Wednesday, June 1, 2011

About The Book

List of Topics

Fundamental Thesis of This Book
The goal behind Science is to put together a large puzzle, where all the pieces fit perfectly together. Together, the puzzle pieces attempt to explain the fundamental cause for everything we observe. This huge mosaic is a combination of both uncontroversial facts and debatable logical inferences.
Scientific facts are considered uncontroversial because they are based on repeatable observations. For example, if you doubt that Newton’s laws accurately describe the effect of gravity in the environment of earth, you can conduct your own experiments and test Newton’s laws yourself.
Scientists strive to merge empirical facts with logical inferences to create a mosaic of cause and effect relationships. Logical inferences introduce controversy into the scientific process because they are made by fallible human beings (i.e., scientists). They are not as certain as scientific facts.
The so-called Fact of Evolution is a mosaic built from both scientific facts and logical inferences. The pieces of this huge mosaic have been obtained from many different fields of science. For example, Paleontologists, Molecular Biologists, and Geneticists all strive to paste bits and pieces into this mosaic.
The fundamental thesis of this book is that it is improper to classify Evolution as a scientific fact. This thesis does not challenge the pieces of the Fact of Evolution that are directly connected to empirical facts. Rather, it challenges the speculative logical inferences that bind these empirical facts together.

Challenges to my Thesis
The main thesis that I present in this book is that it is improper to classify Evolution as a scientific fact. There are two major ways to dispute my thesis. The first is to argue that the mosaic I have painted for the Fact of Evolution is inaccurate. The second is to argue that my analysis of this mosaic is inaccurate.
I welcome all challenges to my thesis. I believe that this subject should be debated in the public domain. I hope that any challenger will take the time to read what I have written and accurately quote me. Within the bounds of my human fallibility, and the time constraints we all have, I have tried to do this for the sources that I have quoted.

