Evolution and Creation Table of Contents
                                                       [Click on any topic to go there.]
1.    Introduction
2.    General References on the Relationship of  Religion and  Theology to Science
3.    General References for Philosophy of Science
4.    Genesis
5.    General References for Evolutionary Theory
6.    Evolution as Fact and Theory
7.     Introduction to Evolutionary Theory
8.     Natural Selection
                8.1  Natural Selection and Speciation
                8.2  Darwin's Finches
                8.3  Peppered Moths
                8.4  Colin Patterson
9.     Genetics and Mutation
                9.5  HOX Genes
10.   The Fossil Record
               10.1  General References on Fossils
               10.2  The Vertebrate Sequence
               10.3  Reptiles to Birds: Archaeopteryx and Longisquama
               10.4  Fish to Amphibian
               10.5  Dinosaur Fossils
               10.6 Polystrate Fossils
               10.7 Whale Fossils
11.   Punctuated Equilibrium
           11.11 The Cambrian Explosion
12.     Anatomy and Physiology
              12.1 The Giant Panda
              12.2. The human eye
              12.3  Vestigial Organs
13.     Molecular Evidence
14.     Evolutionary Developmental Biology
                14.2. Ernst Haeckel
15.     Biochemical Complexity
            15.5 Michael Behe
16.     Biogeography
17.     Origin of Life, Information and Complexity
                    Karl Woese
18.     Stephen Jay Gould and Richard Dawkins
19.     Legal and Educational Issues
20.     Intelligent Design
          20.6 Jonathan Wells
          20.7 William Dembski
21.     General References for Geology and Radiometric Dating
22.     General References for Young Earth Creationism
23.     Young Earth Creationist Arguments for a Young Earth
24.     Young Earth Creationist Arguments for the Coexistence of Humans and Dinosaurs
25.     The Noachian Flood
26.     Progressive (Old Earth) Creationism
27.     Theistic Evolution
                27.1    Catholicism
                27.2    Other Theistic Evolutionists
28.     Sociobiology
29.     Thermodynamics
30.     Human Evolution
31.     Evolution and Creation in the Popular Press

1a. Here are some useful weblogs and news groups for discussion of evolution and creation.
      Others can be found by clicking on the appropriate topic above.

Click Here  for Talk.origins,
         Click Here for the talk.origins discussion forum.
Click Here for TrueOrigin, a creationist response to Talk.origins.
Click Here for The Panda's Thumb
Click Here for Pharyngula by P.Z. Myers.
Click Here for The Loom by Carl Zimmer.
Click Here for The Austringer, The Weblog of Wesley R. Elsberry.
Click Here for The Sandwalk by Larry Moran.
Click Here for The Questionable Authority by Mike Dunford.
Click Here for Science, AntiScience, and Geology, by Joe Meert.
Click Here for Uncommon Descent, The Intelligent Design Weblog of William Dembski, Denyse O' Leary, and Friends.
Click Here for an Index to Creationist Claims edited by Mark Isaak.
Click Here for Alec's Evolution Pages by Alec MacAndrew.
Click Here for The Lancelet by Martin Brazeau.
Click Here for Playing Chess with Pigeons by Troy Britain.
Click Here for Genomicron by T Ryan Gregory.
Click Here for Quintessence of Dust by Stephen Matheson.
 

         Some primary texts and authors often or sometimes used for the course:

1.1   Darwin on Trial, by Phillip Johnson
1.1a    Click Here for Johnson's home page.
1.1b    Click here for links to most of Johnson's publications compiled by Stephen Jones.
1.1c    Click Here  for a 1999 intervew with Johnson hosted by Communique.
1.1d    Click Here  for a video study guide to a debate between Johnson and William Provine provided by the Access Research Network.
1.1e Click Here  for a November 2000 interview of Johnson for Touchstone: A Journal of Mere Christianity.
1.1f    Click Here  for an August 14, 2000 interview with Phillip Johnson about his book The Wedge of Truth.
           1.1fa Click Here  for a review of The Wedge of Truth by Edward Oakes.
           1.1fb Click Here  for reaction to this review and response from Oakes.
1.1g    Click Here for Johnson's 1989 "Position Paper on Darwinism".
 

1.2    Finding Darwin's God: A Scientist's Search for Common Ground Between God and Evolution, by
         Kenneth Miller
1.2a    Click Here for Miller's home page.
1.2b    Click Here for "The Evolution of Ken Miller: How a Roman Catholic cell biologist became one of the country's leading defenders of evolution - and what's at stake".
                                        [Nov/Dec 2005]
1.2c    Click Here for Miller's article, "Life's Grand Design".
1.2d    Click Here  for Miller's 2000 keynote address in Kansas, "Finding Darwin's God: The New Battle over Evolution".
1.2e    Click Here  for "Finding Darwin's God", adapted from Miller's book.
1.2f    Click Here for a December 2004 interview.
 

1.3  Science on Trial: The Case for Evolution, by Douglas Futuyma
1.3a    Click Here  for brief information on Futuyma.
1.3b    Click Here  for Futuyma's lecture "Evolution, Science and Society".

