Intelligent Design, Creationism, and a panda with a sore thumb

Dear Discovery Institute,

Today we will be discussing Dean Kenyon and whether or not Intelligent Design is linked to Creation Science. It is perhaps best to let Kenyon's own words express his viewpoint, so let's let his own words speak for him.

Dean Kenyon is a prominent defender of Creation science. In fact,Answers in Genesis lists him in a listing of Creation Scientists (see list http://www.answersingenesis.org/home/area/bios/default.asp), and he was a witness in the Edwards v. Aquillard evolution-creation case in favor of Creation Science(see link for trial transcript with Kenyon)(http://www.talkorigins.org/faqs/edwards-v-aguillard/kenyon.html ). Let's consider parts of his affidavit:

" It is my opinion, although not in the area of my expertise, that creation-science is as nonreligious as evolution."

This shows that Kenyon accepts Creation Science as scientifically valid. Thus, it calls into question the validity of Pandas...ie could Of Pandas and People be a Creationist text in disguise? Let's see another quote from the above link:

"Creation-science means origin through abrupt appearance in complex form, and includes biological creation, biochemical creation (or chemical creation), and cosmic creation. Evolution-science is equivalent to evolution. Evolution is generally understood by scientists (although some would disagree) to include biological evolution (or organic evolution) from simple life to all plants and animals, biochemical evolution (or chemical evolution or prebiotic evolution of the first life), and cosmic evolution (including stellar evolution) (of the universe). Creation-science does not include as essential parts the concepts of catastrophism, a world-wide flood, a recent inception of the earth or life, from nothingness (ex nihilo), the concept of kinds, or any concepts from Genesis or other religious texts. The subject of origins is a part of evolution, and the origin of the first life and tre-origin of the universe are generally regarded by the scientific community as part of evolution."

This almost sounds like an early discussion of Intelligent Design. Perhaps that is because it is. In "Of Pandas and People", Kenyon and Davis state the following:

"Intelligent Design means that various forms of life began abruptly through an abrupt agency, with their distinctive features already intact--fish with fins and scales, birds with feathers, beaks, and wings, etc." (Kenyon and Davis 1989)

Intelligent Design appears to be the same thing as Creation Science according to Kenyon. Would the Discovery Institute support such a text? If yes, then it would be evidence that the Discovery Institute accepts Intelligent Design as Creation Science. Here, we see Stephen Meyer, a major player at the Discovery Institute, actually writing a "note to teachers" to be published within the textbook supplement ( http://www.discovery.org/scripts/viewDB/index.php?command=view&id=1671 ). Shows that at least some at Discovery Institute at one point at least accepted the validity of the textbook, and thus Creation Science as a whole. Is it possible that the book itself never was a Creationist textbook supplement? No. In 1986, this exact textbook was published as "Creation and Biology". The only differences between the 2 books are the name and the fact that Creation science is changed to intelligent design in the 1989 edition. Telling. So the Discovery Institute (or at least some of its higher-ups) support an initially Creationist textbook supplement.

Time for another statement by Kenyon (from the trial transcript linked):

"The creationist scientific conclusion is that empirical data currently in hand demand the inference that the first living organisms were created. This view of the origin of life is based on a detailed analysis of laboratory information from molecular biology, biochemistry, organic chemistry, the simulation experiments on chemical evolution, as well as relevant aspects of physics, geology, astrophysics, probability and information theory."

Again, sounds exactly like Intelligent Design theory. There seems to be some sort of pattern here. Let's read some more from the trial transcript:

"At the heart of the molecular activity of all living cells is the genetic coding and protein-synthesizing machinery which stores and translates biologic information. This information is contained in the specific linear sequences of the subunits of DNA, RNA and proteins. At least 20 different proteins are required for the replication of DNA. At least another 50 proteins are needed to transcribe and translate the information stored in the DNA molecules into the amino acid sequences of proteins (J. Fox 1978; Sheeler and Bianchi 1980). Among these proteins are the aminoacylsynthetases, the enzymes that link the various amino acids to their respective transfer RNA molecules. In the absence of even one of these enzymes, protein synthesis does not take place. The genetic code is actually read by the aminoacylsynthetases since they match an amino acid with its own transfer-RNA molecule. If we go back into the past to the first time the protein-synthesizing machinery functioned, we are faced with the problem of the origin of the necessary aminoacylsynthetases. Where did the proteins come from before the protein-synthesizing system originated? One can postulate that the necessary proteins formed abiotically in the primitive ocean, but there is virtually no experimental evidence for such a postulate. "

Here we have Behe's Irreducible Complexity concept, proposed as part of Creation Science. But Intelligent Design isn't the same thing as Creation Science. Or is it? What can one do to explain these extremely close similarities without accepting the two "sciences" as one in the same? Perhaps ignore the evidence and paper trail? Let's look at one final quote from the trial transcript:

"These scientific considerations form the core of biochemical creation, and show that it is as scientific as chemical evolution, and in fact is preferable in scientific plausibility to chemical evolution. These are weighty issues of fact. Evidence often taken to support a naturalistic chemical origin of life, actually, upon close analysis, points in another direction, namely, toward the conclusion that the first life was created. The data of molecular biology, especially the details of the genetic-coding and protein-synthesizing systems, lend further powerful support to this view. Probability arguments applied to the problem of the origin of genetic information also confirm the creationist view of origins. Laboratory data and theoretic arguments concerning the origin of the first life lead one to doubt the evolution of subsequent forms of life. The fossil record and other lines of evidence confirm this suspicion. In short, when all the available evidence is carefully assessed in toto, the evolutionary story of origins appears significantly less probable than the creationist view."

Attacks on naturalistic explanations for life? Sounds like...Wedge Strategy. Probability attacks? Brings to mind the work of William Dembski. Sounds like Intelligent Design really does have a lot in common with Creation Science after all! What would be thoroughly damning for Discovery Institute's claim that Intelligent Design is not science would be to have a Creation Scientist, such as Kenyon, as a member. And surprisingly enough, Dean Kenyon is indeed a fellow of the Discovery Institute! http://www.discovery.org/scripts/viewDB/index.php?command=view&id=89&isFellow=true

Dear Discovery Institute, if you hope to uphold any scientific validity, you have a lot of explaining to do. It seems as if Intelligent Design is closer to Creation Science than you claim to accept. Perhaps we are not getting the whole story from you.



Davis, P. and Kenyon, D. "Of Pandas and People: The Central Question of Biological Origins". Haughton Publishing Company. Dallas. 1989

Edwards Vs Aguillard trial transcript links:

http://www.law.cornell.edu/supct/html/historics/USSC_CR_0482_0578_ZD.html
http://www.talkorigins.org/faqs/edwards-v-aguillard/kenyon.html (Kenyon's affidavit)
http://supreme.justia.com/us/482/578/case.html

The Wedge Document...so what?

Dear Discovery Institute,

Now it is time to face one of our biggest issues, namely, the Wedge Document itself. First, lets see the document itself. It is visible at http://www.discovery.org/scripts/viewDB/filesDB-download.php?id=349 , but I will include text of the Wedge Document on this blog as well:

"CENTER FOR THE RENEWAL OF SCIENCE & CULTURE


INTRODUCTION

The proposition that human beings are created in the image of God is one of the bedrock principles on which Western civilization was built. Its influence can be detected in most, if not all, of the West's greatest achievements, including representative democracy, human rights, free enterprise, and progress in the arts and sciences.


Yet a little over a century ago, this cardinal idea came under wholesale attack by intellectuals drawing on the discoveries of modern science. Debunking the traditional conceptions of both God and man, thinkers such as Charles Darwin, Karl Marx, and Sigmund Freud portrayed humans not as moral and spiritual beings, but as animals or machines who inhabited a universe ruled by purely impersonal forces and whose behavior and very thoughts were dictated by the unbending forces of biology, chemistry, and environment. This materialistic conception of reality eventually infected virtually every area of our culture, from politics and economics to literature and art


The cultural consequences of this triumph of materialism were devastating. Materialists denied the existence of objective moral standards, claiming that environment dictates our behavior and beliefs. Such moral relativism was uncritically adopted by much of the social sciences, and it still undergirds much of modern economics, political science, psychology and sociology.


Materialists also undermined personal responsibility by asserting that human thoughts and behaviors are dictated by our biology and environment. The results can be seen in modern approaches to criminal justice, product liability, and welfare. In the materialist scheme of things, everyone is a victim and no one can be held accountable for his or her actions.


Finally, materialism spawned a virulent strain of utopianism. Thinking they could engineer the perfect society through the application of scientific knowledge, materialist reformers advocated coercive government programs that falsely promised to create heaven on earth.


Discovery Institute's Center for the Renewal of Science and Culture seeks nothing less than the overthrow of materialism and its cultural legacies. Bringing together leading scholars from the natural sciences and those from the humanities and social sciences, the Center explores how new developments in biology, physics and cognitive science raise serious doubts about scientific materialism and have re-opened the case for a broadly theistic understanding of nature. The Center awards fellowships for original research, holds conferences, and briefs policymakers about the opportunities for life after materialism.


The Center is directed by Discovery Senior Fellow Dr. Stephen Meyer. An Associate Professor of Philosophy at Whitworth College, Dr. Meyer holds a Ph.D. in the History and Philosophy of Science from Cambridge University. He formerly worked as a geophysicist for the Atlantic Richfield Company.


THE WEDGE STRATEGY


Phase I.


* Scientific Research, Writing & Publicity


Phase II.


* Publicity & Opinion-making


Phase III.


* Cultural Confrontation & Renewal


THE WEDGE PROJECTS


Phase I. Scientific Research, Writing & Publication


* Individual Research Fellowship Program

* Paleontology Research program (Dr. Paul Chien et al.)

* Molecular Biology Research Program (Dr. Douglas Axe et al.)


