Darwin's Doubt

Stephen C. Meyer


p v Recap of Signature in the Cell to make the point that it dealt with the origin of life and the information required.

p viii After commenting that critics responded to the book he didn't write, i.e., a book challenging Darwin's main thesis, he decided to write that book.

p viii Dobzhansky's quote "Pre-biological natural selection is a contradiction in terms."

p x-xi Comments on the different uses of the word evolution. Contrasts between public and private statements of biologists, and between those of research biologists and journalists & popularizers of biology. E.g."There is no credible scientific challenge to the theory of evolution as an explanation for the complexity and diversity of life on earth" by New York Times science writer Cornelia Dean and "There are no weaknesses in the theory of evolution" by Eugenie Scott of National Center for Science Education.

1.Darwin's Nemesis

About Darwin and Louis Agassiz

p 3 Darwin's twin pillars - universal common ancestry and natural selection. Darwin "all the organic beings which have ever lived on this earth have descended from some one primordial form."

p 4 Illustration of Darwin's evolutionary tree from Haekel. "descent with modification"

p 8 Agassiz concluded that the Cambrian explosion was "an insuperable difficulty for Darwin's theory."

p13 Murchison, Sedgwick and the Cambrian fossils of Wales

p14 Sedgewick - species suddenly appear and then disappear.

p15 Dating by discontinuity - William Smith in his canal excavations found distinct fossil changes that permitted the identification of strata.

p16 Illustration of geologic periods.

p18 The cast of Darwin supporters: Joseph Hooker, Thomas Huxley, Ernst Haeckel, Asa Gray.

p18-22 Darwin-Agassiz dialog. More details on Agassiz

p23 Darwin quote, having accepted the validity of Agassiz's objections, in Origin "To the question why we do not find rich fossiliferous deposits belonging to these assumed earliest periods prior to the Cambrian system, I can give no satisfactory answer .. The case at present must remain inexplicable; and may be truly urged as a valid argument against the views here entertained."

2. The Burgess Bestiary

p29 >65,000 specimens collected in Burgess shale. Diagrams of marrella and hallucigenia.

p31 About 20 of the 26 total phyla present in the fossil record

p31 Goes through organization from phylum to smaller divisions

p32 Illustration of time periods and phyla

p33 Fig 2.6 on marine invertebrates

p34 A puzzling pattern: the four problems from a Darwinian point of view

  1. The sudden appearance of the Cambrian life forms
  2. An absence of transitional intermediate fossils
  3. Startling array of completely novel animal forms with novel body plans
  4. A pattern in which radical differences in form in the fossil record arise before minor, small-scale diversification and variations.

p35 Fig 2.7 Illustration of the tree and how it doesn't fit fossil evidence

p36 Fig 2.8 another illustration of fossil record vs neo-darwinian theory.

p39 Stephen Jay Gould enters the picture.

p41 By Darwin's tree, even as told by Dawkins, diversity would precede disparity and so on to more major differences - but the fossil record contradicts this. More "top down" as termed by Roger Lewin. Or from Douglas Erwin, James Valentine and Jack Sepkoski "The higher taxa do not seem to have diverged through an accumulation of lower taxa."

p45 Description of event which formed Burgess Shale, a unique geological event with major tectonic movements and relatively sudden events to preserve the fossils.

p46 Walcott's efforts for explaining the Cambrian and absence of intermediates - some kind of selection process

3. Soft Bodies and Hard Facts

p50 J. Y. Chen and the Chenjiang, China fossils.

p51 Even more explosive appearance than Burgess Shale.

p52 Chen at meeting "In China we can criticize Darwin, but not the government. In America, you can criticize the government, but not Darwin." "As Chen explained, the Chinese fossils turn Darwin's tree of life 'upside down'."

p52-54 Harry Whittington with then graduate students Simon Conway Morris and Derek Briggs did extensive work at Burgess Shale and further broke with Walcott's bridging strategy. They discovered wider morphological disparities.

p55 Understanding that subducting plates would destroy precambrian fossils did away with testing of Walcott's idea that precambrian fossils could be found in the sea floor. So land samples were best shot at precambrian fossils

p58 Schopf and observation of microorganism fossils like cyanobacteria in >3Gy collections worked against the idea that precambian fossils hadn't been seen because they were microscopic.