1.4  Refuting Evolution & Refuting Evolution2 by Jonathan Sarfati  Click Here for the PBS series on Evolution and
                         Click Here for the Scientific American article by John Rennie. Sarfati's book is a response to this production and article.
1.4a     Click Here  for Sarfati's homepage and links to many of his publications.
1.4b    Click Here for Sarfati's "Variation and natural selection versus evolution" from Chapter 2 of Refuting Evolution.
1.4c     Click Here  for Chapter 4 of Refuting Evolution: "Bird Evolution?".
1.4d     Click Here  for discussion of Sarfati's concept of "kinds" by David Thomas.
1.4e    Click Here for "Rejoinder to Sarfati and Humphreys's Responses"  by Perry G. Phillips of the Interdisciplinary Biblical Research Institute.

1.5    Click Here for information on Evolution vs. Creationism: An Introduction by Eugenie C. Scott. She is the director of the National Center for Science Education.
                                1.5a    Click Here for a review by John Burgeson.
 

1.6     Click Here  for an overview developed by the Ontario Consultants on Religious Tolerance: "The Theory of Evolution and Creation Science".
1.7     Click Here for the American Scientific Affiliation Commission on Creation.
1.8     Click Here for "Who Believes What? Clearing up Confusion over Intelligent Design and Young-Earth Creationism", by Marcus R. Ross.

2.1     Click Here  for The American Scientific Affiliation. The Affiliation is described as "a fellowship of  men and women of science and disciplines
                            that relate to science who share a common fidelity to the Word of God and a commitment to integrity in the practice of science."
                            Click Here for the ASA Creation/Evolution Page.
2.2    Click here   for "Truth and Religion Reconsidered: An Analytic Approach", by Andrzej Bronk.
2.3    Click Here  for "The Relation of Science, Factual Statements and the Doctrine of Biblical Inerrancy", by Bernard Ramm, former Professor of Christian
                           Theology at the American Baptist Seminary of the West.
2.4    Click Here  for "Can Science Prove that God Does Not Exist?" by Theodore Schick, Jr.
2.5    Click Here  for "Has Science Found God?" by Victor J. Stenger.
2.6    Click Here  for "Rational Methodology for Identifying Supernatural Power and Purpose" by  Steve Hinrichs .

2.7     Click Here  for a course developed by Deborah and Loren Haarsma: "Science and Spirituality: Is Harmony Possible?"
           2.7a    Click Here  for "Are Science and Religion at War?".
           2.7b    Click Here  for "Is the Creator Infinitely Lazy?".
           2.7c    Click Here  for "If Science is Right, is Genesis Wrong?".
           2.7d    Click Here  for "Can Creation and Evolution Both be Right?".
           2.7e    Click Here  for "If Evolution is Messy, can Creation be Good?".
            2.7f    Click Here for additional resources related to the Haarsmas' book, Origins: A Reformed Look at Creation, Design, & Evolution.

2.8      Click Here  for "Beyond War and Peace: A Reappraisal of the Encounter between Christianity and Science", David Lindberg and Ronald Numbers.
2.9      Click Here  for "Bishop Barnes, Science and Religion" by Steve Bishop.
2.10    Click Here  for "Important Primary Texts on Religion and Science in America" by   Edward B. Davis .
2.11    Click Here for Myths, Models and Paradigms: A Comparative Study in Science and Religion by  Ian Barbour (1976).
2.12    Click Here for "An Open Letter Concerning Religion and Science", distributed by the "Clergy Letter Project".
                                Click Here for a response from Rev. Mark H. Creech, executive director of the Christian Action League of North Carolina, Inc.
2.13    Click Here  for "Understanding American Evangelicals", a lecture by Mark A. Noll, McManis Professor of Christian Thought at Wheaton College.
2.14    Click Here  for some sample articles from Science and Christian Belief.
2.15    Click Here  for "Science, Religion, and the Teaching of Evolution in Public School Science Classes", issued by the National Council of Churches
                             Committee on Public Education and Literacy.
2.16    Click Here for the Nebraska Religious Coalition for Science Education (NRCSE).
2.17    Click Here for Beyond Belief: Science, Religion, Reason and Survival.
2.18    Click Here for Counterbalance: New Views on Complex Issues.
2.19    Click Here for "An Evangelical Manifesto: A Declaration of Evangelical Identity and Public Commitment"; 7 May, 2008 by the Evangelical Manifesto Steering Committee.

3.1                Karl Popper
3.1a    Click Here  for excerpts from "Science as Falsification" by Karl Popper.
3.1b    For some comments on Johnson's references to Karl Popper, click here to see a review of Darwin on Trial by Gert Korthof.
3.1c       Click Here  for a discussion of Popper's demarcation criterion, "The Separation of Science From Non-Science and Pseudo-Science and the
                                General Problem of Rationality and Openness to Argument: A Critical Exposition" by Ray Scott Percival.
3.1d    Click Here  for essays on Popper by Rafe Champion.

3.2                          Thomas Kuhn
    3.2a       Click Here  for a short discussion of Thomas Kuhn by Frank Pajares of Emory University.
    3.2b       Click Here  for an outline of Kuhn's The Structure of Scientific Revolutions composed by Frank Pajares.
                  Click Here for a short synopsis of this outline.
    3.2c       Click Here  for "Thomas Kuhn: Paradigms Die Hard" by Imran Javaid.
    3.2d       Click Here for "Popper and Kuhn on the Evolution of Science" by Pat Duffy Hutcheon.