Phase II. Publicity & Opinion-making


* Book Publicity

* Opinion-Maker Conferences

* Apologetics Seminars

* Teacher Training Program

* Op-ed Fellow

* PBS (or other TV) Co-production

* Publicity Materials / Publications


Phase III. Cultural Confrontation & Renewal


* Academic and Scientific Challenge Conferences

* Potential Legal Action for Teacher Training

* Research Fellowship Program: shift to social sciences and humanities


FIVE YEAR STRATEGIC PLAN SUMMARY


The social consequences of materialism have been devastating. As symptoms, those consequences are certainly worth treating. However, we are convinced that in order to defeat materialism, we must cut it off at its source. That source is scientific materialism. This is precisely our strategy. If we view the predominant materialistic science as a giant tree, our strategy is intended to function as a "wedge" that, while relatively small, can split the trunk when applied at its weakest points. The very beginning of this strategy, the "thin edge of the wedge," was Phillip ]ohnson's critique of Darwinism begun in 1991 in Darwinism on Trial, and continued in Reason in the Balance and Defeatng Darwinism by Opening Minds. Michael Behe's highly successful Darwin's Black Box followed Johnson's work. We are building on this momentum, broadening the wedge with a positive scientific alternative to materialistic scientific theories, which has come to be called the theory of intelligent design (ID). Design theory promises to reverse the stifling dominance of the materialist worldview, and to replace it with a science consonant with Christian and theistic convictions.


The Wedge strategy can be divided into three distinct but interdependent phases, which are roughly but not strictly chronological. We believe that, with adequate support, we can accomplish many of the objectives of Phases I and II in the next five years (1999-2003), and begin Phase III (See "Goals/ Five Year Objectives/Activities").


Phase I: Research, Writing and Publication


Phase II: Publicity and Opinion-making


Phase III: Cultural Confrontation and Renewal


Phase I is the essential component of everything that comes afterward. Without solid scholarship, research and argument, the project would be just another attempt to indoctrinate instead of persuade. A lesson we have learned from the history of science is that it is unnecessary to outnumber the opposing establishment. Scientific revolutions are usually staged by an initially small and relatively young group of scientists who are not blinded by the prevailing prejudices and who are able to do creative work at the pressure points, that is, on those critical issues upon which whole systems of thought hinge. So, in Phase I we are supporting vital witting and research at the sites most likely to crack the materialist edifice.


Phase II. The pnmary purpose of Phase II is to prepare the popular reception of our ideas. The best and truest research can languish unread and unused unless it is properly publicized. For this reason we seek to cultivate and convince influential individuals in pnnt and broadcast media, as well as think tank leaders, scientists and academics, congressional staff, talk show hosts, college and seminary presidents and faculty, future talent and potential academic allies. Because of his long tenure in politics, journalism and public policy, Discovery President Bruce Chapman brings to the project rare knowledge and acquaintance of key op-ed writers, journalists, and political leaders. This combination of scientific and scholarly expertise and media and political connections makes the Wedge unique, and also prevents it from being "merely academic." Other activities include production of a PBS documentary on intelligent design and its implications, and popular op-ed publishing. Alongside a focus on influential opinion-makers, we also seek to build up a popular base of support among our natural constituency, namely, Chnstians. We will do this primarily through apologetics seminars. We intend these to encourage and equip believers with new scientific evidence's that support the faith, as well as to "popularize" our ideas in the broader culture.


Phase III. Once our research and writing have had time to mature, and the public prepared for the reception of design theory, we will move toward direct confrontation with the advocates of materialist science through challenge conferences in significant academic settings. We will also pursue possible legal assistance in response to resistance to the integration of design theory into public school science curricula. The attention, publicity, and influence of design theory should draw scientific materialists into open debate with design theorists, and we will be ready. With an added emphasis to the social sciences and humanities, we will begin to address the specific social consequences of materialism and the Darwinist theory that supports it in the sciences.


GOALS


Governing Goals


* To defeat scientific materialism and its destructive moral, cultural and political legacies.

* To replace materialistic explanations with the theistic understanding that nature and hurnan beings are created by God.


Five Year Goals


* To see intelligent design theory as an accepted alternative in the sciences and scientific research being done from the perspective of design theory.

* To see the beginning of the influence of design theory in spheres other than natural science.

* To see major new debates in education, life issues, legal and personal responsibility pushed to the front of the national agenda.


Twenty Year Goals


* To see intelligent design theory as the dominant perspective in science.

* To see design theory application in specific fields, including molecular biology, biochemistry, paleontology, physics and cosmology in the natural sciences, psychology, ethics, politics, theology and philosophy in the humanities; to see its innuence in the fine arts.

* To see design theory permeate our religious, cultural, moral and political life.


FIVE YEAR OBJECTIVES


1. A major public debate between design theorists and Darwinists (by 2003)


2. Thirty published books on design and its cultural implications (sex, gender issues, medicine, law, and religion)


3. One hundred scientific, academic and technical articles by our fellows


4. Significant coverage in national media:


* Cover story on major news magazine such as Time or Newsweek

* PBS show such as Nova treating design theory fairly

* Regular press coverage on developments in design theory

* Favorable op-ed pieces and columns on the design movement by 3rd party media


5. Spiritual & cultural renewal:

* Mainline renewal movements begin to appropriate insights from design theory, and to repudiate theologies influenced by materialism

* Major Christian denomination(s) defend(s) traditional doctrine of creation & repudiate(s)

* Darwinism Seminaries increasingly recognize & repudiate naturalistic presuppositions

* Positive uptake in public opinion polls on issues such as sexuality, abortion and belief in God


6. Ten states begin to rectify ideological imbalance in their science curricula & include design theory


7. Scientific achievements:


* An active design movement in Israel, the UK and other influential countries outside the US

* Ten CRSC Fellows teaching at major universities

* Two universities where design theory has become the dominant view

* Design becomes a key concept in the social sciences Legal reform movements base legislative proposals on design theory


ACTVITIES


(1) Research Fellowship Program (for writing and publishing)

(2) Front line research funding at the "pressure points" (e.g., Daul Chien's Chengjiang Cambrian Fossil Find in paleontology, and Doug Axe's research laboratory in molecular biology)


(3) Teacher training


(4) Academic Conferences


(5) Opinion-maker Events & Conferences


(6) Alliance-building, recruitment of future scientists and leaders, and strategic partnerships with think tanks, social advocacy groups, educational organizations and institutions, churches, religious groups, foundations and media outlets


(7) Apologetics seminars and public speaking


(8) Op-ed and popular writing


(9) Documentaries and other media productions


(10) Academic debates


(11) Fund Raising and Development


(12) General Administrative support


THE WEDGE STRATEGY PROGRESS SUMMARY


Books


William Dembski and Paul Nelson, two CRSC Fellows, will very soon have books published by major secular university publishers, Cambridge University Press and The University of Chicago Press, respectively. (One critiques Darwinian materialism; the other offers a powerful altenative.)


Nelson's book, On Common Descent, is the seventeenth book in the prestigious University of Chicago "Evolutionary Monographs" series and the first to critique neo-Dacwinism. Dembski's book, The Design Inference, was back-ordered in June, two months prior to its release date.


These books follow hard on the heals of Michael Behe's Darwin's Black Box (The Free Press) which is now in paperback after nine print runs in hard cover. So far it has been translated into six foreign languages. The success of his book has led to other secular publishers such as McGraw Hill requesting future titles from us. This is a breakthrough.


InterVarsity will publish our large anthology, Mere Creation (based upon the Mere Creation conference) this fall, and Zondervan is publishing Maker of Heaven and Earth: Three Views of the Creation-Evolution Contoversy, edited by fellows John Mark Reynolds and J.P. Moreland.


McGraw Hill solicited an expedited proposal from Meyer, Dembski and Nelson on their book Uncommmon Descent. Finally, Discovery Fellow Ed Larson has won the Pulitzer Prize for Summer for the Gods, his retelling of the Scopes Trial, and InterVarsity has just published his co-authored attack on assisted suicide, A Different Death.


Academic Articles


Our fellows recently have been featured or published articles in major sciendfic and academic journals in The Proceedings to the National Academy of Sciences, Nature, The Scientist, The American Biology Teacher, Biochemical and Biophysical Research Communications, Biochemirtry, Philosophy and Biology, Faith & Philosophy, American Philosophical Quarterly, Rhetoric & Public Affairs, Analysis, Book & Culture, Ethics & Medicine, Zygon, Perspectives on Science and the Christian Faith, Relgious Studies, Christian Scholars' Review, The Southern Journal ofPhilosophy, and the Journal of Psychalogy and Theology. Many more such articles are now in press or awaiting review at major secular journals as a result of our first round of research fellowships. Our own journal, Origins & Design, continues to feature scholarly contribudons from CRSC Fellows and other scientists.


Television and Radio Appearances


During 1997 our fellows appeared on numerous radio programs (both Christian and secular) and five nationally televised programs, TechnoPolitics, Hardball with Chris Matthews, Inside the Law, Freedom Speaks, and Firing Line. The special edition of TechnoPolitics that we produced with PBS in November elicited such an unprecedented audience response that the producer Neil Freeman decided to air a second episode from the "out takes." His enthusiasm for our intellectual agenda helped stimulate a special edition of William F. Buckley's Firing Line, featuring Phillip Johnson and two of our fellows, Michael Behe and David Berlinski. At Ed Atsinger's invitation, Phil Johnson and Steve Meyer addressed Salem Communications' Talk Show Host conference in Dallas last November. As a result, Phil and Steve have been interviewed several times on Salem talk shows across the country. For example, in ]uly Steve Meyer and Mike Behe were interviewed for two hours on the nationally broadcast radio show ]anet Parshall's America. Canadian Public Radio (CBC) recently featured Steve Meyer on their Tapestry program. The episode, "God & the Scientists," has aired all across Canada. And in April, William Craig debated Oxford atheist Peter Atkins in Atlanta before a large audience (moderated by William F. Buckley), which was broadcast live via satellite link, local radio, and intenet "webcast."


Newspaper and Magazine Articles


The Firing Line debate generated positive press coverage for our movement in, of all places, The New York Times, as well as a column by Bill Buckley. In addition, our fellows have published recent articles & op-eds in both the secular and Christian press, including, for example, The Wall Street Journal, The New York Times, The Washington Times, National Review, Commentary, Touchstone, The Detroit News, The Boston Review, The Seattle Post-lntelligenter, Christianity Toady, Cosmic Pursuits and World. An op-ed piece by Jonathan Wells and Steve Meyer is awaiting publication in the Washington Post. Their article criticizes the National Academy of Science book Teaching about Evolution for its selective and ideological presentation of scientific evidence. Similar articles are in the works."