p62 The Chengjiang explosion proved that soft body parts could be preserved.

p63 The story of the Chengjiang discovery -

p63 Xian-Guang Hou and Chengjiang discovery - got team of farm workers to dig out mudstone blocks and found exquisitely preserved fossils including soft body parts. Much more detailed than Burgess fossils.

p66 J Y Chen and Paul Chien discovered sponge embryo fossils, showing that precambrian soft bodies can be preserved.

p69-70 Foote's analysis - more evidence against assumption that lack of intermediates is an artifact of selection.

p70 "paleontologists have utterly failed to find forms that would fill these yawning chasms in what biologists call 'morphological space'."

p70 "extensive sampling of the fossil record has confirmed a strikingly discontinuous pattern in which representatives of the major phyla stand in stark isolation from members of other phyla, without intermediate forms filling the intervening morphological space."

p71 Radiometric dating has narrowed the time window from 570-510My to a 20-40My window. This includes 1993 zircon crystal dating on both sides of the window.

p72 Diagram which posits 530-525 Mya as the window, which compared to 3Gy of life is like one minute of a 24 hour clock.

p73 Mentions problem of Vendian organisms, which I must have missed in the text - like microscopic precambrian? See p79-81

p73 Neighborhood of 6 My for appearance of maybe 13 new phyla, including trilobites with their complex lens-focusing compound eyes.

p74 "Top-down" pattern evidence strengthens at the expense of the "bottom-up" Darwinian pattern with the discovery of eel and fish-like creatures in the Chengjiang fossils. Simon Conway Morris is involved in this.

p76 Chapter ends with Darwin's tree of life upside down.

4. The Not Missing Fossils?

p78 Has described tension surrounding showing of film "Darwin's Doubt" and describes the Vendian or Ediacaran fossils dated to 565 Mya. Those were part of the topic of a critical lecture before the film.

p79-81 Section on the Ediacaran Fauna and Vendian Radiation. From Ediacaran Hills in outback of southeastern Australia. The last period of precambrian time has been named the Ediacaran period, but is also called the Vendian period. In neighborhood of 570-543 My . Some sponges in era, but distinctive group from Ediacaran Hills

p81-86 Detailed discussion of the four or so types of fossils and the debate about whether they were the "fuse" that set off the Cambrian explosion. Is decidedly skeptical about their role.

p87 Raises the issue that these Ediacarans represent an earlier but more minor explosion of information.

p88 "late Precambrian fossils have not solved, but rather deepened, the mystery of the origin of animal form."

p97 Summarizes some frustration at the end of a detailed chapter challenging the role of Ediacaran fossils as precursors for the Cambrian explosion. Well-argued chapter on a still-controversial matter of precambrian life forms.

5. The Genes Tell the Story?

p98 Using the analogy of a detective story to describe the study of the history of life: "Perhaps the most obvious surviving traces of ancient life are fossils. But as evolutionary biologists and paleontologists have come to realize that the Precambrian fossil record has not furnished the confirmation that Darwin hoped it would, many have looked to other kinds of clues to establish the gradual emergence of Cambrian animal life from a common ancestor."

p99 Discusses "homologies" in the usual man to horse to whale to bat five-digit homology - diagram.

p100 Discusses using "degree of difference" as a kind of clock of divergence time.

p100 "By analyzing the genes of existing animals representing phyla that first arose in the Cambrian, scientists have attempted to establish when the common ancestor of the Cambrian animal forms lived."

p101 The "Deep Divergence" hypothesis. Sort of concedes that the fossils can't do it, but maybe gene pointers can.

p102 The "molecular clock" Diagram fig 5.2, looking at mutation rate.

p103 Can be used with similar genes, RNA molecules or proteins in pairs of animals belonging to phyla that first arose in the Cambrian era. Use as pointer to precambrian ancestor.

p103-104 One study 1.2 Gy, one 800 My as projection of first animal. These studies sought to challenge the Cambrian explosion idea.

p111 Interesting idea in the section on the "Shmoo". The precursor to the Cambrian explosion, if it is to be the ancestor of the 20+ Cambrian phyla, has to lack the specific characteristics that distinguish the phyla from each other. So it had to be extremely simple, leading to the "shmoo" picture.

p113 Very interesting discussion in which he pretty thoroughly trashes the idea that such time projections have any validity. Ends with a section titled "Deep Trouble".