3.6       Click Here  for "Evolution and Philosophy - An Introduction" by John Wilkins.
3.7       Click Here  for "Methodological Naturalism?" by Alvin Plantinga.
3.8       Click Here  for "Methodological Naturalism ? Part 2" by Alvin Plantinga
3.9       Click Here  for "Naturalism is an Essential Part of Science and Critical Inquiry", by Steven D. Schafersman.
3.10     Click Here  for "Science as Successful Prediction" by Imre Lakatos.
3.11    Click Here for "Methodological Naturalism and Philosophical Naturalism: Clarifying the Connection", by Barbara Forrest, author of Creationism's Trojan Horse.

4. GENESIS

           4.2.Interpretations of Genesis
4.2a    Click Here  for "The Literary History of the Pentateuch (Documentary Hypothesis)", by John Barton.
4.2b    Click Here  for a diagramatic representation of the documentary hypothesis and an application to Noah's flood.
4.2c    Professor Barry Bandstra at  Hope College teaches a course using the documentary hypothesis called  Reading the Old Testament .
4.2d    Click Here  for Bandstra's color-coded combined Yahwist-Priestly Flood text.
4.2e    Saint Augustine offers an interesting early example of how Genesis was interpreted at the end of the fourth century. See John McCarthy's
                                                     The Days of   Creation According to St. Augustine .
4.2f    For Thomas Aquinas's influential thirteenth century commentary on Genesis, see John McCarthy's The First Four Days According to St. Thomas .
4.2g    Click Here for Aquinas' commentary on the "days" of creation in his Summa Theologica.
4.2h    Click Here  for "Because it had not Rained", a 1958 argument for the "framework" interpretation by Meredith Kline.
4.2i     Click Here  for "The First Four Days of Genesis in Concordist Theory and the Biblical Context", by Paul Seely.
4.2j     Click Here  for "Genesis Reconsidered" by Armin Held and Peter Ruest.
4.2k    Click Here for "Why I Believe Genesis is Historically Accurate", by  Glenn Morton.
4.2L    Click Here for "The Antiquity and the Unity of the Human Race Revisited", by Davis A. Young
4.2m   Click Here for "Dinosaur Religion: On Interpreting and Misinterpreting the Creation Texts", by Conrad Hyers.
4.2n    Click Here  for  "Does the Bible Teach a Spherical Earth?", by Robert J. Schneider.
4.2O    Click Here for "The Three Storied Universe", by Paul Seely.

                                    4.3       "The Fundamentals" and "Fundamentalism"
4.3a    See Jerry Bergman's  A Brief History of the Modern American Creation Movement .
4.3b    Although the term "fundamentalism" is used in a variety of manners today, the term has its origin in a pamphlet series entitled  The Fundamentals: A Testimony to the Truth and published between 1910 and 1915.
Especially relevant for the discussion of evolution and creation are the following two essays from The Fundamentals:
4.3c    Professor George Frederick Wright, DD, LLD:  The Mosaic Authorship of the Pentateuch
4.3d    Rev. Dyson Hague, M.A.:  The Doctrinal Value of the First Chapters of Genesis
 

                                                4.4    Biblical Literalism
4.4a    Click Here for "The Bible Is a Textbook of Science", a position statement by Henry Morris of the  Institute for Creation Research.
4.4b    Click Here  for "The Days Of Creation", a Special Committee Report of the Reformed Church in the United States, adopted by the 253rd Synod May 17-20, 1999.
4.4c    Click Here  for the 2000 Report of the Creation Study Committee by the Presbyterian Church in America .
4.4d    Click Here for "Biblical Literalism: Constricting the Cosmic Dance", by Conrad Hyers.
4.4e   Click Here for the Westminster Theological Seminary and the Days of Creation.
4.4f     Click Here for "The Meaning of the Chronogenealogies of Genesis 5 and 11", by Gerhard F. Hasel.
4.4g    Click Here for "The non-moving Earth & anti-evolution web page of The Fair Education Foundation, Inc"

                                        4.5 Death and Sin in Genesis
4.5a   Click Here  for "Death Before Sin?", an Institute for Creation Research essay that interprets Genesis to say that death began only after the sin of Adam and Eve.
4.5b   Click Here  for "Theological Analysis of Selected Recent Creationist Assertions Concerning the Occurrence of Death before Sin", by Gary Emberger.
4.5c   Click Here for "Disease and Dying in the Fossil Record: Implications for Christian Theology" by Clarence Menninga.                                          
4.5d   Click Here for "Creature Mortality: From Creation or the Fall?", by John Munday.
4.5e   Click Here for "A young Earth - it's not the issue!", by  Ken Ham.
4.5f    Click Here for "Why is there death and suffering?", by  Ken Ham and Jonathan Sarfati.
4.5g   Click Here for "Two histories of death", by  Ken Ham.
4.5h    Click Here for "Animal Death before Human Sin ...does the Bible really teach that there was no animal death before human sin?", by Craig Rusbult.
4.5i    Click Here for "Death before Sin", a collection of sources compiled by Answers in Creation.
4.5j    Click Here for "Does Death before Sin Destroy the Plan of Salvation?", by Dalton D. Baldwin. (Or Click Here.)

 

5.1 Charles Darwin
    5.1a    Click Here  for an electronic version of Charles Darwin's On the Origin of Species, with a search option.
    5.1b    Click Here for an electronic version of Darwin's 1871 Descent of Man.
    5.1c    Click Here The Complete Works of Charles Darwin Online.
    5.1d    Click Here for "Evolution and Wonder: Understanding Charles Darwin".
    5.1e    Click Here for the Darwin Correspondence Project.