What does the Discovery Institute say about all this? They attempt to explain away the document as nothing more than a modest fundraising proposal. (see link) However, note that they do not attempt to debunk the validity of the document, and indeed admit to its authenticity. Note also that "Wedge Strategy" has been incorporated into the work of many ID theorists (for example, Jonathan Wells). The paper trail that has been pointed to throughout these blogs show that the Wedge Strategy is an attempt to redefine the definition of science itself. The Discovery Institute admits this fact as well, and complain that science is controlled by "Scientific materialists". However, the fact is that science cannot deal with that which can't be touched or percieved, and therefore by nature the supernatural is not part of science.

In "The Wedge Document, So What?" (see link), the Discovery Institute argues that they are not trying to force a theocracy. However, that is besides the point. The question is whether or not they are attempting to push religion into science classrooms. Although the Discovery Institute maintains that the Designer is not named (ie no religion is favored), lets look at a quote from the Wedge Document:


"Alongside a focus on influential opinion-makers, we also seek to build up a popular base of support among our natural constituency, namely, Chnstians. We will do this primarily through apologetics seminars. We intend these to encourage and equip believers with new scientific evidence's that support the faith, as well as to "popularize" our ideas in the broader culture. "

This statement shows the fact that they are in fact (apparently) attempting to use Intelligent Design to support Christianity. Not a theocracy, but it is a practice that has been declared unconstitutional (if the Discovery Institute hopes to one day put Intelligent Design into the classroom). This action would violate the seperation of church and state clause in the Constitution, and similar attempts to do this have been repeatedly shot down by the Supreme Court.

Let's consider another short quote for more damning evidence:

"Governing Goals


* To defeat scientific materialism and its destructive moral, cultural and political legacies.

* To replace materialistic explanations with the theistic understanding that nature and hurnan beings are created by God. "

Let's look at Discovery Institute's comment on a similar statement from the Wedge Document (taken from linked article):

"Discovery Institute's Center...wants to reverse the stifling dominance of the materialist worldview, and to replace it with a science consonant with Christian and theistic convictions. [from Wedge Document]

This passage instead was referring to our conviction that sceince, rather than supporting a materialistic philosophy, is at least consistent with theistic belief, including Christian belief. In fact, some of our fellows actually go further than this. They think that new developments in science may actually support a theistic worldview or have "theistic implications," even though they do not think that science can "prove" the existence of God or specific religious doctrines"

Again, telling. This shows that the Discovery Institute does, indeed, aim to redefine science to include the supernatural. Under the definition of science required to incorporate Intelligent Design, astrology would also be considered a science. Also please note the Discovery Institute quote that ends with "even though they do not think that science can 'prove' the existence of God" (above). If you can't prove a Designer exists, then Intelligent Design necessarily fails the test of science, even if science were redefined to include the supernatural. As shown, Intelligent Design is not science. Besides, even if the definition of science were changed so that Intelligent Design could be considered science, it would fail the burden of proof. I have shown this before by showing evolutionary pathways for structures that the ID movement claims to be "irreducibly complex", and the Discovery Institute shows us that by admitting that you cannot prove the existence of "God" (the "Creator"). Game over.

Is there a lawyer in the house?

Dear Discovery Institute,

Today we will be looking at one of the star witnesses for the Intelligent Design movement, namely lawyer Phillip E. Johnson. With the publication of "Darwin on Trial" in 1991, Johnson instantly became a celebrity to those that would argue against evolutionary theory. Let's look at some of his works.

First, is Johnson's work consistent with the Discovery Institute's Wedge Strategy? Let's let his own words speak for him. The following is from his article "Evolution as Dogma: The Establishment of Naturalism":

"There are no scientific points in favor of creation and there never will be any as long as naturalists control the definition of science, because creationist explanations by definition violate the fundamental commitment of science to naturalism" (Johnson 2006 p. 32).

Johnson here precisely explains why Creationism is scientifically untenable. But Intelligent Design isn't creationism...is it? Johnson seems to think so:

"All persons who affirm that "God creates" are in an important sense creationists, even if they believe that the Genesis story is a myth and that God created gradually through evolution over billions of years" (Johnson 2006 p.28).

Johnson considers anyone who accepts the presence of a Creator, for scientific purposes especially or otherwise, a Creationist. And Johnson's entire attempt within the article cited is to overthrow "Scientific Naturalism" and replace it with a Theistic mindset, which aligns beautifully with the Wedge Strategy. Johnson's statement in "Darwin on Trial" thoroughly reveals his mindset:

"Darwinist evolution is an imaginative story about who we are and where we came from, which is to say it is a creation myth" (Johnson 1993 p. 133)

Telling. Can Phillip Johnson really be ignoring all evidence in favor of evolution? Not all of it. He mainly ignores the fossil record, which we will return to later. First, lets look at one of the evidences in favor of evolution that Johnson accepts:

"The most famous piece of evidence for Darwinsism is a study of an English peppered-moth population consisting of both dark- and light-colored moths. When industrial smoke darkened the trees that were the moths' habitat, the percentage of dark moths increased, because of their relative advantage in hiding from predators. When the air pollution was reduced, the trees became lighter and more light moths survived. Both colors were present throughout, and so no new characteristics emerged, but the percentage of dark moths in the population went up and down as chagning conditions affected their relative ability to survive and produce offspring." (Johnson 2006 p. 24)

This is at least an admission that microevolution can occur. To see how microevolution and macroevolution can occur together in a population, refer to my discussion of ceratopsians in my fossil record blog.

What does Johnson have to say about fossils? Let's consider "Darwin on Trial":

[in reference to Darwinian Natural Selection] "There was a way to test the theoryby fossil evidence, however, if Darwin and his followers had wanted a test. Darwin was emphatic that the number of transitional intermediates must have been imense, even "inconceivable". Perhapse evidence of their existence was missing because in 1859 only a small part of the world's fossil beds had been searched, and because the explorers had not known what to look for. Once paneontologists accepted Darwinism as a working hypothesis, however, and explored many new fossil beds in an effort to confirm the theory, this situation ought to change. In time the fossil record could be expected to look very different, and very much more Darwinian.

The test would not be fair to the skeptics, however, unless it was also possible for the theory to fail. Imagine, for example, that belief in Darwin's theory were to sweep through the scientific world with such irresistible power that it very quickly beecame an orthodoxy. Suppose that the tide was so irrestible that even the most prestigious of scientists---Harvard's Louis Agassiz, for example---became an instant has-been for failing to join the movement. Suppose that aplentologists became so committed to the new way of thinking that fossi lstudies were published onliy hf they supported the theory, and were discarded as failures if they showed an absense of evolutionary change. As we shall see, that is what happened. Darwinism apparently passed the fossil test, but only because it was not allowed to fail." (Johnson 1993 p. 48)

First, evidence of stasis (periods of no evolutionary change) is published, as with Eldredge and Gould's work on Punctuated Equilibrium. Second, there are ways for evolution to fail the fossil record test. For example, show me a panda in the Permian, and you have disproven evolution. Third, evolution has passed the test. There are huge volumes of known transitional fossils (see my fossil record blog for just a few examples) available to paleontologists. It is when authors such as Johnson, who have no background in paleontology, brush past known fossil evidence in an attempt to support their ideas that there are problems with grasping the fact that the fossil record does indeed support evolutionary theory. See, for example, the following quote:

"The story to be tested is that a fish species developed the ability to climb out of the water and move on land, while evolving the peculiar reproductive system of amphibians and other amphibian features more or less concurrently. No specific fossil fish species has been identified as an amphibian ancestor, but there is an extinct order of fish known as the rhipidistians which Darwinists frequently describe as an "ancestral group" The rhipidistians have skeletal features resembling those of early amphibians, including bones that look like they could have evolved into legs. But according to Barbara J. Stahl's comprehensive textbook, "Vertebrate History", "None of the known fishes is thought to be directly ancestral to the earliest land vertebrates. Most of them lived after the first amphibians appeared, and those that came before show no evidence od feveloping the stout limbs and ribs othat characterized the primitive tetrapods"

In 1938, a coelacanth, an ancient fish thought to have been extinct for about seventy million years, was caught by fishermen in the Indian Ocean. Many paleontologists considered the ceolacanth to be closely related to the rhipidistians, and thus a living specimen was expected to shine light on the soft body parts of the immediate ancestors of amphibians. When the modern coelacanth was dissected, however, its internal organs showed no signs of being preadapted for a land environment and gave no indication of how it might be possible for a fish to become an amphibian. The experience suggests that a rhipidistian fish might be equally disappointing to Darwinists if its soft body parts could be examined." (Johnson 1993 p.76-77).

Johnson seems to ignore transitional fossils that prove a fish ancestry for amphibians. While Tiktaalik wasn't known in 1993, Icthyostega was! Here are the transitional forms Johnson wants (see following link)
http://www.nature.com/nature/journal/v440/n7085/abs/nature04639.html

Kind of kills Johnson's argument. Perhaps his lack of understanding of the fossil record has clouded his judgement, or maybe he has a prior commitment to the Wedge Strategy. Either way, he aims to change the rules of science to incorporate the supernatural, a strategy I've discussed many times before. Johnson is a lawyer, and therefore good at making the most of small amounts of evidence. However, as shown by the above quote on fossils, Johnaon himself does exactly what he accuses "Darwinists" of doing, namely, warping the evidence to suit his views.


Works Cited:
Johnson, P. "Darwin on Trial". Intervarsity Press, Downers Grove. 1993
Johnson, P. "Evolution as Dogma: The Establishment of Naturalism". presented in Dembski's "Uncommon Dissent: Intellectuals who Find Darwinism Unconvincing". ISI Books, Washington. 2006. p. 23-40

Reducing the Irreducibly Complex

Dear Discovery Institute,

Today I have been thinking about the work of Michael Behe of Lehigh University. Behe's concept of irreducible complexity appears sufficient to support Design theory, until it is critically considered at least. Today we will investigate exactly why the concept of irreducible complexity is flawed, and requires more support before it is accepted as a valid scientific concept.

First, we will critically consider some of "Darwin's Black Box", considered by many to be the seminal work (along with Philip Johnson's "Darwin On Trial") on Intelligent Design. First, Behe seems to confuse the definition of evolution (the diversification of life) with that of abiogenesis (the origin of life). Lets hear it in his own words:

evolution means a process whereby life arose from non-living matter and subsequently developed entirely by natural means. (Behe 2006 p.xi).

While the natural cause explanation clause is a major part of the definition of science (Behe has that statement correct),he is obviously confused about the very definition of Darwinian evolution, the theory which his entire book attempts to debunk. That fact raises major credibility questions. However, lets give Behe the benefit of the doubt for now. Let's consider his irreducibly complex structures.