6. The Animal Tree of Life

I think this is a very well-done chapter. He has obviously thought about it a lot, and carefully lays out the case that neither the homology methods nor the genetic methods have produced a self-consistent tree of life. He highlights the abundance of inconsistencies with different starting points and different assumptions.

p115 A sort of tongue-in-cheek summary of the excessive confidence in Darwin's tree of life. Even having raised considerable doubt about the "deep divergence" use of mutations as a clock, he starts "The tree of life as a whole, however, is another matter. Many evolutionary biologists think the case for universal common descent is something close to unassailable because, they argue, analysis of both anatomical and genetic similarities converges on the same basic pattern of descent from a universal common ancestor." Quotes from Dawkins (Greatest Show), Coyne and Atkins, with Atkins being the most outrageous as usual:"There is not a single instance of the molecular traces of change being inconsistent with our observations of whole organisms."

p115 After noting that confidence in the "tree", the trunk of which would have to be in the precambrian, he notes "evolutionary biologists often dismiss the missing Precambrian fossil precursors and intermediates as a minor anomaly - one awaiting explanation by an otherwise completely adequate theory of the history of life."

p116 Another Coyne quote, expressing complete confidence in a universal common ancestor. "It stands to reason that if the history of life forms a tree, with all species originating from a single trunk, then one can find a common origin for every pair of twigs (existing species) by tracing each twig back through its branches until they intersect at the branch they have in common. This node, as we've seen, is their common ancestor."

p116 "evolutionary biologists have long used methods that assume that both molecular sequences and anatomical similarities provide an accurate historical sign about the past." "assume that the degree of difference between molecular or anatomical features in pairs of organisms indicates how long ago they diverged from a common ancestor."

p120 Meyer proceeds to give a string of examples that undermines these assumptions. Syvanen of U. Cal Davis studied 2000 genes, 6 animals and got no consistent tree-like pattern. His comment "We've just annihilated the tree of life." Rokas of Vanderbilt 50 genes, 17 taxa, found numerous conflicting phylogenies. Copublished with Sean Carroll the following year - skeptical about tree.

p124 After detailing a particularly strong disagreement between anatomical and molecular approaches "the statements of Dawkins, Coyne and many others about all the evidence (molecular and anatomical) supporting a single, unambiguous animal tree are manifestly false."

p125 He proceeds with a number of other examples and comes down to the conclusion that "there is no basis for the 'molecular assumption'."

p127 Example of the method of sperm cell production, which is scattered nearly randomly among animal groups, so couldn't form a coherent tree.

p133 Discussion of convergent evolution - i.e., similar individual traits in otherwise different body plans. If you have to evoke it often, it undermines the whole basis of phylogenetic reconstruction of the tree of life.

7. Punk Eek!

p137 Eldridge and Gould with many papers 1972-80 proposed "punctuated equilibrium" as an alternative to neodarwinian gradualism. They were joined by Stanley.

p138 Proposed "allotropic speciation" as a "fast engine" for producing the rapid change that was indicated, followed by long periods of stasis. They typically evoked small populations and geographical isolation.

p143 While punk eek had promise for explaining the lack of fossils as precursors to the Cambrian explosion, the different phyla represented a major problem for punk eek as well because it, like neo-darwinism, presumed a bottom-up pattern. Erwin and Valentine challenged both punk eek and neo-darwinism based on these problems.

p148 Neither species selection nor allotropic speciation accounts for the higher taxonomic categories appearing first.

p149 Gould had to drop back to natural selection in his major book in 2002, the year he died. So few evolutionary biologists regard punk eek as a solution.

p151 "in the end, punctuated equilibrium highlighted rather than resolved a profound dilemma for evolutionary theory .."

p151 Last paragraph a good general overview of the failure of both punctuated equilibrium and neo-darwinism to explain the features of life observed.