Why is the Debate over Evolution Important?
Because this book challenges the validity of the Fact of Evolution, it is reasonable to ask this question: Why is the debate over Evolution important? There is no doubt that Evolution is often presented as being vitally important to science. For example, consider this quote from Richard Dawkins’ The Selfish Gene:
If superior creatures from space ever visit the earth, the first question they will ask, in order to assess the level of our civilization, is: ‘Have they discovered evolution yet?’[1]
However, there is a good reason to believe that Dawkins drastically overemphasizes the importance of Evolution. Because Evolution relies on an unpredictable set of random genetic mutations, it can make no predictions about the future. One might argue that this is unimportant, since the primary focus of Evolution is to explain the past. However, the explanation of the past promoted by Evolutionists is just as murky.
In The Blind Watchmaker, Richard Dawkins devotes a whole chapter to describing the fierce fights about the evolutionary Tree of Life.[2] Stephen Jay Gould went as far as to suggest that taxonomy should be labeled “names and nastiness” because of the sharp differences of opinion between advocates for different classification methods.[3] Thus, Evolution can neither explain the past nor predict the future with any certainty.
Science without certainty has little value. The primary value of science stems from the certainty of repeatable observations. Repeatable observations are largely undisputed and uncontroversial, except for cases of outright fraud or careless methodology. This quote from the Nobel-Prize winning physicist Emilio Segrè[4] suggests that science needs to keep its focus on empirically derived data, and avoid the danger of non-empirical conclusions:
In an enterprise such as the building of the atomic bomb the difference between ideas, hopes, suggestions and theoretical calculations, and solid numbers based on measurements is paramount. All the committees, the politicking and the plans would have come to naught if a few unpredictable nuclear cross sections had been different from what they are by a fact of two. [NOTE: A cross section is the probability that a particular nuclear reaction will or will not happen].[5]
As Segrè’s quote suggests, no team of scientists – no matter how distinguished – can avoid the necessity of focusing on the laws of physics. That is probably why Ernest Rutherford[6] (another Nobel-Prize winning scientist) made this statement: “All science is either physics or stamp collecting.”[7] Rutherford was not knocking the value of chemistry, as he was actually awarded the Noble Prize for chemistry, although he was a physicist.[8]
But Rutherford would probably have hit the roof if he read Bruce Alberts description of how “many talented young biologists feel that mathematics, chemistry, and physics are of minor importance to their careers.”[9] I find Alberts’ statement to be a sad commentary on the relation of modern biology to empirical science. In my opinion, biology is simply the branch of physics that deals with the operation of living organisms.
According to Molecular Biology of the Cell (Alberts et al.), “there is nothing in living organisms that disobeys chemical and physical laws.”[10] Therefore, if the aim of biology is to understand how living organisms work, it needs to be tightly coupled to the laws of physics and chemistry. This makes one wonder what value Evolution offers to scientific advancement, if it takes the focus of biologists away from physics and chemistry.
Memorizing the entire content of Darwin’s Origin of the Species or Dawkins’ The Blind Watchmaker will not help anybody understand how nerve cells work, or how bacteria propel themselves with the aid of ultra-efficient miniature motors. If you want to understand how any biological system functions, you need to study physics and chemistry. Worshiping the dogma of the Fact of Evolution will not aid you in this task.
Anybody who thinks that dogmatic beliefs are restricted to religion should consider this quote from Michael Polanyi[11] (Chemist and Philosopher of Science):
Any account of science which does not explicitly describe it as something we believe in is essentially incomplete and a false pretense. It amounts to a claim that science is essentially different from and superior to all human beliefs that are not scientific statements – and this is untrue.[12]
As an engineer, I doubt the scientific usefulness of the Fact of Evolution. As a Christian, I think the basic principles of the Fact of Evolution are inconsistent with basic Christian doctrine. For example, a 1950 encyclical of Pope Pius XII describes the conflict between Catholic theology and standard claims associated with the Fact of Evolution:
For the faithful cannot embrace that opinion which maintains that either after Adam there existed on this earth true men who did not take their origin through natural generation from him as from the first parent of all, or that Adam represents a certain number of first parents.[13]
There is no doubt the National Academy of Sciences (NAS) promotes Theistic Evolution as a religious alternative that is consistent with the Fact of Evolution.[14] However, the Bible clearly teaches that death came into the world through the sin of Adam and Eve.[15] The concept of the fall of man through Original Sin is inconsistent with a group of ape-like creatures slowly evolving into a group of the first human beings.[16]
In various places throughout this book, I challenge the dogma of scientific naturalism – i.e., the a priori assumption that a supernatural God is unable or unwilling to interact with the natural world. If one concedes that a supernatural God may have designed the natural world (as the NAS does), any opinions about Gods interaction with it are metaphysical rather than scientific.
My goal in challenging the Fact of Evolution is not to drag religious dogma into science, but to encourage science to focus on its empirical roots. In both modern physics and modern biology, scientists have taken to promoting their speculative metaphysical opinions with the authority of scientific facts. The uncertainty of metaphysical opinions is far different than the certainty of empirical evidence. Mixing the two is not good science.

Why Does The Title End With A Question Mark?
The title of this book has a question mark at the end to emphasize a fundamental question – i.e., is Evolution a Fact?

Why Italicize the Fact of Evolution?
The Fact of Evolution is italicized throughout this book to emphasize the fundamental question suggested by the title – i.e. is Evolution a Fact?

Why Does This Book Use So Many Quotations?
Consider the saying, “standing on the shoulders of giants.”[17] This saying implies that much of the knowledge we possess comes from other people – i.e., it is not self-derived. The most accurate way to acknowledge that others have contributed to the knowledge we possess is to quote them.
The Apostle Paul has stated, “What do you have that you did not receive?”[18] If you consider the knowledge you possess, this is true for almost all of it. Much of what each of us knows has been learned from reading what others have written and listening to what others have said.
If you seek to evaluate the reliability of the knowledge you possess, it is necessary to evaluate the integrity of the sources you learned it from. For example, the Apostle Paul based much of his New Testament writing on a source he considered infinitely reliable – The Old Testament Scriptures.
The logical reasoning I used in this book is based upon the style of reasoning practiced by the Apostle Paul – frame an argument by quoting reliable sources. In Paul’s case, he quoted the Old Testament Scriptures as a reliable source. Some of the major sources that I have chosen to quote as a reference for reliable information are listed below.
The quotes I have selected are meant to encourage readers to consider where their knowledge comes from and how reliable it is. All of us are guilty of thinking we know things for sure, even when such certainty is unjustified. The combination of sources I quote illustrate that the Fact of Evolution is not as certain as many claim it to be.
Human knowledge is a tangled web that is not easily traced back to an original source. Thus, my quoting a particular source is not intended to imply that I came to learn a particular piece of information through this specific source only. Nor does it imply that a particular piece of information originated with this source.