Behe's poster child for irreducible complexity is the bacterial flagellum. If this stucture can be shown to be "evolvable", then this raises major questions about the validity of irreducible complexity. NJ Matzke has done just that with his article "Evolution in (Brownian) space: a model for the origin of the bacterial flagellum". While I suggest reading his entire piece (cited and linked below), here is the abstract of Matzke's piece, which shows exactly why the words "irreducibly complex" fail to describe the bacterial flagellum:


"The bacterial flagellum is a complex molecular system with multiple components required for functional motility. Such systems are sometimes proposed as puzzles for evolutionary theory on the assumption that selection would have no function to act on until all components are in place. Previous work (Thornhill and Ussery, 2000, A classification of possible routes of Darwinian evolution. J Theor Biol. 203 (2), 111-116) has outlined the general pathways by which Darwinian mechanisms can produce multi-component systems. However, published attempts to explain flagellar origins suffer from vagueness and are inconsistent with recent discoveries and the constraints imposed by Brownian motion. A new model is proposed based on two major arguments. First, analysis of dispersal at low Reynolds numbers indicates that even very crude motility can be beneficial for large bacteria. Second, homologies between flagellar and nonflagellar proteins suggest ancestral systems with functions other than motility. The model consists of six major stages: export apparatus, secretion system, adhesion system, pilus, undirected motility, and taxis-enabled motility. The selectability of each stage is documented using analogies with present-day systems. Conclusions include: (1) There is a strong possibility, previously unrecognized, of further homologies between the type III export apparatus and F1F0-ATP synthetase. (2) Much of the flagellum’s complexity evolved after crude motility was in place, via internal gene duplications and subfunctionalization. (3) Only one major system-level change of function, and four minor shifts of function, need be invoked to explain the origin of the flagellum; this involves five subsystem-level cooption events. (4) The transition between each stage is bridgeable by the evolution of a single new binding site, coupling two pre-existing subsystems, followed by coevolutionary optimization of components. Therefore, like the eye contemplated by Darwin, careful analysis shows that there are no major obstacles to gradual evolution of the flagellum." (Matzke 2006).

There it is, right in Matzke's article. An allegedly "irreducibly complex" structure shown to be evolvable. Science once again trumps the Intelligent Design movement. Bad arguments in favor of supposed design do not qualify as science, especially when the "designer" in question, as well as the presence of "design" itself, remains inherently untestable.

But let's play Behe's game. The blood clotting mechanism in blood is Behe's other major "irreducible complex" structure. And as with the bacterial flagellum, it is shown to be evolvable. For example, check out the work of Kenneth Miller (a good rebuttal to Behe's blood clotting argument is available on the following site, which will not be cited because it is linked within the text: http://www.millerandlevine.com/km/evol/DI/Clotting.html )

On the site linked, Kenneth Miller does an absolutely beautiful job of refuting Behe's research on "irreducible complexity". It's sad that so many people have accepted Behe's concept of irreducible complexity when he has not even been able to provide an "irreducibly complex" structure that has withstood scrutiny. All of his examples have been shown to be evolvable. The argument from personal incredulity is not a valid argument to use to disprove Darwinian evolution. Strong evidence in favor of your viewpoint is provided. Behe has failed to provide this.

In conclusion, while scientists are still working to understand the exact nature of abiogenesis (the origin of life), that fact does not make Darwinian evolution false. Darwinian evolution does not attempt to explain how life arose; it only explains how it has subsequentially diversified. Those people claiming that evolutionary theory is sufficient to explain the origin of life are grasping at straws. Darwinian Natural Selection, by nature, requires reproduction to occur, which, in turn, requires life to be in existance. Darwin's black box? Not quite.







Works Cited:
Behe, MJ. "Darwin's Black Box: The Biochemical Challenge to Evolution". Free Press, NY. 2006. 10th Anniversary edition.
Matzke, NJ. "Evolution in (Brownian) space: a model for the origin of the bacterial flagellum". originally published 2003, updated 2006. http://www.talkdesign.org/faqs/flagellum.html

The strange case of Dr. Discovery and Mr. Hide

Dear Discovery Institute,

How are you today? I am doing quite well, thank you for asking. You may perhaps appreciate me noting some discrepancies I've noted in books connected to your Institute, however. We'll start with William Dembski, one of the most well-known individuals connected with your institution.

In Dembski 1999, the author states the following (printed on Brockman 2006 p. 3and checked for validity in Dembski 1999):

"Any view of the sciences that leaves Christ out of the picture must be seen as fundamentally deficient...The conceptual soundness of a scientific theory cannot be maintained apart from Christ"

As shown by our previous discussions on the Wedge Document, this statement correlates perfectly with the Discovery Institute's ideals. However, apparently in order to sell Intelligent Design to the general public, Dembski states (Dembski 2004, and quoted in Brockman 2006 p. 3):

"Intelligent Design is not an evangelic Christian thing, or a generally Christian thing or even a generally theistic thing...Intelligent design is an emerging scientific research program. Design theorists attempt to demonstrate its merits fair and square in the scientific world---without appealing to religious authority"

Both statements have been made by the same author. Which is correct? Perhaps we should examine "Of Pandas and People", an old ID textbook, for answers? Lets start with a quote from the book defining Intelligent Design:

"Evolutionists object to the view of intelligent design because it does not give a natural cause explanation of how the various forms of life started in the first place. Intelligent design means that various forms of life began abruptly through an intelligent agency, with their distinctive features already intact---fish with fins and scales, birds with feathers, beaks, and wings, etc." (Davis and Kenyon 1989 p. 99-100)

Is it just me, or does this definition of Intelligent Design reek of Creationist theory? Perhaps this resemblance is because the book was originally a Creationist book titled "Creation Biology" (Shermer 2006 p. 102-3, Humes 2007 p. 285). It is also telling that Stephen Meyer, of the Discovery Institute, has affiliated himself with the book by publishing a "Note to teachers" within its pages, especially in the 1993 edition (www.discovery.org/scripts/viewDB/indexphp?commonand=view&ID=1671
see for web posting of this note).

In today's discussion, as inspired by the conflicting claims of William Dembski, we've seen evidence of "Pandas"' Creationist ancestry, conflicting claims by William Dembski (both supporting and suppressing Discovery Institute's Wedge Strategy), and even the support of "Pandas" by some of Discovery Institute's own. My dear friends at the Discovery Institute, for the sake of ID's survival as a science, please step away from the Wedge Strategy and stop contradicting yourselves so that it will one day be possible to give credibility to your researchers.



Works Cited:

Brockman, J. "Intelligent Thought: Science Versus the Intelligent Design Movement". 2006
Davis, P. and Kenyon, D. "Of Pandas and People: The Central Question of Biological Origins". 1989
Dembski, W. "Intelligent Design: the Bridge Between Science & Theology. 1999
Dembski, W. "The Design Revolution". 2004
Humes, E. "Monkey Girl: Evolution, Education, Religion, and the Battle for America's Soul". 2007
Shermer, M. "Why Darwin Matters: The Case Against Intelligent Design". 2006

Climate Change

Dear Discovery Institute,

How are you today? I am doing quite well, thank you for asking. However, I have been reading "The Politically Incorrect Guide to Science", written by Tom Bethell, and given great reviews from some of your own scientists (David Berlinski, Jonathan Wells, Phillip E. Johnson, and George Gilder). I just finished the section on Global Warming, and noticed some problems in the text.

On page 2, Bethell gives decent explanation of the Greenhouse Effect:

"Environmentalists believe that the twentieth-century warming was caused by human activity, primarily the burning of fossil fuels. Their combustion producese carbon dioxide--- one of several "greenhouse gases." Methane is another. The argument is that their release into the atmosphere wraps the Earth in an invisible shroud. It makes the escape of heat into outer space slightly miore difficult than its initial absorption by the Earth (from sunlight). This is the Greenhouse Effect. And the result is that the Earth warms." (Bethell 2005 p. 2)

However, Bethell continues to claim that humans are having no effect on global climate change. This is in stark contrast to the majority of the scientific community. While Bethell implies that humans have had NO effect on global climate change, the fact is that, by burning fossil fuels, destroying forests, etc., humans have at least served to accelerate it. This fact is accepted by most mainstream scientists. Indeed, many geologists who have worked on the subject have stated that the current warming trend is much faster than at other points in history. This is not based on the work of Al Gore, but rather on living, breathing (and CO2 producing) geologists. Factors responsible for global climate change in the past include volcanic outgassing and a large amount of CO2 and Methane producing organisms. One of the main explanations for the Snowball Earth occurance in early geologic history is the presence of large amounts of Oxygen in the atmosphere, produced by stromatolites early in Earth's history, that served to alter Earth's climate.

Where do we stand today? Humanity has destroyed much of the Earth's forested area, especially within the Amazon region of South America. We are producing large amounts of CO2, large enough to at least partially alter Earth's climate. This trend has been illustrated with the Hockey Stick graph published by Mann (more about this later). The Arctic and Antarctic ice caps are melting much faster than scientists have predicted, which is evidence of increased global warming, effected by human activity. Methane is a much more potent greenhouse gas than Carbon Dioxide, and there are huge amoutns of it trapped in the Arctic permafrost (Jacquot 2008). Heating of the ice that traps this methane will result in its release, and thus, subesquent faster warming. Whether humans are affecting it or not, the hockey stick model of global warming, in general, is accurate. We are witnessing something unique in geologic history with regards to the rate of warming on Earth.

Bethell's work claims that the Hockey Stick model is flawed, However, this mindset goes against the mainstream scientific community. Bethell ignores both computer models projecting massive increases in global temperature in the near future ( http://www.sciencedaily.com/releases/2003/02/030217120135.htm ), and scientific data arrived at independently of Mann's Hockey-Stick model that corraborate his model (http://www.globalwarmingart.com/wiki/Image:2000_Year_Temperature_Comparison_png). While Bethell also claims that humans are not affecting Global Warming because "the atmosphere is not increasing in temperature". This statement is addressed in the following article ( http://archives.cnn.com/2000/NATURE/01/13/global.warming/ ). Bethell's anti-global-warming arguments, thus far, fail to hold water.