8. The Cambrian Information Explosion

p155 "to build a new form of life from a simpler preexisting form requires new information."

p156 "between 1870 and 1920 classical Darwinism entered a period of eclipse, because many scientists thought that it could not explain the origin and transmission of new heritable variation."

p156 Mendel's contributions.

p158 Discovery of genetic mutations brought both Mendel's genetics and natural selection back into play. The synthesis of Darwinism with Mendelian genetics is called the "new synthesis" or neo-Darwinism.

p159 Julian Huxley's quote

p159 In 1959 "Darwinism has come of age, so to speak. We are no longer having to bother about establishing the fact of evolution." Julian Huxley. The discovery of DNA structure in 1953 by Watson & Crick added to this euphoria.

p161 The Cambrian information explosion involved jump in Ediacaran period 555-570My with maybe 10 cell types, then at Cambrian explosion 50 or more cell types.

p164 Discussion of Shannon information. Then moves on to functional information.

9. Combinatorial Inflation

p170 Work of Murray Eden, "'No currently existing formal language can tolerate random changes in the symbol sequences which express its sentences. Meaning is almost invariably destroyed.' Thus, he suspected that the need for specificity in the arrangement of DNA bases made it extremely improbable that random mutations would generate new functional genes or proteins as opposed to degrading existing ones."

p170-177 Discussion of the Wistar Institute Conference in which Eden and other combinatorial math experts expressed pessimism about the efficacy of random variations in the DNA code producing new information.

p178 Michael Denton's input

p180 Role of Robert Sauer. Also Hubert Yockey. Behe mentioned.

10. The Origin of Genes and Proteins

p185 Douglas Axe, assessment of Dawkins program in The Blind Watchmaker, assessment of conference "Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution" and Robert Sauer's papers.

p187 Start of a detailed description of Axe's work at Cambridge where he challenged Sauer's work and tried to assess the possibilities for making proteins, or changing one protein into another similar one by natural selection. Found great difficulties with this, so tried the "scaling mount improbable" route of starting from nonfunctional or neutral regions of genome.

p207 Thorough experiments and calculations led to the conclusion of "extreme rarity of protein folds in sequence space also show why random changes to existing genes inevitably efface or destroy function before they generate fundamentally new folds or functions." The odds of 1 in 1077 that Axe came up with are pretty hard to get by.

p207 Summarizes as a "catch 22" that the low odds of natural selection generating a new gene means a mutation would have to scale Mount Improbable in a single leap. Also a summary statement that this study of mutations implies that neo-Darwinism can't explain the Cambrian explosion.

11. Assume a Gene

p209 Story about Meyer citing Axe's work in the article that caused so much furor that it led to the sacking of Sternberg, the editor of Proc of Bio Soc of Washington.

p211 Conclusion of no new genes finally got challenged by references to Long of U of Chicago article pointing to origin of new genetic information.

p213 Diagram of proposed types of mutations that have been alleged to modify genes

  1. Exon shuffling
  2. Retropositioning of messenger RNA transcript
  3. Lateral gene transfer
  4. Gene fusion
  5. Gene duplication

p214-229 Detailed examination of the supposed roles of these processes

12. Complex Adaptations and the Neo-Darwinian Math

p230 Story of Tom Frazzetta and his study of the extra hinge in the upper jaw of the bolyerine snakes of the Island of Mauritius. (diagram p231).

p233 Good quote of Frazzetta outlining the difficulty of modification of existing structures by natural selection: "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 next 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."

p240 Discusses Behe and Snoke's paper in Protein Science discusses the difficulty of the multiple coordinated mutations that could be required to achieve a new function. Evaluated probability of two coordinated mutation, then three - precipitous drops in probability when such coordination is required. Behe explored this idea in his book Edge of Evolution.

p250 Axe and Gauger explored literature for proteins as close to each other as possible and tried to convert one to the function of the other. Found that coordinated changes were required, and three coordinated changes would take longer than the age of life on earth. Bottom line was that co-option model was not viable.

p254 "the neo-Darwinian math is itself showing that the neo-Darwinian mechanism cannot build complex adaptations - including the new information-rich genes and proteins that would have been necessary to build the Cambrian animals."