Four Categories of Quotes
Each field of science is a highly technical subject. Nobody is an expert in all of these fields. In order to understand the huge mosaic of the Fact of Evolution, everybody must rely on the work done by many different experts.
In order to provide a thorough analysis of the so-called Fact of Evolution, this book includes many short quotations from a large number of experts in a wide variety of technical fields. These quotes fall into four basic categories:
  • Category 1: Uncontroversial Scientific Facts
  • Category 2: Scientific Speculation from Physics, Geology, and Biology
  • Category 3: Arguments for the Fact of Evolution
  • Category 4: Arguments against the Fact of Evolution
In this book, I tie together the words of experts from all four categories of quotes to analyze what is commonly called the Fact of Evolution. My goal is to create a mosaic that is as accurate as possible because it uses pieces directly attributable to experts.
Although I am not an expert in any field directly related to Evolution, I do have a lot of expertise in creating huge technical mosaics. In my technical career, I have designed many pieces of computer logic that tied together millions of little pieces (transistors and gates) to paint complex mosaics.

My Quoting Practices
This is a summary of my typical quoting practices:
  • I identify the author and/or the source for quoted material. Detailed source information for each quote is provided in the footnotes.
  • The first time I identify an author in a Chapter, I use both the first and last name. In additional references, I use only the last name.
  • In referring to authors, I have dropped the formality of titles. However, nearly all the quoted scientists have PhD degrees, and it would be proper to refer to most of these authors as Doctor or Professor.
  • I distinguish quoted material from my own words by placing larger quotes in a slightly indented paragraph with a slightly smaller font. I use quotation marks around short in-line quotes.
  • I keep any emphasis used in the original source (i.e., italics, bold-font, and underlining).
  • I don’t add extra emphasis to quoted passages.
  • I delete hyperlinks and footnote numbers from quoted material.
  • I use an ellipsis (…) anytime quoted material is skipped.
  • If a quote starts in the middle of a sentence, I begin the quote with an ellipsis.
  • If a quote spans multiple paragraphs of the original text, I use an ellipsis to indicate that one or more paragraphs are being skipped.
  • I add brackets “[]” to delineate any additional text I have added for clarification. For example, I use bracketed text to summarize deleted context or clarify the meaning of technical words.
Return to List of Topics