5.2    Click Here  for a website dedicated to Alfred Russell Wallace.
5.3    Click Here  for a website dedicated to Thomas H. Huxley.

5.4  Some useful sources for the study of evolution have been compiled by CSUF Professor Douglas Eernisse  for his course Biology 404: Evolution :
        5.4a Links to Topics in Richard Cowen's The History of Life (with Cowen's links for paleontology in the news)
        5.4b Links for Study of Evolution
        5.4c Organism WWW links

5.5    Click Here for the contents for the journal Evolution.

5.6    To look at the present reconstruction of the history of life, see  The Tree of Life .
5.7      Center for the Study of Evolution and the Origin of Life at UCLA.
5.8       SEE: Semiosis, Evolution, Energy - a virtual research project exploring the transformation of energy within evolutionary semiotic or codal organization.
5.7      Click Here  for the American Association for the Advancement of Science Evolution Resources site.
5.8      Click Here for Understanding Evolution: An Evolution website for Teachers.
5.9      Click Here for a collection of on-line peer-reviewed articles on various aspects of evolutionary biology.
5.10    Click Here for the Society for the Study of Evolution.
5.11    Click Here for Educational Resources developed by the Evolution and the Nature of Science Institutes.

6. Evolution as Fact and Theory

6.1    Click Here for Stephen J. Gould, "Evolution as Fact and Theory", May 1981.
           6.1a     Click Here  for an abridged version.

excerpt:

"Well evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts don't go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's in this century, but apples didn't suspend themselves in mid-air, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered.
Moreover, "fact" doesn't mean "absolute certainty"; there ain't no such animal in an exciting and complex world. The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are NOT about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us falsely for a style of argument that they themselves favour). In science 'fact' can only mean 'confirmed to such a degree that it would be perverse to withhold provisional consent'. I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
     Evolutionists have been very clear about this distinction of fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred. Darwin continually emphasized the difference between his two great and separate accomplishments: establishing the fact of evolution, and proposing a theory - natural selection - to explain the mechanism of evolution."

7.1    For a survey article by a famous evolutionary theorist, Stephen Jay Gould, see The Evolution of Life on Earth .
7.2    Click Here for  "Understanding Evolution".
7.3    Click Here for the PBS series on Evolution.
7.4    Click Here for Educational Resources developed by the Evolution and the Nature of Science Institutes.
7.5    Click Here for the Darwin Correspondence Project.

8. NATURAL SELECTION

8.1    Natural Selection and Speciation
8.1a    Speciation via Natural Selection
8.1b    Some More Speciation via Natural Selection
8.1c    Click Here  for "Nonrandom mating in drosophila melanogaster laboratory populations derived from closely adjacent ecologically contrasting slopes at Evolution Canyon by Abraham Korol et al.
8.1d    Click Here  for "Natural selection and speciation" by Christopher Schneider.
8.1e    Click Here for "An Interventionist Theory of Natural Selection and Biological Change within Limits" by Leonard Brand and L. James Gibson.
8.1f     Click Here  for a young-earth creationist analysis of "kinds": "Baraminology - Classification of Created Organisms", by Wayne Frair; archived from the CRS Quarterly by the  Creation Research Society .
8.1g    Click Here for "How the Horned Lizard Got Its Horns", by K.V. Young, E.D. Brodie Jr., and E.D. Brodie III. Click Here for additional material.
                            8.1ga    Click Here for commentary by S. J. Agosta and A.E. Dunham.
                            8.1gb    Click Here for a response by Young, Brodie and Brodie.
                            8.1gc    Click Here for additional commentary.

8.2 Darwin's Finches
8.2a    For an application of a young-earth creationist perspective on the biological concept of species to Darwin's finches see Kenneth Cumming's article
           Reticulate Evolution . Phillip Johnson discusses this case on page 25 of Darwin on Trial.
8.2b    Click Here  for "Darwin's Finches: Evidence supporting rapid post-Flood adaptation", by Carl Wieland of Answers in Genesis.
8.2c    Click Here for "Phylogeny of Darwin's finches as revealed by mtDNA sequences" by Akie Sato, Colm O'hUigin, Felipe Figueroa, Peter R. Grant, B. Rosemary
                                                                                                                                                                                         Grant, Herbert Tichy, and Jan Klein.
8.2d    Click Here  for "Genetics and the origin of bird species" by Peter R. Grant and B. Rosemary Grant.
8.2e    Click Here  for the Galapagos finch page of   Robert Rothman .

8.3 Peppered Moths
An interesting case of the role of natural selection in evolutionary change is provided by melanism in peppered moths. Johnson mentions this case on pages 26 and 176-177 of Darwin on Trial.
8.3a   Click Here for a summary by Bruce Grant, "Fine Tuning the Peppered Moth Paradigm".
                              8.3aa    Click Here for Bruce Grant's home page and a link to his review of Judith Hooper's Of Moths and Men.
8.3b   Click Here for "Goodbye, peppered moths", by young earth creationist Carl Wieland.
8.3c   Click Here  For "Second Thoughts about Peppered Moths", by  Jonathan Wells.
                                      Click Here  for other articles on evolution by Wells, and  Click Here  for other articles by Wells.
8.3d   Click Here  for a review of Wells' book, Icons of Evolution, by  David Ussery.  Click Here for analysis by Massimo Pigliucci. 
          Click Here  for "Icon of Obfuscation: Jonathan Wells's book Icons of Evolution and why most of what it teaches about evolution is wrong", by Nick Matzke.
          Click Here  for a critique of Wells by Alan Gishlick for the National Center of Science Education.
8.3e   Click Here  for Kenneth Miller's comments on peppered moths.
8.3f    Click Here for "Moonshine: Why the Peppered Moth Remains An Icon of Evolution", by Matt Young.
8.3g   Click Here for the home page of Michael Majerus, which includes links to his lecture "The Peppered Moth: The Proof of Darwinian Evolution", given at the ESAB meeting in Uppsala on 23
                            August, 2007 and his "Peppered Moth: Decline of a Darwinian Disciple", delivered to the British Humanist Society on 12 February 2004.