13. The Origin of Body Plans

This is the chapter that I feel I learned the most from. It clarified the picture that mutations must come early in development to have a chance at macroevolutionary change in body plan, but that experiments show that such early mutations don't work because of the chain of coordinated steps downstream from such a mutation no longer work. Takes you to consider the development of an animal as a tightly coordinated process, so for an early mutation to work, you would have to change the rest of the process to fit it. This appears to be a fatal blow to neo-Darwinism, because by its very nature it can't help with all those other steps that fit the non-mutated pathway. Shows the picture of a whole system of coordinated epigenetic information and mechanism which supports the embryonic development toward the animal.

p255 Nobel prize of 1995 awarded to Christiane Nusslein-Volhard and Eric Wieshaus for their work in doing saturation mutagenesis of fruit flies, creating so many thousand mutations that you could reasonably judge that they had done a sampling of the available "mutation space". Dubbed the "Heidelberg screens", these experiments reverse-engineered the fly's genome to determine the function of the different genes.

p256 In response to a question in 1982 AAAS meeting, Weishaus replied "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, I guess, is what are - or what would be - the right mutations for major evolutionary change? And we don't know the answer to that."

The picture that emerged from this saturation mutation experiment is that, since all these major mutations died, and since major mutations are needed to create a new body plan, this seems to be a roadblock to the creation of new species by mutation.

p257 "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 body plans in the first place.?"

p257 "But even if mutation and selection could generate fundamentally new genes and proteins, a more formidable problem remains. To build a new animal and establish its body plan, proteins need to be organized into higher-level structures. In other words, once new proteins arise, something must arrange them to play their parts in distinctive cell types. These distinctive cell types must, in turn, be organized to form distinctive tissues, organs, and body plans. This process of organization occurs during embryological development."

p258 "Specific proteins play active roles in regulating the expression of genes for building other proteins. The protein actors playing these coordinating roles are known as transcription regulators (TRs) or transcription factors (TFs). .. usually bind directly to specific sites in DNA, either preventing (repressing) or enabling (activating) the transcription of specific genes into RNA.

p259 "Mutations that are expressed early in development, however, may affect many cells and could conceivably produce significant changes in the form or body plan, especially if these changes occur in key regulatory genes. Thus, mutations that are expressed early in the development of animals have probably the only realistic chance of producing large-scale macroevolutionary change."

  • Bernard John & George Miklos: "macroevolutionary change" requires changes in "very early embryogenesis"
  • Keith Thomson: only mutations expressed early in the development of organisms can produce large-scale macroevolutionary change.

But such early mutations are almost never viable

  • T H Morgan: mutation of fruit flies from early 20th century inevitably damage the organism
  • R A Fisher: early mutations "either definitely pathological (most often lethal) in their effects" or results in animals that cannot survive "in the wild state"

p260 From this point Meyer starts developing the picture of embryonic development as a regulated process with multiple coordinated agents.

p260 "Normal development in an animal can be represented as an expanding network of decisions, where the earliest (upstream) decisions have greater impact than those occurring later. Regulatory genes and their DNA-binding protein products help to control this unfolding network of decisions - such that if regulatory proteins are altered or destroyed by mutation, the effects cascade downstream into the whole developmental process. The earlier the failure, the more widespread the destruction."

p260 Geneticist Bruce Wallace "The extreme difficulty encountered when attempting to transform one organism into another .. still functional one lies in the difficulty in resetting a number of the many controlling switches in a manner that still allows for the individual's orderly (somatic) development."

p260 Nusslein-Vorhaus & Vieschaus discuss proteins that influence the organization of cells in fruitfly development - they called them "morphogens" - one they called bicoid which established the fruit fly's head-to-tail axis. If one of these "body-plan-affecting" molecules was damaged then development shuts down.

p260 Meyer has a good mechanical analog - if you change the length of the piston rod in a car's engine without modifying the crankshaft accordingly .. but late in the process you could change a minor control variable , like the paint color, without noticeable ill effects.

p261 "Similarly, animal development is a tightly integrated process in which various proteins and cell structures depend upon each other for their function, and later events depend crucially on earlier events. As a result, one change early in the development of an animal will require a host of other coordinated changes in separate but functionally interrelated developmental processes and entities downstream. This tight functional integration helps explain why mutations early in development inevitably result in embryonic death and why even mutations expressed somewhat later in development commonly leave organisms crippled."

p261 Illustration of fruit fly mutations.

p262 Georgia Tech geneticist John F. McDonald "great Darwinian paradox" "the genes that are obviously 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."