Summary of Major Sources
The following is a brief summary of some of the major sources I have chosen to quote. I have grouped these sources into a number of basic categories.
Technical Information:
  • I reference a set of university-level textbooks for information on Biochemistry, Molecular Biology, and Genetics. The versions that I reference are available from the National Center for Biotechnology Information (NCBI) website.
  • I reference a set of articles from a number of scientific journals for information on a wide variety of scientific topics (i.e., Science, Nature, New Scientist, and other more specialized publications).
General Promotion of the Fact of Evolution:
  • I reference Science and Creationism: A View from the National Academy of Sciences to demonstrate the promotion of the Fact of Evolution by the mainstream scientific community.
  • I reference a set of books by the renowned Evolutionist Richard Dawkins as a representative source of scientific arguments for the Fact of Evolution.
  • I reference a set of articles posted on the Talk Origins website as an example of typical responses offered in response to criticism of the Fact of Evolution.
The Metaphysical Aspect of Modern Physics:
  • I quote passages from a set of books by Physicists Stephen Hawking, David Deutsch, David Lindley, and Paul Davies to illustrate the metaphysical speculation that has become common in modern physics.
  • I reference a Time Magazine article on String Theory by Michael Lemonic as a typical example of the rampant speculation that is common in modern physics.
The Naturalistic Origin of Life:
  • I reference a set of books and articles by Biochemist Robert Shapiro and the Physicist’s Fred Hoyle and Paul Davies to illustrate the uncertainty surrounding scientific theories for the naturalistic origin of life.
  • I reference an article by Creationist John Baumgardner to illustrate the vast improbability associated with the random formation of vital cellular proteins.
  • I reference an article posted on the Talk Origins website as an example of a typical response by Evolutionists to the claims of Creationists like Baumgardner.
A Discussion of the Fossil Evidence for Evolution:
  • I reference articles by Paleontologists Stephen Jay Gould and Niles Eldredge to illustrate that the fossil record contains very little evidence supporting the Evolutionary transition between different species.
A Discussion of Various Genetic Conclusions
  • I reference Jonathan Marks What it Means to be 98% Chimpanzee to illustrate that genetic conclusions are far from infallible.
Challenges to the Fact of Evolution made by advocates for Intelligent Design:
  • I reference a set of books by Michael Behe, Michael Denton, and Phillip Johnson as a representative source of the Intelligent Design movement.
  • I reference a set of articles posted on Discovery Institute and the Access Research Network (ARN) websites as a representative source for Intelligent Design.
Challenges to the Fact of Evolution made by advocates for Biblical Creation:
  • I reference a variety of books by these leading Creationists: Jonathan Sarfati, Henry and John Morris, Duane Gish, Gary Parker, Lee Strobel, and Luther Patterson.
  • I reference a variety of articles posted on the websites of Answers in Genesis, Creations Ministries International, and the Institute for Creation Research.
The above list is far from exhaustive. I quote many other sources that are not included in this list. The details for each source I use are documented in “Notes and References” section, located at the end of each chapter.

Footnote Formats
The details for each source I use are documented in “Notes and References” section, located at the end of each chapter. The format for my footnotes is based on the Chicago-Turabian style for footnotes, with some minor alterations.[19] A summary of my footnote format is given here:
For Books:
<Author-List>, <Book-Title>, (Location: Publisher, Date), <Page>.
For Scientific Journals:
<Author-List>, <Article-Title>, <Source-Title>, < Date>, <Page>, <Web-URL>.
For Newspapers, Magazines, or Journals:
<Author-List>, <Article-Title>, <Source-Title>, < Date>, <Page>, <Web-URL>.
For Web Pages:
<Author-List>, <Article-Title>, <Website-Name>, < Date>, <Web-URL>.
Where:
  • Each author on the <Author-List> is identified by “First-Name, Middle-Initial, Last-Name.” For books, I try to list all authors in the footnotes, rather than using the “et al.” abbreviation (et al. means “and others”). For journal articles, I use the et al. abbreviation for three or more authors.
  • The <Book-Title> is italicized. I include the subtitle if I think it is necessary to identify the book.
  • The <Article-Title> is listed in quotes.
  • The <Source-Title> is italicized.
  • Journals with pages number restarted each issue typically include a field of the form “Volume (Issue-Number):<Page-Range>.”
  • Journals with pages number consecutively throughout the year/volume may include a field of the form “Volume (Year) (Issue-Number):<Page-Range>” or Volume (Issue-Number):<Page-Range>, Year.
  • The <Location> indicates the “City and State” of publication (using two digit state abbreviations).[20] Several major cities (i.e. New York or Boston) do not have the state abbreviation.
  • The <Date> for articles is listed as: <Day Month Year>. If an article is undated, I skip this field. Unless otherwise noted, all web pages were accessible in 2010.
  • The <Page> number is prefixed by the abbreviations “p. or pp.” For PDF files, I use the original page number if it is present. Otherwise, I use the PDF page.
  • I list details for all footnotes rather than using the “ibid.” abbreviation.
Acknowledgments
Endnotes are contained in the following section. The following shorthand notation connects the numbered endnotes to permission statements:
            N(x, y, z, …) indicates endnotes numbered ‘x’, ‘y’, ‘z’.
I gratefully acknowledge permission to reproduce quotes from the following copyrighted material:
N(15): Used with permission from Answers in Genesis – www.answersingenesis.org.
N(15): Used with permission of Creation Ministries International – www.creation.com.
N(18): Scripture taken from the HOLY BIBLE, NEW INTERNATIONAL VERSION®. Copyright © 1973, 1978, 1984 by International Bible Society. Used by permission of Zondervan. All rights reserved.