Bethell is also mistaken in arguing that the urban heat island idea somehow nullifies the claim that humans are causing global warming. He implies that the temperature increases we see are due to skewed data as a result of temperature measurements being taken in cities, and as a result of the increased heat in cities. Bethell ignores the fact that temperatures are increasing over oceans and rural areas as well. This would appear to partially nullify his arguments. The IPCC strikes the killing blow to this line of argument by Bethell: "Urban heat island effects are real but local, and have a negligible influence (less than 0.006°C per decade over land and zero over the oceans) on these values". (IPCC)


Bethell also argues that Global Warming is beneficial;

"The Warmer period [in reference to the Medieval Warm Period], accompanied by a flowering of prosperity, knowledge, and art in Europe, seems to have been wholly beneficial. Agricultural yields increased along with the temperature. Marshes and swamps---today they would be called wetlands---dried up, removing the breeding grounds of mosquitoes that spread malaria. Infant mortality fell; the population grew." (Bethell 2005, p. 7-8).

This statement may be true for a small amount of global warming. However, we are talking about a much greater amount of temperature increase today. With the melting of Antartica's ice caps, as well as much of the ice in the Arctic (which are over land), more water will be added to the ocean, which will cause an increase in sea level. The fact is, this phenomena, whether affected by humans or not, is something that we need to be prepared for. And the majority of the scientific community agrees that humans have played a part in the increase of greenhouse gasses, and, thus, in the increase of global temperature as a whole. It's no longer a question as to whether or not we've had an impact, but rather a question as to how much of an impact we've had.

Before my works cited, here's a good site for those interested in global warming to check out. I'm not an expert on the topic myself, but the author of the blog knows his stuff.

http://chriscolose.wordpress.com/

Works Cited:
Bethell, T. "The Politically Incorrect Guide to Science". Regenry, Washington DC. 2005.
Jacquot, J. "Come On, Bubble, Light my Fire". Discover magazine, February 2008. p. 14

Jonathan Wells and the Wedge Strategy

At the end of the Washington Monument rally in September, 1976, I was admitted to the second entering class at Unification Theological Seminary. During the next two years, I took a long prayer walk every morning. I asked God what He wanted me to do with my life, and the answer came not only through my prayers, but also through Father’s many alks to us, and through my studies. Father encouraged us to set our sights high and accomplish great things

He also spoke out against the evils in the world; among them, he frequently criticized Darwin’s theory that living things originated without God’s purposeful, creative activity. My studies included modern theologians who took Darwinism for granted and thus saw no room for God’s involvement in nature or history; in the process, they reinterpreted the fall, the incarnation, and even God as products of human imagination

Father’s [Reverend Moon of Unification church], my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When father chose me (along with about a dozen other seminary graduates) to enter a PhD program in 1978, I welcomed the opportunity to prepare myself for battle. ---Jonathan Wells

The above words, from Jonathan Wells’ piece titled "Darwinism: Why I Went for a Second PhD" (also covered in Dawkins article in Brockman 2006 p. 92-3, and Shermer 2006 p.109-111 and Humes 2007 p. 165) show an inherent bias in Wells’ work. Wells, a member of the Unification Church, is apparently attempting (like many at the Discovery Institute) to destroy Darwinism as a result of his chosen worldview. While most of the Discovery Institute is only trying to change the definition of science, Wells appears to be attacking Darwinian evolution as a result of a mission given by his religious leader, ie he seems to be on a mission from God, at least in his mind. While a religious background is no reason to question a scientist’s work, it is when the scientific work done by the individual is only being done in an attempt to push a religious goal that the individual’s research should be called into question, if it is indeed flawed. We will consider Wells’ research in this blog.

Before addressing the scientific validity of Wells’ claims (I do a relatively quick explanation of Icons of Evolution in an attempt to keep this blog of a bearable length for the reader, and also due to the fact that this book has been rebutted by many authors already), it is worth noting that he is yet another key member of the Discovery Institute. Therefore, one would expect the validity of his claims to be telling with regards to the nature of Discovery Institute’s scientific claims as a whole. Let’s compare the above passage to the Discovery Institute’s Wedge Document:

The proposition that human beings are created in the image of God is one of the bedrock principles on which Western Civilization was built. Its influence can be detected in most, if not all, of the West’s greatest achievements, including representative democracy, human rights, free enterprise, and progrerss in the arts and sciences.

Yet a little over a century ago, this cardinal idea came under wholesale attack by intellectuals drawing on the discoveries of modern science. Debunking the traditional conceptions of both God and man, thinkers such as Charles Darwin, Karl Marx, and Sigmund Freud portrayed humans not as moral and spiritual beings, but as animals or machines who inhabited a universe ruled by purely impersonal forces and whose behavior and very thoughts were dictated by the unbending forces of biology, chemistry, and environment. This materialistic conception of reality eventually infected every area of our culture, from politics and economics to literature and art…

Discovery Institute’s Center for the Renewal of Science and Culture [now named the Center for Science and Culture] seeks nothing less than the overthrow of materialism and its cultural legacies. Bringing together leading scholars from the natural sciences and those from the humanities and social sciences, the Center explores how new developments in biology, physics, and cognitive science raise serious doubts about scientific materialism and have re-opened the case for a broadly theistic understanding of nature. (taken from the Discovery Institute’s press release "The "Wedge Document": "So What?"")

[another Wedge Document quote, same source]:

The social consequences of materialism have been devastating. As symptoms, those consequences are certainly worth treating. However, we are convinced that in order to defeat materialism, we must cut it off at its source. That cource is scientific materialism. This is precisely our strategy.

As shown by the above quotes, Jonathan Wells’ personal religious convictions and goals fit in perfectly with the Discovery Institute’s plan to undermine scientific materialism, ie. the clause in the definition of science requiring testability of ideas and essentially removing appeals to the supernatural from the realm of science. Many leaders of the Intelligent Design movement are in favor of changing the definition of science to include the supernatural, and this pattern will be illustrated throughout the course of this blog. Now that Wells’ religious convictions and goals have been shown to line up with Discovery Institute’s Wedge strategy, we can critically consider some of Wells’ writings.

Wells’ book Icons of Evolution, Science or Myth?: Why Much of What we Teach About Evolution is Wrong, published in 2000, attempts to undermine the scientific validity of evolutionary theory by attacking ten pieces of evidence for evolution that Wells claims have been debunked, and as a result, somehow undermine the validity of Darwinian evolution.
Wells’ first "Icon" is the Miller-Urey experiment. Wells here explains that there are flaws in the Miler-Urey experiment. While some of the questions he raises may be valid, there are some points worth noting in the defense of evolutionary theory. First, Wells is attacking abiogenesis (the origin of life) rather than Darwinian evolution (the diversification of life) here. Even if the Miller-Urey experiment is eventually proven to be completely worthless to science, its falsification would not in any way serve to falsify Darwinian evolution. Natural selection works only after life has originated; it cannot function until that point because by nature natural selection requires life to be in existence to operate.

Secondly, if all else fails, the Miller-Urey experiment did serve to produce amino acids. Amino acids are some of the major building blocks of life, and the creation of these acids is fundamental to scientifically explaining the origin of life. The next question that one could raise in reference to this experiment is the question of replication. How could the acids replicate? Robert Hazen raises a possibility in his article titled "Life’s Rocky Start" (2001). Perhaps the amino acids utilized mineral facies present upon formation in order to replicate. This would not only provide a framework for the creation of complex protein strings, but would also serve to explain the presence of a large bias in handedness in amino acids.

Wells’ next "Icon" is the Darwinian "tree" of life. Wells attacks this point by using the Cambrian explosion; since diversification apparently occurred rapidly at the Cambrian explosion, it serves to nullify the commonly-held interpretation of evolution, namely, that evolution leads to gradual increases in diversity through nature. Stephen Jay Gould does an outstanding job at explaining the trend Wells is using as evidence "against" evolution in his book Wonderful Life: The Burgess Shale and the Nature of History (Gould 1989 p. 23-52), and I recommend reading this piece to anyone questioning the validity of the fossil record. Also worth noting in reference to the fossil record and the Cambrian explosion is the fact that there are known predecessors to the Burgess organisms in earlier sediments. While these organisms may not be closely related to the Burgess animals (there is a Chinese assemblage from the early Cambrian that preserves some Burgess-type organisms, such as simple chordates. However, the Ediacaran fauna, for example, are not known to be closely related to the Burgess fauna. What is important to note, however, is the extreme bias against soft-body preservation in the fossil record, and thus, how rare early soft-bodied organism fossils are), there are fossils present that show transitional phases leading up to the Burgess organisms in at least a few cases.

Wells’ third "Icon" is homology. However, the tetrapod body form, and derivations of the tetrapod limb, are so obvious to those with a background in the subject that is tough to misunderstand the implications of homology. While convergent evolution can produce similar features, in some cases, extremely similar features, good phylogenic data derived from a combination of features serves to nullify any confusion caused by apparent similarities caused by convergent evolution.

Wells’ next "Icon" is Haekel’s embryo drawings. Wells claims that Haeckel’s embryo drawings are used to indoctrinate biology students into an acceptance of evolution (Haeckel’s embryo drawings are known to be embellished in order to better illustrate the evolutionary evidences shown, and thus show bad scientific research practices which undermine Haeckel’s credibility in this case). However, that assumption is false. See Randy Olson’s recent film Flock of Dodos: the Evolution-Intelligent Design Circus for a short, crisp, yet nice destruction of this claim. While Haeckel’s embryo drawings have been proven to be scientifically inaccurate, the general trend in embryology does show the evidence that Haeckel embellished his embryo drawings with in an attempt to illustrate.

Next, we see Archaeopteryx. Wells essentially claims that Archaeopteryx is not evidence of evolution because Archaeopteryx lived before more-dinosaur-like relatives of Archaeopteryx. See my blog on the fossil record for a discussion of Archaeopteryx as a valid transitional fossil.
Wells next attacks the validity of experiments done on peppered moths that appeared to show that changes in moth color occur in response to pollution levels. Wells claims that photographs in textbooks are staged in order to make them appear viable, and that this disproves the research. The key point is that, while the photographs themselves were staged, they were used to illustrate actual experimental data dealing with the evolution of the moths (Humes 2007 p. 171).
While Humes’ statement (see source) initially appears to be a last-ditch effort to defend evolution, when his entire book is read, it becomes apparent that it is not. See the following statement:

Adaptation of peppered moths has been proved to occur across multiple generations, regardless of the staged illustrations (Humes 2007 p. 174)

Most modern scientists would agree with Humes here. In fact, the website of the National Center for Science Education has an entire page dedicated to rebutting Wells’ work in Icons. For the discussion of peppered moths, see www.natcenscied.org/icons/icon6moths.html. The site rebuts Wells’ other claims within the book as well.