262 Cites Paul Nelson's summary:

  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 determine 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.

p263 Nelson "those premises strongly imply that the neo-Darwinian mechanism does not - and indeed cannot - provide an adequate mechanism for producing new animal body plans."

p264 Nelson "Research on animal development and macroevolution over the last thirty years - research done from within the neo-Darwinian framework - has shown that the neo-Darwinian explanation for the origin of new body plans is overwhelmingly likely to be false - and for reasons that Darwin himself would have understood."

p264 DEVELOPMENTAL GENE REGULATORY NETWORKS "many gene products (proteins and RNAs) needed for the development of specific animal body plans transmit signals that influence the way individual cells develop and differentiate themselves. Additionally, these signals affect how cells are organized and interact with each other during embryological development. These signaling molecules influence each other to form circuits or networks of coordinated interaction, much like integrated circuits on a circuitboard. For example, exactly when a signaling molecule gets transmitted often depends upon when a signal from another molecule is received, which in turn affects the transmission of still others - all of which are coordinated and integrated to perform specific time-critical functions. The coordination and integration of these signalling molecules in cells ensures the proper differentiation and organization of distinct cell types during the development of an animal body plan. Consequently, just as mutating and individual regulatory gene early in the development of an animal will inevitably shut down development, so too will mutations or alterations in the whole network of interacting signaling molecules destroy a developing embryo."

p265 Cites Eric Davidson of Cal Tech. "Davidson observed that the cells of an individual animal, no matter how varied in form or function, 'generally contain identical genomes'. During the life cycle of an organism, the genomes of these specialized cells express only a small fraction of their DNA at any given time and produce different RNAs as a result. These facts strongly suggest that some animal-wide system of genetic control functions to turn specific genes on and off as needed during the development of an animal from egg to adult as different cell types are being constructed."

p265 Some summary statements for Davidson & Britten's deductions:

  1. Tens or hundreds of specialized cell types arise during the development of animals.
  2. Each cell contains the same genome
  3. Some control system must determine which genes are expressed in different cells at different times to ensure the differentiation of cell types from each other.
  4. Some system-wide regulatory logic must oversee and coordinate the expression of the genome.

p265 "non-protein-coding regions of the genome control and regulate the timing of the expression of the protein-coding regions of the genome.

p266 Illustration of a control system

p267 Davidson, working since 1971 with the purple sea urchin as his experimental model system, has gone a long way toward modeling this control system. He refers to regions of the DNA which regulate and control gene expression as dGRNs(developmental gene regulatory networks).

p268 These dGRNs cannot vary without causing catastrophic effects to the organism.

p268 "Davidson's findings present a profound challenge to the adequacy of the neo-Darwinian mechanism. Building a new animal body plan requires not just new genes and proteins, but new dGRNs. "

p269 "Davidson's work highlights a profound contradiction between the neo-Darwinian account of how new animal body plans are built and one of the most basic principles of engineering - the principle of constraints. Engineers have long understood that the more functionally integrated a system is, the more difficult it is to change any part of it without damaging or destroying the system as a whole. " "The system of gene regulation that controls animal-body-plan development is exquisitely integrated, so that significant alterations in these gene regulatory networks inevitably damage or destroy the developing animal. But given this, how could a new animal body plan, and the new dGRNs necessary to produce it, ever evolve gradually via mutation and selection from a preexisting body plan and set of dGRNs?"

p269 Davidson "Neo-Darwinian evolution .. assumes that all processes work the same way, so that evolution of enzymes or flower colors can be used as current proxies for study of evolution of the body plan. It erroneously assumes that change in protein-coding sequence is the basic cause of change in developmental program; and it erroneously assumes that evolutionary change in body-plan occurs by a continuous process. All of these assumptions are basically counterfactual. This cannot be surprising, since the neo-Darwinian synthesis from which these ideas stem was a premolecular biology concoction focused on population genetics and .. natural history, neither of which have any direct mechanistic import for the genomic regulatory systems that drive embryonic development of the body plan."