Notes and References
[1].   Richard Dawkins, The Selfish Gene, 30th annv. ed. (New York: Oxford University Press, 2006), p. 1.

[2].   Richard Dawkins, The Blind Watchmaker, 2006 Edition (New York: W.W. Norton, 2006), pp. 363-405; Richard Dawkins, The Blind Watchmaker (New York: W.W. Norton, 1986), pp. 255-284 from Chapter 10 “The one true tree of life.”

[3].   Richard Dawkins, The Blind Watchmaker, 2006 Edition (New York: W.W. Norton, 2006), p. 393; Richard Dawkins, The Blind Watchmaker (New York: W.W. Norton, 1986), p. 275 from Chapter 10 “The one true tree of life.”

[4].   “Biography – Emilio Segrè,” NobelPrize.Org, http://nobelprize.org/nobel_prizes/physics/laureates/1959/segre-bio.html.

[5].   Richard Rhodes, The Making of the Atomic Bomb (New York: Simon and Schuster, 1986), pp. 8, 282.

[6].   “Biography – Ernest Rutherford,” NobelPrize.Org, http://nobelprize.org/nobel_prizes/chemistry/laureates/1908/rutherford-bio.html.

[7].   “People and Discoveries – Ernest Rutherford,” PBS, 1998, http://www.pbs.org/wgbh/aso/databank/entries/bpruth.html.

[8].   Richard Rhodes, The Making of the Atomic Bomb (New York: Simon and Schuster, 1986), p. 45. Because he was a physicist, Rutherford found his noble prize in Chemistry amusing. I believe it is proper to view Chemistry as the branch of Physics that deals with atomic level reactions.

[9].   Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell 92(3):291-4, 6 February 1998, p. 293, as referenced from Science Direct, http://www.sciencedirect.com/science/article/B6WSN-419K592-1/2/fc6ab6ca1e175d970b76c6a10ad6e81a.

[10]. Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter, Molecular Biology of the Cell, 4th ed. (New York: Garland Science, 2002), Chapter 2, “Cell Chemistry and Biosynthesis,” http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=chemistry,cell&rid=mboc4.chapter.163.

[11].See http://en.wikipedia.org/wiki/Michael_Polanyi for background information.

[12]. Richard Rhodes, The Making of the Atomic Bomb (New York: Simon and Schuster, 1986), p. 33.

[13]. “His Holiness Pope Pius XII: Encyclical Letter Concerning Some False Opinions Which Threaten to Undermine the Foundations of Catholic Doctrine,” (Par. 37), 12 August 1950, New Advent, http://www.newadvent.org/library/docs_pi12hg.htm.

[14]. Science and Creationism: A View from the National Academy of Sciences, 2nd ed. (Washington, DC: National Academies Press, 1999), p. 7, http://www.nap.edu/openbook.php?record_id=6024&page=7.

[15]. Bodie Hodge, “Biblically, Could Death Have Existed before Sin?” 2 March 2010, http://www.answersingenesis.org/articles/2010/03/02/satan-the-fall-good-evil-could-death-exist-before-sin; Jonathan Sarfati, The Fall: a cosmic catastrophe,” Journal of Creation 19(3):60–64, December 2005, http://creation.com/the-fall-a-cosmic-catastrophe.

[16]. “The Catholic Encyclopedia – Original Sin,” New Advent, http://www.newadvent.org/cathen/11312a.htm.

[18]. 1 Corinthians 4:7 (NIV) – For who makes you different from anyone else? What do you have that you did not receive? And if you did receive it, why do you boast as though you did not?. See BibleGateway.com: http://www.biblegateway.com/passage/?search=1%20Corinthians%204:7&version=NIV.

[19]. “Turabian and Chicago Style Citations,” University of California Berkeley Library, http://www.lib.berkeley.edu/instruct/guides/chicago-turabianstyle.pdf.

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