Wells’ next "Icon" is the experimentation done on fruit flies. The important concepts to take out of the fruit fly research deal with genetics. The key point behind these experiments is the fact that they show that certain genetic changes can produce new features (ie extra wings) in organisms. This fact is not questioned by the scientific community because it is scientifically proven; the experiments have been done.

Yet another Wells "Icon" is that of Darwin’s finches. However, these are evidences of microevolution, as conceded by many Design theorists. Design theorists, and even some Young Earth Creationists, do not attempt to refute microevolution as a rule, so this example is not as strong as Wells would expect it to be. The same is true with regards to the moth experiments listed above.

Next, Jonathan Wells discusses evolution in fossil horses. Wells’ major argument against the validity of these fossil horses is the fact that they show evidence as branching as opposed to linear evolution. The initial interpretation of these fossils was that they did show evidences of linear evolution, while that is false. This is perhaps a relict of the way Victorians approached evolutionary theory, in an attempt to find "direction" in evolutionary patterns. Gould again hits home on this "Icon" in Gould 1989. I strongly suggest reading that book to anyone with an interest in evolutionary theory.

Wells’ final "Icon" is that of human evolution. Consult my fossil record blog for a few links on this subject. Talk.Origins also has good sources on both human evolution and evolution as a whole. The evidence in favor of human evolution is so strong that I currently employ only a few references on the subject, allowing those with a background in anthropology to cover that area while I cover the fossil record as a whole and other subjects I am more familiar with. However, consider that one of the most damning evidences against Wells’ research here goes right back to the Wedge Strategy:

Governing Goals:
To defeat scientific materialism and its destructive moral, cultural and political legacies
To replace materialistic explanations with the theistic understanding that nature and human beings are created by God. (Discovery Institute, "The "Wedge Strategy": "So What?"")

This strategy was developed before Wells published his book; the Wedge Document was leaked to the public in 1999, Icons of Evolution was published in 2000. Coincidence?

As shown by the short discussion of Icons of Evolution, Wells here has created a straw-man version of evolutionary theory, a theory in crisis, a theory not supported by the evidence. Later in the book, Wells suggests putting warning stickers on textbooks, and even provides some for readers to cut out themselves and paste in. What Wells does not note is the fact that these warning labels fit perfectly with the Discovery Institute Wedge strategy. By attacking evolutionary theory at the grassroots level, in our nation’s schools/with our nation’s young ones, they will have much greater success in their attempt to undermine scientific materialism, just as the Wedge strategy requires. However, the warning label path has been blocked by courts time and time again. I believe that the lack of compelling evidence as to why evolutionary theory should be challenged in Icons of Evolution betrays the true purpose of the book. If the purpose of the book were to scientifically undermine evolution, it fails miserably because it does not attack the most important evidences in favor of evolutionary theory; rather, it attacks "problems" that are not seen as problematic by any mainstream evolutionary theorist. This betrays the fact that the book was written to push a political/religious motive, not to improve science. Consider the Wedge Document goals already quoted here as well as the next one in reference to classroom policies:

[from the Wedge Document’s 5 Year Goals] To see major new debates in education, life issues, legal and personal responsibility pushed to the front of the national agenda. (Discovery Institute, "The "Wedge Document": "So What?"")

This appears to line up quite nicely with Wells’ textbook stickers and attacks on the teaching of evolutionary theory as presented in Icons of Evolution.

Next, we’ll consider Wells’ The Politically Incorrect Guide to Darwinism and Intelligent Design. Let’s start off with another statement dealing with the Wedge Strategy’s educational goals.

The Discovery Institute defends the right of teachers to discuss ID if they choose to do so, but it opposes requiring ID until it becomes better established in the scientific community (Wells 2006 p. 155).

Apparently we must wait until the Wedge Strategy succeeds in changing the definition of science to include appeals to the supernatural, a situation that will never happen if the scientific community as a whole holds its ground. Currently, the Discovery Institute pushes a "Teach the Controversy" agenda rather than explicitly mentioning ID. Wells, its seems, agrees with this plan:

As Congress was debating the No Child Left Behind Act of 2001, Republican senator Rick Santorum of Pennsylvania proposed a "Sense of the Senate" amendment that subsequently became part of the joint House-Senate Conference Report accompanying the final bill. "The conferees recognize," stated the report, "that a quality science education should prepare students to distinguish the data and testable theories of science from religious or philosophical claims that are made in the name of science. Where topics are taught that may generate controversy (such as biological evolution), the curriculum should help students to understand the full range of scientific views that exist, why such topics may generate controversy, and how scientific discoveries can profoundly affect society"

…Many Darwinists refuse to acknowledge that there are "differing scientific views" on biological evolution…(Here Wells goes on to discuss Eugenie Scott’s statement against anti-evolution arguments, and Stephen Meyer [of Discovery Institute fame] responding to these arguments)...As we have seen in the previous chapters, Darwinism has serious problems with the evidence, and some highly qualified scientists are skeptical of its exaggerated claims. Shouldn’t science students be permitted to learn about them? (Wells 2006 p.145-7)

As shown here, Wells is all in favor of teaching "alternates" to evolution, as well as problems with the theory. This would allow the Wedge Strategy to begin to gain a foothold in the American education system. Also, Wells’ arguments in the "previous chapters" mentioned in the above quote are not nearly as compelling as one would expect to be made by an individual attempting to undermine Darwinism. We will examine some of these arguments in this blog, but first, in accordance with the Wedge Document’s claims in reference to the cultural evils of Darwinian evolution and scientific materialism as a whole, here is a quote pitting Darwin against religion:

Many Darwinists are virulently anti-Christian. Richard Dawkins once said religion "is one of the world’s great evils, comparable to the smallpox virus but harder to eradicate," and Daniel C. Dennett thinks Christianity should be "preserved in cultural zoos". A common sight in American college towns is cars displaying Darwin fish---deliberate mockeries of the traditional symbol of Christianity, with feet underneath and "Darwin" inside. One variant has a Darwin fish raping a Christian fish.

Anti-Christian zealots are often in the forefront of attacks on intelligent design. In 2005, the chairman of the University of Kansas Religious Studies Department, atheist Paul Mirecki, proposed to teach a course titled "Intelligent Design Creationism and Other Mythologies." Mirecki boasted on a web site that "fundies" would see the course as a "slap in their big fat face." He also endorsed a description of Pope John Paul II as "a corpse in a funny hat wearing a dress."

Even disregarding such excesses, it is clear that there is a fundamental conflict here. It is not between religion and science, or even between Christianity and evolution, but between traditional Christianity and Darwinism. Although the latter may allow for the existence of a deity, it is not the God of traditional Christianity, who created human beings in His image. The contradiction couldn’t be sharper, and most attempts to blunt it end up by abandoning traditional Christianity. (Wells 2006 p. 173).

This passage is inherently dishonest. Wells uses the most militantly anti-religious atheist proponents of Darwinian evolution and attempts to paint all proponents in such a light. Even if this is not the intent, Wells only highlights the most militant evolutionary theorists. Dawkins misuses evolutionary theory in an attempt to push an atheistic agenda. Dennett also feels that evolution supports atheism. While they are both extremely intelligent individuals, they are misguided in their attempt to use evolution to push a religious agenda. The moderate proponents of evolution represent what many of us think. There is no inherent conflict between science and religion because they occupy two separate realms; science tells us physically how we exist, and religion deals with the spiritual realm. Science is testable, concrete. Religion is spiritual and mystical. Science must be proven. Religion is based on faith. Evolutionary theorists such as Stephen Jay Gould and Kenneth Miller are perhaps the most well-known advocates of this mindset. Darwinian evolution need not be anti-religion, and it inherently isn’t.

What is also telling about this passage is that Wells fails to mention any of the extreme radicals on the anti-Darwin side. Wells himself has admitted to devoting his life to "destroying Darwinism", so naturally he only picks the most radical evolutionary theorists in attempt to portray evolutionary biology in a bad light. Wells makes the major mistake of claiming that Darwinian evolution is inherently anti-Christianity, when, in reality, it isn’t. The Roman Catholic Church sees no problem with evolutionary theory, although the Church would tend to disagree with such loose cannons as Richard Dawkins and Paul Mirecki (after all, Pope John Paul II does deserve much more respect than to be called "a corpse in a funny hat wearing a dress". I’m not sure if this claim is valid, but it would not surprise me given the nature of some attacks by atheists on religion. These atheists make the same mistake Design theorists do, namely, attempting to include religious implications in a scientific theory. Again, religion is inherently outside the realm of science due to the definition of science. Science cannot prove or disprove the presence of a deity. This is where faith must be applied. ). See for example the following quote, and also Gould 1997:

Religious faith is not the problem here, and I do not wish to state otherwise. What Is problematic is when religion is removed from its proper role. Science and religion are not mutually exclusive (Truth cannot contradict Truth), as they deal with two wholly different realms: religion dealing with how to live our lives in a moral sense, and how to interact with other people to a certain extent; and science dealing with how to live in and interact with a constantly changing world. Religion is a powerful force that can bring out the best in people when exercised in its proper element, and science can be a dangerous tool when taken out of context. The mirror statements also apply, such that religion is also dangerous when taken out of context, and science is a powerful positive force when applied in its proper element. When religious doctrines are forced into a science classroom, no good can come of it. Let us keep religion in the realm of religion, and leave the science classrooms to what they are meant for, the teaching of science. (Bertasso 2006)


Perhaps Wells feels that one must choose between religion and "Darwinism" because he feels a religious calling to destroy Darwinism. However, many in the scientific community would agree with the statement above.

Next, we will compare Wells’ writings with the ID textbook supplement Of Pandas and People. In The Politically Incorrect Guide to Darwinism and Intelligent Design, Wells states that:

Intelligent design is compatible with some aspects of Darwinian evolution. ID does not deny the reality of variation and natural selection. It just denies that those phenomena can accomplish all that Darwinists claim they can accomplish. ID does not maintain that all species were created in their present form: Indeed, some ID advocates have no quarrel with the idea that all living things are descended from a common ancestor (Wells 2006 p.8-9)

This explains the viewpoint of ID theorist Michael Behe. Behe accepts macroevolution, but argues against evolution creating the complex building blocks of life. It appears that his criticisms of Darwinian natural selection are misguided, however. Behe appears to be questioning abiogenesis rather than evolution itself (a distinction present in many of these blogs). Natural selection, by nature, cannot apply to abiogenesis; abiogenesis deals with the origin of life while natural selection deals with the subsequent diversification of forms after life has originated.