14. The Epigenetic Revolution

This adds to the picture of the excellent Ch 13 and provides some detail about the nature of the epigenetic coordinated system necessary for the whole process of reproduction to work.

p271 Pointers to epigenetic, influences on cell development outside the DNA.

  • 1924 Spemann and Mangold- portion of newt embryo planted in another embryo caused a double body, so something outside DNA affects gross body shape.
  • 1930-40 Harvey - sea urchin to 500 cells without nucleus, so early division is guided by something outside DNA.

"DNA is not the whole story."

p273-274 "beyond the gene" conference, Muller & Newman, "neo-Darwinian paradigm ..[has] no theory of the generative."

p273 In 1993, Meyer and Jonathan Wells on way to "private meeting of Darwin-doubting scientists". Meyer asked why developmental biology was so important to evolutionary theory "I'll never forget his reply. 'Because' he said, 'that's where the whole theory is going to unravel.'"

p274 Discusses Shannon information and functional information in DNA and outside it. DNA and RNA are not the sole repositories of information.

p276 Good summary of the situation:

"DNA helps direct protein synthesis. Parts of the DNA molecule also help to regulate the timing and expression of genetic information and the synthesis of various proteins within cells. Yet 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. Similarly, distinctive 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 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."

p277 Analogies: "At a construction 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 low level components do not determine their own arrangement in an integrated circuit."

p277 Sources of epigenetic information:

  • Cytoskeletal arrays - arrays of microtubules made of tubulin provide critical structural information for a cell, but that information is not in the nature of the tubulin but in its arrangement.
  • Centrosome - duplicates in cell reproduction to partly determine the nature of the tubulin arrays in both daughter cells.
  • Membrane targets in cell walls provide information for location of proteins after synthesis - involves cytoskeleton
    • Interesting example of Bicoid and Nanos RNAs in fruit fly - info about head and tail
    • Transported by cytoskeleton
    • Membrane target at one end collects Bicoid, at other end collects Nanos to build head and tail
  • Ion channels - their location and pattern on the membrane represent higher level information
  • The sugar code - precisely arranged sugar molecules on cell surface represent another source of higher level information guiding cell surface interactions.
    • Location of specific sugar molecules on the exterior surface of cells represents information beyond the control of the genes.
    • Protein patterns in cell membrane transmitted from parent membrane to daughter membrane during cell division

p281 Epigenetic information challenges neo-Darwinism. Neo-Darwinism depends on mutation and natural selection at the level of the genetic text. "Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn't wholly responsible for the way an embryo develops - for body-plan morphogenesis - then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand."

p282 "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."

p286-287 "Darwin's Growing Anomaly" - good general discussion, which I will represent with the quote from Gilbert, Opitz and Raff:

"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.' "

p287 Points out that Gilbert and colleagues approached the problem by invoking mutations in Hox genes.

p287 "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."

15. The Post-Darwinian World and Self-Organization

p291 Simon Conway Morris unresolved problems exposed by the Cambrian explosion have, in Conway Morris's view "opened the way to a post-Darwinian world."

p292 A group called the Altenberg-16 biologists considered alternatives to the "neo-Darwinian triad"

  1. evolutionary change occurs as the result of random, minute variations or mutations
  2. the process of natural selection sifts among those variations and mutations such that some organisms leave more offspring
  3. favored variations must be inherited faithfully in subsequent generations.

p293-305 Detailed discussion of the proposals for self-organizational strategies by Stuart Kauffmann and Stuart Newman.

p305-310 Argues that the distinction between organization and order and information kills these proposals

16. Other Post-Neo-Darwinian Models

p312 "evo-devo" with Rudolf Raff, Sean B. Carroll and Wallace Arthur, achieving effectively large mutations by mutations of developmental genes.