8.4 Colin Patterson
8.4a    On page 10 of Darwin on Trial, Johnson cites an oft-quoted statement by Colin Patterson. Click Here for correspondence from Patterson concerning this passage in a report by Lionel Theunissen.
8.4b     Click Here  for an alternative account by  Paul Nelson.
8.4c     Click Here  for a 1981 speech by Patterson transcribed by Stephen Jones. 

8.5     Click here for information on the Coelacanth, one of the most famous of the "living fossils" discussed by Johnson on page 29.

9.1     Click Here  for DNA From The Beginning: an animated primer on the basics of DNA, genes and heredity.
        9.1a    Click Here for a review of DNA structure and protein synthesis.
        9.1b    Click Here for a summary of various types of mutation.
        9.1c    Click Here for a summary of an interesting experiment by  Joshua Lederberg. This is an example of a bacteria mutation that resulted in
                                      adaptive change in a specific environment.
9.2    Click here for a discussion of the distinction between genetic "microevolution" and larger scale "macroevolution".

9.3   Debate over the role of random mutations in adaptive change.
    9.3a   Click Here  for "The Evolution of Improved Fitness by random mutation plus selection" by Edward Max. This includes a link to correspondence
                                 with a critic, Lee Spetner.
    9.3b   Click Here  for Spetner's update of his critique: "A Scientific Critique of Evolution".
    9.3c   Click Here for  "Spetner and Biological Information" by Ian Musgrave.
    9.3d   Click Here  for "Evolutionary Increases in Information" by  Wesley Elsberry.
    9.3e   Click Here  for a report on the role of chance in the history of amino acid sequences.
    9.3f    Click Here  for "Evolution and Information: The Nylon Bug", by Dave Thomas.
                                    9.3fa    Click Here for further discussion of this case.
    9.3g     Click Here for "Evolution of Biological Information" by Tom Schneider.
    9.3h     Click Here  for "Examples of Beneficial Mutations and Natural Selection" by Robert Williams.
    9.3i      Click Here  for a discussion of "delta 32", a mutation studied by Stephen O'Brien.
    9.3j      Click Here  for an article by O'Brien on the relevance of "delta 32" to research on HIV and AIDS.
    9.3k     Click Here for "Apolipoprotein AI Mutations and Information" by Ian Musgrave and Steven Pirie-Shepherd.
    9.3L     Click Here for "Information Theory and Creationism", by Ian Musgrave, Rich Baldwin, and others.
    9.3m    Click Here for the abstract of "Myosin gene mutation correlates with anatomical changes in human lineage" (2004)
                                    9.3ma    Click here for more information on myosin.
                                    9.3mb    Click Here for pdf files (2004).
    9.3m    Click Here  for "Evolution and Chance" by John Wilkins and Chance from a Theistic Perspective by Loren Haarsma.
    9.3n     Click Here for "Evolution by Accident" by Laurence A. Moran.
    9.3O    Click Here for "Are Mutations Harmful?"
    9.3p    Click Here for "Examples of Beneficial Mutations in Humans ".
    9.3q    Click Here for discussion of the origins of the SETMAR gene.

                                                  9.4    Mutation and the Evolution of Vision
9.4a  On a computer simulation of the evolution of vision, see Richard Dawkins' Where d'you get those peepers .
9.4b  For a controversial genetic argument that the eye has only evolved once, see Eye-opening Gene by John Travis.

9.5    HOX GENES AND OTHER REGULATORY GENES
9.5d    Click Here  for "Establishment of Spatial Patterns of Gene Expression During Early Vertebrate Development: Hox Genes" by Derrick Rancourt.
9.5e    Click Here  for "Interpreting the Homeobox: Metaphors of Gene Action and Activation in Development and Evolution" by Jason Scot Robert
9.5f     Click Here  for "Hox (homeobox) Genes - Evolution's Saviour?" by Don Batten of Answers in Genesis.
9.5g    Click Here  for "It's not just the genes, it's the links between them", by P.Z. Myers.
9.5h    Click Here  for "Natural Genetic Engineering -- the Toolbox for Evolution: Prokaryotes", by Dr. Jim Shapiro.

                                                            9.6    Technical Articles
9.6a    Click here  or Click Here for an interesting experiment by  Joshua Lederberg  discussed by Futuyma on page 137 of Science on Trial. This is an example of a bacteria mutation that was adaptive in a specific environment. Click Here for a summary of this experiment.
9.6b    Click Here  for "Evolution of an Escherichia coli Protein with Increased Resistance to Oxidative Stress" by E.C.C. Lin et al. This case is discussed
                              by Miller on pages 105-107 of Finding Darwin's God.
9.6c    Click Here   for a collection of articles on horizontal gene transfer by Michael Syvanen.
9.6d    Click Here   for "Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and
                               dominance of horizontal gene transfer in the evolution of prokaryotes" by Boris G. Mirkin et al.
9.7      Click Here  for a report on gene swapping among bacteria.