On to the question as to whether Pandas agrees with the work of Wells. Consider the following quote:

Evolutionists object to the view of intelligent design because it does not give a natural cause explanation of how the various forms of life started in the first place. Intelligent design means that various forms of life began abruptly through an intelligent agency, with their distinctive features already intact---fish with fins and scales, birds with feathers, beaks, and wings, etc. "(Davis and Kenyon 1989, p.99-100)

Apparently either the ID textbook supplement or Jonathan Wells is mistaken here. While some may claim that the ID movement does not attest to the validity of Pandas, it is worth noting that Stephen C. Meyer approves the book, indeed he even wrote a note to teachers in the 1993 edition. The Discovery Institute appears, overall, to accept the validity of the textbook, as evidenced by the May 1st 1993 "A Note to Teachers" article on the Discovery Institute’s website. Somewhere here, things do not add up. Which publication is correct?

In conjunction with the Discovery Institute’s Wedge Strategy, Wells devotes a section of his Politically Incorrect Guide to railing against the evils of methodological naturalism in the scientific community. This term coincides with the definition of "scientific materialism". This book is apparently one of the Discovery Institute’s attempts to undermine scientific materialism. It certainly lives up to the goals set out by the Wedge Document.

Wells also argues against evidences for microevolution in his book, such as bacterial resistance to antibiotics. This shows a pattern common in Wells’ works. Point out evidences of microevolution in action, point out that they are "only microevolution", and then claim that they serve to not show any evidence for "macroevolution", which is essentially the same as microevolution, except on a larger scale. See for example my ceratopsian evolution discussion present on this webpage (fossil record blog).

Wells also claims that DNA shows evidence of "Design". By nature, this needn’t be taken as an argument against natural selection. Wells seems to have a problem with the origin of DNA, not necessarily mutations that occur after DNA has originated. Again, while natural selection may have some impact on the formation of DNA, the origin of DNA is again going back to the science of abiogenesis, and not evolution. Natural selection essentially fails to operate until we have competition, which occurs long after the first DNA strand was formed. Therefore, natural selection has nothing to do with the initial formation of DNA, only subsequent variation of DNA, which Darwinian natural selection has been shown to be able to explain. Wells also attacks evolutionary theory, using for example the bacterial flagellum, which has already shown to have been able to evolve.

What does Jonathan Wells believe about the fossil record? Let’s see it in his own words:
It turns out that the problem with fossils is not that transitional forms are missing, but that fossil evidence in principle cannot provide evidence for descent with modification (Wells 2006 p. 20).

This statement is so patently false that it requires a blog to answer in full. See my fossil record blog for an explanation as to why this is false. This statement by Wells showcases a massive misunderstanding of the fossil record, and calls into question his credibility to be discussing the subject.

As shown in this blog, Wells’ work has been shown to drastically misinterpret the data in favor of evolutionary theory in an attempt to falsify evolution as a science. This work comes hand-in-hand with an intriguing similarity to Discovery Institute’s Wedge Strategy. While Wells’ claims have across the board been shown to be either wrong or irrelevant, he still continues to be billed as one of the leaders of the Discovery Institute’s attack on Darwinian evolution. Is the best that the Discovery Institute can do with $5 million a year? Objections to Darwinian theory that have been repeatedly shown to be false do not constitute a strong objection to Darwinian evolution. With nearly all arguments made by Design theorists, the mainstream scientific community has been able to prove the Design theorists false. This leads one to ask the question "Is Intelligent Design science?" The answer is no. It is nothing more and nothing less than attempt to undermine the definition of science and return America to a Christian, theistic worldview. But don’t take my word for it…read the Wedge Document and compare it to the work of some Design theorists such as Wells!


Works Cited:
Behe, MJ. Darwin’s Black Box: The Biochemical Challenge to Evolution. Free Press NY, 2006. 10th Anniversary Edition
Bertasso, M. "Evolutionary Theory in an Insecure World". First published November 2006. www.nileseldredge.com/darwin_blogs_037.htm accessed 1/3/08
Brockman, J. Intelligent Thought: Science Versus the Intelligent Design Movement. Vintage Books. NY 2006
Davis, P., and Kenyon, DH. Of Pandas and People: The Central Question of Biological Origins. Haughton Publishing Company, Dallas, 1989.
Discovery Institute. "The "Wedge Document": "So What?"". Available on Discovery Institute’s website www.discovery.org. Just search for "Wedge Document" and it will come up.
Gould, SJ. Wonderful Life: The Burgess Shale and the Nature of History. WW Norton& Company NY. 1989
Gould, SJ. "Nonoverlapping Magisteria". Natural History 106, p.16-22. printed March 1997. Also available at www.stephenjaygould.org/library/gould_noma.html
Hartwig, M., and Meyer, SC. "A Note to Teachers". www.discovery.org/scripts/viewDB/indexphp?command=view&ID=1671 accessed 1/2/08, published 5/1/1993
Hazen, R. "Life’s Rocky Start". Scientific American. Vol. 284 # 14. p. 76-84. Printed April 2001.
Humes, E. Monkey Girl: Evolution, Education, Religion, and the Battle for America’s Soul. HarperCollins NY, 2007. First Edition
National Center for Science Education "Icons of Evolution? Why Much of What Jonathan Wells Writes About Evolution is Wrong." www.natcenscied.org/icons
Also cited www.natcenscied.org/icons/icon6moths.html. Accessed 1/3/08
Olson, R. Flock of Dodos: the Evolution-Intelligent Design Circus. Docuramafilms, 2006. video/DVD
Shermer, M. Why Darwin Matters: the Case Against Intelligent Design. Times Books, NY. 2006
Wells, J. "Darwinism: Why I Went for a Second Ph.D.". www.tparents.org/library/unification/talks/wells/darwin.htm. Accessed 1/2/08
Wells, J. Icons of Evolution, Science or Myth?: Why Much of What we Teach About Evolution is Wrong. Regnery Publishing, Inc, Washington DC, 2000
Wells, J. The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc, Washington DC, 2006

Transitional fossils/fossil record

Introduction

Intelligent design is not science. This fact has never been as clear as it was on December 20th, 2005, in Dover, PA when Judge John E. Jones III declared that Intelligent Design had no place in the science curriculum in the region. In Jones’ words:

"After this searching and careful review of ID [Intelligent Design]
as espoused by its proponents, as elaborated upon in submissions
to the Court, and as scrutinized over a six-week trial, we find that ID
is not science and cannot be adjudged a valid, accepted scientific theory,
as it has failed to publish in peer-reviewed journals, engage in research
and testing, and gain acceptance in the scientific community. ID,
as noted, is grounded in theology, not science." (Brockman 2006 p.252)

The implications of this statement are obvious to anyone with a background in the debate. However, for those individuals unfamiliar with the issue, and also for those individuals desiring to understand exactly why Intelligent Design [ID hereafter] is nothing more than an unintelligently designed challenge to evolutionary theory that clings to Young Earth Creationism [YEC] even when the "Designer" of ID is never identified, an inquiry into the works of the theory’s proponents is required.

That is the intent of this essay; in an attempt to illustrate why ID is a non-scientific idea that is strongly tied to its Creationist heritage, the works of leading ID proponents and also major documents from the ID movement will be considered, and compared to YEC theory. This essay will focus mainly on the ID, YEC, and mainstream science arguments dealing with the fossil record.

Historical background

Ever since Darwin, the fossil record has been cited as one of the best sources of evidence in favor of evolutionary theory. However, many leaders of the YEC movement (Duane Gish for example) point to gaps in the fossil record as "proof" that God created "kinds" of animals that cannot be crossed by evolution; ie. evolution can occur within a "kind", but never between "kinds". What is a "created kind"? You won’t find the answer in many YEC works. However, Of Pandas and People, the textbook that the ID movement has repeatedly attempted to push into classrooms, does indeed offer a definition of a "created kind" within its definition of ID, which, ironically, also nullifies ID’s claim to be a scientific theory:

"Evolutionists object to the view of intelligent design because it does not give a natural cause explanation of how the various forms of life started in the first place. Intelligent design means that various forms of life began abruptly through an intelligent agency, with their distinctive features already intact---fish with fins and scales, birds with feathers, beaks, and wings, etc. "[Davis and Kenyon 1989, p.99-100)

As shown by the quote above, the ID movement essentially gives up all scientific validity within its own textbook by appealing to the supernatural. In fact, during the Dover trial, Michael Behe, one of the leaders of the ID movement, acknowledged the fact that if the rules of science were changed to include ID, by definition astrology would also be considered science (Humes 2007 p. 301).

Also telling with regards to the above quote is the fact that if the term "intelligent design" were changed to "creationism", one would have no problem accepting the quote as being from a YEC publication. Perhaps this is because the book was initially a Creationist textbook initially titled Biology and Creation (Shermer 2006 p. 103). Also worth noting is that the 1989 version of Pandas is the first version of the textbook printed as an ID textbook. The book was printed in 1986 as Biology and Creation.

Anyway, back to the fossil record. The ID movement, in the above passage, appears to claim that evidence of evolution is not to be found in the fossil record. This is a commonly held misunderstanding among ID theorists. While claiming that the fossil record shows no evidence for evolution, they also reveal a major misunderstanding of the way paleontology works.
Other discussions of the fossil record by ID theorists are just as telling. The Design movement, as championed by the Discovery Institute, seems to thoroughly prefer the idea that there are gaps in the fossil record that nullify the fossil record to the idea that most paleontologists hold (the fossil record supports evolution). This is strongly evidenced in the writings of Robert C. Koons in Dembski 2004:

As is well known, the fossil record of the family tree of evolution is so gappy that it consists of a great deal more gap than tree…[Dembski here attests to problems in the invertebrate fossil record]…The missing links that have been found, like the Archaeopteryx or Australopithecus, are better described as mosaics: recombinations of adaptations found in what are assumed to be related families. (Koons in Dembski 2004 p.4)

This blog deals with evolutionary evidences present in vertebrates. The organisms involved are much more well-known to the public than invertebrates are, so it makes sense to consider vertebrates here. Invertebrates will be considered later in these blogs. While Archaeopteryx is called a "mosaic" by Koons, as well as by other Design theorists, it is worth noting that this "mosaic" showcases exactly what one would expect in a transitional form. This idea will be discussed below.

