinism and ID: The theory of ID does not reject evolution s defines by “change over time” or even “uniformal common ancestry”, but it does dispute Darwin’s idea that the cause of major biological change and the appearance of design are wholly blind and undirected (p. 339).

CHAPTER 18: SIGNS OF DESIGN IN THE CAMBRIAN EXPLOSION

99. Characteristics of Whatever Caused the Cambrian Explosion:
    1. Generate new form rapidly
    2. Generate a top-down pattern of appearance
    3. Construct, not merely modify, complex integrated circuits
    4. Not described by any currently proposed theory of micro- or macroevolution
    5. Unlike any observed biological process operating in actual living populations today (p. 357)
100. Why ID is the Best Explanation for the Cambrian Explosion: Standard materialistic evolutionary theories have failed to identify an adequate mechanism or cause for precisely those attributes of living forms that we know from experience only intelligence – conscious, rational activity – is capable of producing. That suggests, in accord with the method of historical scientific reasoning elucidated in the previous chapter, the possibility of making a strong historical inference to intelligent design as the BEST EXPLANATION for the origin of those attributes (p. 358).
101. Why Natural Selection by Random Mutation Fails: Natural selection lacks as a condition of its causal adequacy. We have seen that natural selection lacks the ability to generate novel information precisely because it can only act AFTER new functional information has arisen. Natural selection can favor new proteins and genes, but only after they perform some function (influencing reproductive output).
     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 need is not just a source of variation 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 (p. 361).
102. Top-Down vs Bottom-Up Causation: “Top-Down” Causation begins with a basic architecture, blueprint, or plan and then proceeds to assemble parts in accord with it. The blueprint stands causally prior to the assembly and arrangement of parts. “Bottom-Up” Causation describes a self-assembly in which the gradual production of the components eventually generates the organization of the whole, which implies that the components stand causally prior to the organization as a whole (p. 371).
103. The Problem with “Bottoms-Up” Causation = The fossil record leaves no evidence of such a process and the morphological innovations and transformations that it requires are biologically implausible (p. 371).

CHAPTER 19: THE RULES OF SCIENCE

104. Methodological Naturalism = asserts that to qualify as scientific, a theory must explain phenomena and events in nature – even events such as the origin of the universe and life or phenomena such as human consciousness – by reference to strictly material causes. According to this principle, scientists may not invoke the activity of a mind or, as one philosopher of science puts it, and creative intelligence (p. 383-384).
105. Why Methodological Naturalists Claim ID is Unscientific:
     1. It isn’t testable
     2. It isn’t falsifiable
     3. It doesn’t make predictions
     4. It doesn’t describe repeatable phenomena
     5. It doesn’t explain by reference to natural law
     6. It doesn’t cite a mechanism
     7. It doesn’t make tentative claims
     8. It has no problem-solving capability (p. 389).
106. Stephen Meyer Response: “In Signature of the Cell”, I show that many of the claims are simply false (p. 389).
107. The Question of whether a theory is “scientific” is really a red herring. What we really want to know is whether a theory is TRUE OR FALSE, supported by the EVIDENCE OR NOT, worthy of our belief or not. And we cannot decide those questions by applying a set of abstract criteria that purport to tell in advance what all good scientific theories must look like (p. 389).
108. Explanatory Power of the Evidence = Evolutionary biologists themselves INFER unobserved past mutations and invoke the existence of extinct organisms and transitional forms for which no fossils remain. Such things, like the actions of an intelligent designer, are INFERRED from observable evidence in the present, because of the explanatory power they may offer (p. 390).

CHAPTER 20: WHAT’S AT STAKE

109. The Hard Questions One Must Answer for ID:
     1. How can we detect deign?
     2. Is ID science?
     3. Aren’t we just arguing from ignorance and giving up on science, or at least evolutionary science, too soon?
     4. Who do you think the designer is? (p. 408)
110. Four Scientific Critiques of Neo-Darwinism:
     1. It has no means of efficiently searching combinatorial sequence space for functional genes and proteins
     2. It requires unrealistically long waiting times to generate even a single new gene or protein
     3. It cannot produce new body plans because early acting mutations, the only kind capable of generating large-scale changes, are also invariably deleterious
     4. Genetic mutations cannot generate the epigenetic information necessary to build a body plan (p. 411).
111. ID vs. Theistic Evolution: Unlike the theistic evolution of Francis Collins, the theory of ID does not seek to confine the activity of an intelligent agent to the beginning of the universe, conveying the impression of a decidedly remote and impersonal deistic entity.
112. ID vs. Neo-Darwinistic Atheism: The case for design supports us in our existential confrontation with the void and the seeming meaninglessness of physical existence – the sense of survival for survival’s sake that follows inexorably from the materialist worldview.
     Richard Dawkins and other New Atheists may find it untroubling, even amusing and certainly profitable, to muse over the prospect of a universe without purpose. But for the vast majority of thoughtful people, that idea is tinged with terror.
     Modern life suspends many of us, so we feel, high over a chasm of despair. It provokes feelings of dizzying anxiety – in a word, vertigo. The evidence of a purposeful design behind life, on the other hand, offers the prospect of significance, wholeness and hope.