                                                            9.8    The Genetic Code
9.8a   Click Here  for an introduction to the research of Laura Landweber.
9.8b   Click Here  for "Do Non-standard Genetic Codes Present a Challenge to Evolutionary Theories?", by R. Joel Duff.
9.8c   Click Here  for "The Universal Genetic Code Seen from an ID Perspective", by Mike Gene.
9.8d   Click Here  for the PBS production "Cracking the Code of Life".

10.1  General References on Fossils and the Fossil Record
10.1a    Click Here for a general introduction to fossils: "Fossils - Windows to the past".
10.1b    Click Here  for "Fossilization" by Chris Nedin.
10.1c    The University of California Museum of Paleontology maintains a valuable online collection called Paleontology Without Walls

10.1d    Don Lindsay  has a nicely illustrated set of speciation examples he calls  Smooth Change in the Fossil Record .
                10.1da    Click Here  OR HERE   for further discussion of  Foraminifera.
                10.1db    Click Here for The Micropaleontological Society.
                10.1dc    Click Here for "Microfossil Statigraphy Presents Problems for the Flood" by Glenn Morton.
                10.1dd    Click Here for Dan Georgescu's page on foraminifera.

10.1e    Kathleen Hunt compiled a long list for the talkorigins archive: Transitional Fossils .
10.1f    Click Here  for Paleo Links - 2002, maintained by James Mahaffy of Dordt College.
10.1g    Click Here  for "Fossils" compiled by computer scientist  Don Lindsay.
10.1h    Click Here  for information on how fossils are dated.
10.1i     Click Here  for the Geoscience Research Institute: a research and communication institute serving the Seventh-day Adventist church.
10.1j     Click Here  for an on-line introduction to earth history.
10.1k    Click Here  for "Zeno's Paradox and the Creationist Demand for Transitional Forms" by  Glenn Morton .

10.1L    Click Here for "Estimation at Age of Death" by Nancy Lovell.
10.1m   Click Here  for "Sex Determination" by Nancy Lovell.

10.1n    Click Here  for "What Are Conodonts?" by Jim Davison.
10.1o    Click Here for Palaeontologia Electronica.
10.1p    Click Here for discussion of trace fossils.
10.1q    Click Here for a 1815-1817 geologic map prepared by William Smith and two accompanying publications: "WILLIAM "STRATA" SMITH ON THE WEB", produced by Cecil J. Schneer, Professor Emeritus of Geology and the History of Science at the University of New Hampshire.
10.1r    Click Here    for some examples of index fossils.
10.1s    Click Here for "Taxonomy, Transitional Forms, and the Fossil Record", by Keith B. Miller.
 

10.2The Vertebrate Sequence

10.2a    A good place to start is a 1994 compilation by Kathleen Hunt on Transitional Fossils
 

10.3 Reptiles to Birds: Archaeopteryx and Longisquama
10.3a    Although Johnson is ambivalent about the import of Archaeopteryx for the evolution of birds from reptiles, other creationists, such as Duane Gish, take more extreme exception to evolutionary arguments. Click Here  for "Archaeopteryx: Answering the Challenge of the Fossil Record", a response to Gish by Chris Nedin.
10.3b   Click Here  for "All About Archaeopteryx" by Chris Nedin.
10.3c   Click Here for The Archaeopteryx Pages .
10.3d   Click Here  for links on Archaeopteryx, ancient birds and dinosaur-bird relationships.
10.3e   Click Here for "Half-evolved feathers and Christian Accountability" by Glenn Morton .
10.3f    Click Here  for a very good Archaeopteryx page by daily-tangents.
10.3g    Click Here    for the Archaeopteryx page of Nick Longrich.
10.3h    Click Here    for "Structure and function of hindlimb feathers in Archaeopteryx lithographica", by Nick Longrich.

10.3h Longisquama insignis
10.3ha   Click Here for "Wings on Hind Legs", with links to photos of fossils of Longisquama insignis, a Triassic thecodont reptile with feather-like scales.
              Click Here for another description of Langisquama.
10.3hb   Click Here for a report on the claim that Longisquama had feathers.
10.3hc   Click here for a proposed revision of bird geneology in light of Longisquama.
10.3hd   Click Here for a September 2000 update on Longisquama.

10.3i Other fossils with feathers and "feathered dinosaurs".
10.3ia    Dinosaur-bird link smashed in fossil flap.
10.3ib    Click Here for another article on Archaeoraptor.
10.3ic    Click Here for "Dinos of a Feather: Evidence Mounts of Feathered Lizards".
10.3id    Click Here  for a 7 December, 2000 report on Protopteryx: "Ancient Chinese 'Bird' Used Feathers to Fly".
10.3ie    Click Here  for an April 2001 report by Mark Norell on a new dinosaur specimen unearthed in the Liaoning Province of the China that is said to demonstrate "exceptional preservation of
                                     integumentary structures akin to primitive feathers."
                   Click Here  for a press release from the American Museum of Natural History.
                   Click Here  for an ABC News report.
                   Click Here  for a CNN report.
10.3if     Click Here  for Yale University's Peabody Museum Exhibit: "China's Feathered Dinosaurs".
10.3ig    Click Here  for "Are Birds Really Dinosaurs?", by  John R. Hutchinson.
10.3ih    Click Here  for Chapter 4 of Sarfati's Refuting Evolution: "Bird Evolution?".
10.3ii     Click Here  for a report on recent evolutionary developmental biological research into the origin of feathers.
10.3ij     Click Here for "Feathers, scutes, and the origin of birds", by Jeff Poling.
10.3j      Click Here for the homepage of bambiraptor.
10.3k     Click Here for "Development of teeth in chick embryos after mouse neural crest transplantations", by Thimios A. Mitsiadis, Yvonnick Chéraud , Paul
                                                                                                                                                                                                                           Sharpe and Josiane Fontaine-Pérus.