p313 Illustration of the variations of non-ND models

p314 "Some evo-devo advocates such as Sean B. Carroll and Jeffrey Schwartz have pointed specifically to homeotic (or Hox) genes - master regulatory genes that affect the location, timing and expression of other genes - as entities capable of producing such large-scale change in animal form. These evo-devo advocates have broken with classical neo-Darwinism primarily in their understanding of the size or increment of mutational change."

p314 Meyer pretty well dismisses evo-devo on the basis of the experiments that indicate that major effects must come early, but are not viable. To be viable, they must be late, and therefore small effects.

p316 Some of the discussion centers on "cis-regulatory" genes, the claims that they can have major effects and the denial of same by others. They refer to an article by Sean Carroll and two others.

p317 "many evolutionary biologists recognize that such regulatory mutations do not explain the evolution of new body plans. Cites article by Hoekstra and Coyne critical of this idea "Genomic studies lend little support to the cis-regulatory theory" of evolutionary change.

p317 In section "What about Hox genes? he does provide a careful discussion of why he doesn't consider them a viable candidate for an agent of major body plan change.

p318 Quotes rather extravagant claims for Hox genes by Jeffrey Schwartz. In response "precisely because Hox genes coordinate the expression of so many other different genes, experimentally generated mutations in Hox genes have proven harmful." Cites McGinnis and Kuziora whose experimental studies of such lead them to state "most mutations in homeotic [Hox] genes cause fatal birth defects." Cites the legs for antennae substitution in fruit fly.

p319 A second objection to the Hox pathway is "Hox genes in all animal forms are expressed after the beginning of animal development, and well after the body plan has begun to be established. In fruit flies, by the time the Hox genes are expressed, roughly 6000 cells have already formed, and the basic geometry of the fly - its anterior, posterior, dorsal and ventral axes - is already well established. So Hox genes don't determine body-plan formation. Eric Davidson and Douglas Erwin have pointed out that Hox gene expression, although necessary for correct regional or local differentiation within a body plan, occurs much later during embryogenesis than global body-plan specification itself, which is regulated by entirely different genes. Thus, the primary origin of animal body plans in the Cambrian explosion is not merely a question of Hox gene action, but of the appearance of much deeper control elements - Davidson's 'developmental gene regulatory networks' (dGRNs). ..Davidson argues that it is extremely difficult to alter dGRNs without damaging their ability to regulate animal development."

p320 A third objection to the Hox gene scenario is "Hox genes only provide information for building proteins that function as switches that turn other genes on and off. The genes that they regulate contain information for building proteins that form the parts of other structures and organs. The Hox genes themselves, however, do not contain information for building these structural parts. In other words, mutations in Hox genes do not have all the genetic information necessary to generate new tissues, organs or body plans."

p321 Discussion of Michael Lynch and neutral or nonadaptive evolution

p332 Discussion of Shapiro's "natural genetic engineering" model.

17. The Possibility of Intelligent Design

A discussion of intelligent design and a defense of that approach to the Cambrian explosion. A defense of abduction and the inference to the best explanation. I have read all of this before in his other writings, so I don't do much detail here.

p340 A bit of Meyer's personal story and tribute to Charles Thaxton who started him on this journey.

18. Signs of Design in the Cambrian Explosion

p354 Discussion of the research of Douglas Erwin and Eric Davidson, who although they don't hold the view of intelligent design, provide evidence that certainly seems compatible with it.

Discussion of the evidence and how it points to intelligent design.

19. The Rules of Science

More detailed defense of intelligent design. Understandable in light of the opposition he gets from the evolutionary community. Includes tribute to Sternberg. Some of the 'What is science?' discussion, demarcation arguments

p400 Discussion of the ENCODE project showing 80% of DNA functional. Actually Shapiro writes an article commending Sternberg.

20. What's at Stake

The most personal chapter articulating the value of the consideration of intelligent design. Pushes away from the new atheism and theistic evolution to argue for an open consideration of intelligence in the process. Discussion of trip to Burgess Shale with son and others with some neat stories of interactions and some sharing about the nature of interactions he has had in discussing intelligent design.




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