10.4 Fish and Early Tetrapods
10.4a    Click Here to see a 2000 fossil find relevant to the relationship of fish to amphibians.
10.4b    Click Here  for "Fish to Amphibian Transition" by Glenn Morton .
10.4c    Click Here  for an interview with Ted Daeschler and Neil Shubin: "How Fish Came Ashore". Their discovery is
                                discussed by Miller on page 125.
10.4d    Click Here  for a 2/28/01 news report on a fossil of an early lobe-finned fish, Achoania.
10.4e    Click Here  for articles on Acanthostega gunnari compiled by Todd Greene .
10.4f     Click Here  for a discussion of  Acanthostega gunnari by Jennifer Clack.
10.4g    Click Here  for a discussion of Ichthyostega  by  Jennifer Clack.
10.4h    Click Here  for discussion of genetic research on digit and limb articulation.
10.4i     Click Here   "Regulation of number and size of digits by posterior Hox genes: A dose-dependent mechanism with potential evolutionary implications" by József
                                                                                                                                                                                                                                               Zákány et.al.
10.4k    Click Here  just for fun, to see The Mudskipper, a little fish that can hop around on mud. (cute)
10.4L    Click Here for ""Discovery of a Transitional in Romer's Gap", by Alec MacAndrew, on Pederpes finneyae.
10.4m   Click Here for "Demorphing the Tetrapodomorpha".
10.4n    Click Here for information on the Coelacanth, one of the most famous of the "living fossils".
10.4O    Click Here for The "GREAT" Transition, by Neil Shubin.
10.4p    Click Here for the University of Chicago site dedicated to Tiktaalik roseae.
10.4q    Click Here for Hynerpeton.

10.5 Dinosaur Fossils
10.5a    Click Here  for "The Therapsid-Mammal Transitional Series" by Lenny Flank.
10.5b    Click Here  for "What really killed T. Rex?", a  report on several explanations of dinosaur extinction.
10.5c    Click Here  for The Pterosaur Home Page.
10.5d    Click Here  for photographs and discussion of "A king-sized theropod coprolite found in Saskatchewan" (discussed by Miller on page 62).
10.5e    Click Here  for an illustrated discussion of the fossilized heart of Thescelosaurus.
10.5f     Click Here for recent dinosaur discoveries by paleontologist Paul Sereno.
10.5g    Click Here  for "Heme Compounds in Dinosaur Trabecular Bone" by Mary Schweitzer et al.
10.5h    Click Here  for a young-earth creationist interpretation of Schweitzer's research by Carl Wieland.
10.5i     Click Here  for "Dino-blood and the Young Earth", by Gary S. Hurd
10.5j     Click Here for ""Dino Blood Redux" by Gary Hurd.
10.5k    Click Here for "Tyrannosaur Morsels" by P.Z. Myers.
10.5k    Click Here  for information on Alaskan dinosaur fossils.
10.5L    Click Here  for comments by Bob Bakker, a famous dinosaur fossil hunter and Pentacostal preacher.
10.5m    Click Here for "The Proof is in the Poop!", by Greg Neyman for Answers in Creation.

10.6    Polystrate Fossils
10.6a   Click Here  for "'Polystrate' Tree Fossils" by Andrew MacRae.
10.6b   Click Here  for "Polystrate Fossils" by Don Lindsay.
10.6c   Click Here  for "What are Polystrate Fossils?" by John Morris of the Institute for Creation Research.
10.6d   Click Here  for an American Scientific Affiliation conversation on polystrate fossils archived in 1997.
10.6e   Click Here  for "The Polystrate Trees and Coal Seams of Joggins Fossil Cliffs" by John Morris.
10.6f    Click Here  for "The Fossil Cliffs of Joggins" by Laing Ferguson.
10.6g    Click Here  for "The Joggins Fossil Cliffs", maintained by the Nova Scotia Museum.
10.6h    Click Here  for discussion of a polystrate whale fossil discovered near Lompoc, California.
10.6i    Click Here for a Wikipedia article on polystrate fossils.

10.7    Whale Fossils
10.7a    Click Here  for discussion of recent  Pakicetidae discoveries by  Hans Thewissen. Click Here for Thewissen's research on the evolution of whale hearing. Click Here for his photos of Indohyus.
10.7b    Click Here  for "The Origin of Whales and the Power of Independent Evidence" by Raymond Sutera.
10.7c    Click Here  for "Hooking Leviathan by Its Past" by Stephen Jay Gould (1994).
10.7d    Click Here  for "Ambulocetus Has No Pelvis and is Largely Incomplete?".
                                10.7da    Click here for Ambulocetus fossils.
10.7e    Click Here for "CETACEAN EVOLUTION (WHALES, DOLPHINS, PORPOISES) by Edward T. Babinski
10.7f     Click Here for "A Whale Fantasy from National Geographic" by Harun Yahya.
10.7g    Click Here for "A whale of a tale?", by Don Batten for Answers in Genesis.
10.7h    Click Here for "Another whale of a tale: creationists without a 'whimper'?", by Mark Looy for Answers in Genesis.
10.7i     Click Here for Chapter 5 from Refuting Evolution by Jonathan Sarfati: "Whale evolution?".
10.7j     Click Here for  a summary of recent developments in whale evolution research,  "The Steps of the Puzzle", by Carl Zimmer.
10.7k    Click Here for  "THE EARLY RADIATIONS OF CETACEA (MAMMALIA): Evolutionary Pattern and Developmental Correlations", by
                              J. G. M. Thewissen and E. M. Williams (2002).
10.7L    Click Here  for "French-Chadian funded scientists reveal origin of hippos", on anthracotheres.
10.7m    Click Here or Click Here for "The position of Hippopotamidae within Cetartiodactyla", by Jean-Renaud Boisserie , Fabrice Lihoreau , and Michel Brunet (2005)
10.7n     Click Here for the Whale website of Philip Gingerich.

10.8    Snakes
10.8a    Click Here for Pachyrhachis problematicus, a fossil snake with legs.
10.8b    Click Here  for Haasiophis terrasanctus, another fossil snake with legs.

11.1    Zoologist Wesley Elsberry  has written a good summary of this topic called Punctuated Equilibrium. He also maintains a page called  Evolution, Anti-Evolution, and SciCre .
11.2    Punctuated equilibrium was initially proposed by  Stephen Jay Gould and  Niles Eldredge in 1972. It was an objection to what Gould has called
           Darwinian Fundamentalism . The second half of this article is called  Evolution: The Pleasures of Pluralism .
11.3    Click Here  for "Snails Caught in Act of Evolution", a report on Gould's study of land snails as discussed by Miller on pages  118-121.
11.4    Eldredge proposed punctuated equilibria partly due to his study of trilobites. Click Here for A Guide to the Orders of Trilobites, maintained by
           Sam Gon III, and  Click Here for his gallery of Phacopida images, an order of trilobites particularly important in Eldredge's research.
11.5    Paleontologist Donald Prothero wrote an article for the Skeptic Society entitled  Punctuated Equilibrium at Twenty: A Paleontological Perspective .
11.6    Although rather abstract by some standards, there is also a "Systems Approach" to punctuated equilibrium, for example, the ideas of F. Heylighen in
           his article Punctuated Equilibrium .
11.7    For rapid evolution of bacteria that has been interpreted as support for punctuated equilibrium, see  Score One for Punk Eek .
11.8    For a young earth catastrophist account of punctuated equilibrium, see PUNC EQ CREATION STYLE by  Kurt Wise .
11.9    There is a wide variety of creationist views about speciation. In an article for Creation Ex Nihilo, young earth creationist Carl Wieland argues that
            relatively rapid speciation is to be expected from a creationist perspective:  Speciation Conference Brings Good News for Creationists .

11.11:    THE CAMBRIAN EXPLOSION
11.11a    Click Here for "Phylum Level Evolution" by Glenn Morton .
11.11b    Click Here  for "When Life Exploded", a 1995 Time cover story on the Cambrian explosion by J. Madeleine Nash.
11.11c    Click Here  for The Cambrian Period, maintained by the UC Berkeley Museum of Paleontology.
11.11d    Click Here  for Burgess Shale fossils, maintained by  Andrew MacRae  of the University of Calgary.
11.11e    Click Here   for an introduction to pre-Cambrian animals, "Learning About Vendian Animals', maintained by the UC Berkeley Museum of
                                 Paleontology.
11.11f    Click Here for a computer simulation of the Cambrian explosion by Glenn Morton .
11.11g    Click Here  for "A Review of The Evidence For Trilobite Predecessors in the Fossil Record" by Robert B. MacNaughton.
11.11h    Click Here for Palaeobiology: "The Realms of Archaean Life" by Euan Nisbet.
                            [Abstract: There is evidence of a variety of early organisms from the Archaean — some 4,000 to 2,500 million years ago. Now life at deep-sea hot springs
                                                  can provisionally be added to the list.]
11.11i      Click Here  for "Fossil Findings May Force Revisions in the History of Life", and Click Here for the technical article that is the basis of this report.
11.11j      Click Here  for "The Cambrian 'explosion': Slow-fuse or megatonnage?" by   Simon Conway Morris.
11.11k     Click Here  for "Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla" by Gregory A. Wray et al.
11.11L    Click Here  for "The Universal Ancestor" by   Carl Woese.
11.11m    Click Here  for "Default taxonomy: Ernst Mayr's view of the microbial world by Carl Woese .
11.11n    Click Here  for "Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria,
                                     and Eukaryotes", by Radhey S. Gupta.
11.11o    Click Here  for "Determining divergence times with a protein clock: Update and reevaluation", by Da-Fei Feng, Glen Cho, and  Russell F. Doolittle
11.11p    Click Here  for 'Fun with geneology", by   W. Ford Doolittle .
11.11q    Click Here  for "The Root of the Universal Tree and the Origin of Eukaryotes Based on Elongation Factor Phylogeny", by Baldauf, Palmer and&nbs