Archaeopteryx

Let us consider the case of Archaeopteryx. While heralded as a perfect transitional form by paleontologists and biologists for more than a century (Thomas Henry Huxley, "Darwin’s Bulldog", used Archaeopteryx and some bird-like dinosaurs such as Compsagnathus to theorize that birds evolved from dinosaurs. This idea was forgotten for decades after his death until it was revived strongly by Bakker and Ostrom in the late 1960’s), the Creationist movement immediately began to call Archaeopteryx "just" a bird, and not a transitional fossil. Indeed, Duane Gish continues with that line of argument even today.

While the classification of Archaeopteryx as "just" a bird is likely partially a product of the Linnaean system (there is no classification for a transitional form between birds and dinosaurs under the Linnaean system, so it is classified as a bird because it is more bird-like than dinosaur-like), it is still used today as an argument against evolution. Jonathan Wells of the Discovery Institute (the main proponent group of ID theory) is militantly against the classification of Archaeopteryx as a transitional form, as shown in his book Icons of Evolution, Science or Myth?: Why Much of What we Teach About Evolution is Wrong. Wells essentially argues that since Archaeopteryx cannot be shown to be an ancestor of modern birds, it does not qualify as a transitional form.

This shows a major misunderstanding of paleontology research, and the classification of a transitional form. Archaeopteryx is a transitional form because it shows both bird-like (feathers, wings, etc) and dinosaurian (teeth, bony tail, etc) features. In fact, until the first feathered specimen of Archaeopteryx was found, the known specimens of Archaeopteryx were instead classified as specimens of the genus Compsagnathus, which was a small bipedal Theropod dinosaur.

However, as conclusive as the evidence in favor of Archaeopteryx being a transitional form is, other ID theorists also misunderstand the basis on which Archaeopteryx is classified as a transitional form. This list includes lawyer Phillip Johnson, who is often credited with beginning the ID movement. While Johnson may be brilliant as a lawyer, he is not qualified to discuss paleontology, as shown by the following passage:

"Archaeopteryx is an impressive mosaic. The question is whether it is proof of a reptile (dinosaur) to bird transition, or whether it is just one of those odd variants, like the contemporary duck-billed platypus, that have features resembling those of another class but are not transitional intermediates in the Darwinian sense. "(Johnson 1993 p. 80)

This passage shows a major misunderstanding as to why Archaeopteryx is considered to be a "transitional intermediate in the Darwinian sense". Archaeopteryx is not considered to show dinosaurian paternity for the avian class merely because it has a few dinosaur-like features. Rather, the fact that the skeleton of Archaeopteryx is similar enough to the Theropod body plan to be mistaken as a small Theropod (Compsagnathus) until feathered specimens were found is why Archaeopteryx is classified as a transitional form. The hips, teeth, claws, shoulders, and skeleton as a whole of Archaeopteryx is essentially dinosaurian. This is why Archaeopteryx is classified as a transitional form, not because of some minor similarities, but rather due to major irrefutable physical similarities between birds and dinosaurs shown in Archaeopteryx. See the National Center for Science Education article cited for an in-depth explanation of Wells’ claims on Archaeopteryx and also the rest of his book.

Dinosaur transitional phases

It is worth noting at this point, while both some ID theorists and also the YEC movement claim that macroevolution is not visible through the fossil record, it is perhaps most visible through some dinosaurian lineages. See for example Ceratopsian dinosaurs. The beautiful thing about the Ceratopsian dinosaurs is the fact that within this group there is present both macroevolution and microevolution, and evidence of both is present. For microevolution, just look at the sacrums of the lineage. It soon becomes obvious that this lineage showcases a trend towards robustness as the Ceratopsians evolve from a bipedal ancestral stock (Psittacosaurus) into a hefty quadruped (Triceratops). The change in habit from biped to quadruped, as well as the appearance of horns through the lineage, seemingly out of nowhere, is proof of macroevolution, and also proof that evolution can indeed "create" information. First, in Protoceratops paleontologists see the appearance of a frill, then in later ceratopsians paleontologists can watch (metaphorically speaking; they use fossils) horns form from regions where no horns were initially present in ancestral forms. Here we have a beautiful example of macroevolution and microevolution working in conjunction in order to form new structures and body plans.

Also worth noting is the fact that not only does Archaeopteryx show us a dinosaurian ancestry for the birds, but also that there are other feathered dinosaurs that show evidence of close relation to birds. These animals include Sinosauropteryx and Caudipteryx, both from China.

Tetrapod/early Amphibian evolution

Other transitional sequences are also present, and often ignored by ID theorists. The most commonly ignored transitional sequence is perhaps the evolution of early amphibians from Crossopterygian fish. With the recent discovery of Tiktaalik rosea, we now have an absolutely beautiful transitional sequence documenting early tetrapod evolution (see for example Shubin p. 82-91 in Brockman 2006). However, a brief survey of some of the major ID works shows yet another misunderstanding of the fossil record in reference to this transitional sequence.
First, let us again consider the 1989 edition of Pandas:

"Evolutionists believe that the first amphibians (the labyrinthodonts[italics in original]) evolved from early fish known as crossopterygians or lobe-fined fish. A very similar lobe-finned fish swims the (sic) Indian Ocean today…[brief reference to figure in book here]…If crossoperygians really did evolve into amphibians, tremendous changes must have taken place. Fins must have been transformed into forelimbs. The skull had to change from two parts to a single, solid piece. The hip bones had to enlarge and become attached to the backbone. As well as changes in the skeleton, not a few changes must have occurred in organs, muscles, and other soft tissues. For example, the air bladder of the fish had to be transformed into the lungs of the amphibian.
Though just a few of the many examples possible, these are enough to show how large the differences between early fish and amphibian really were. How many different transitional species were required to bridge the gap between them? And how many generations of each species must have been involved? Were hundreds or even thousands of species required? We have no way of knowing, but we do know that no such species are found in the fossil record." (Davis and Kenyon 1989 p. 102)

It is worth noting here that even at the time this edition of Pandas was published, there were known transitional fossils bridging the gaps noted here (also please refer to Shubin’s article in Brockman 2006, Icthyostega and tetrapod-like fish were present in the fossil record, and had been discovered. Tiktaalik only filled in yet another gap within that lineage, effectively adding even stronger support to its validity). With the edition of Tiktaalik rosea to this lineage, there is no doubt that we do indeed have a transitional line leading from fish to amphibians and tetrapods as a whole.

Whales

When confronted with the problem of the whale transitional series in The Politically Incorrect Guide to Darwinism and Intelligent Design, Jonathan Wells does accept the presence of the whale transitional lineage. However, he attempts to make their presence irrelevant by essentially claiming that since they did not "give birth to the other" that they do not count, and also by stating the following:

"It turns out that the problem with fossils is not that transitional links are missing, but that the fossil evidence in principle cannot provide evidence for descent with modification" (Wells 2006 p. 20)

However, ask almost any paleontologist and you will find out that the fossil record does, by nature, prove evolutionary theory. This passage by Wells shows a complete and total misunderstanding with regards to the fossil record. For a good discussion of the whale transitional fossils we have, check out the article "Hooking Leviathan by its Past" in Gould 1995.

Humans

The human transitional sequence is perhaps the most hotly debated transitional series known. This is perhaps due to the fact that this exact lineage directly involves our species as a whole. While many ID theorists (and all YEC theorists) deny the existence of human transitional fossils, the evidence is indeed there in favor of evolution for those who look. Since this is not my area of expertise, see for example Ch. 3 (p. 60-89) in Eldredge 1991 for both detailed yet accessible descriptions and also images, and also Tim D White’s article in Brockman 2006. For internet sources, check out the following:

http://www.pandasthumb.org/archives/transitional_fossils/ note that Design advocates will not call themselves creationists and make a distinction between themselves and creation science there.

www.talkorigins.org/indexcc/CC/CC200.html
another decent site. google searches will bring up a whole list of human transitional forms.



Conclusion

A brief foray into the field of vertebrate paleontology shows that the fossil record does indeed support evolutionary theory. While there is no time for more discussion in this blog, the fossil record will serve as an underlying theme of all the blogs presented in this series. As shown, many Design theorists tend to support the idea that there are gaps in the fossil record that somehow serve to disprove evolution. While some ID theorists, like Michael Behe, are open to macroevolution and accept the fossil record for what it is, most seem to misunderstand the nature of the fossil record. This is either due to a lack of expertise or a preconceived notion that for their theory to succeed fossils must be ignored. This works in conjunction with one of the Wedge Document’s major goals, namely, to "Replace materialistic explanations with the theistic understanding that nature and human beings are created by God" (Discovery Institute. "The "Wedge Document": "So What?""). This statement in itself shows why exactly Discovery Institute’s science agenda (and therefore, Intelligent Design as a "science") is flawed. Science does not allow appeals to the supernatural, and the Discovery Institute’s Center for Science and Culture expects science to eventually allow these appeals. However, science will stand its ground, and the fossil record will continue to do what it has for the past 150 years; show strong evidence of evolution itself.

Luckily for Darwin, however, the fossil record does support evolution. And unluckily for the Discover Institute, as shown by history, appeals to the supernatural are a science-stopper, and support the mindset of "God did it, no need to understand why". This is the fatal flaw of the Discovery Institute’s Wedge strategy. Science, by nature, excludes the supernatural, and will continue to do so, even if Discovery Institute plans otherwise. Read the Wedge Document (printed in Humes 2007 p. 356-7, and also the Discovery Institute’s "The "Wedge Document": "So What?"") in order to understand exactly what the "Wedge Strategy" is. It will be discussed throughout these blogs.

Works Cited

Brockman, J. Intelligent Thought: Science Versus the Intelligent Design Movement. Vintage Books. NY 2006. Trial transcript in Appendix, also Neil Shubin article p. 82-91.
Davis, P., and Kenyon, DH. Of Pandas and People: The Central Question of Biological Origins. Haughton Publishing Company, Dallas, 1989. The "Intelligent Design" textbook supplement for biology curriculums
Dembski, W. Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing. ISI Books, Wilmington. 2004 a volume collecting writings of some of the more prominent Design theorists.
Discovery Institute. "The "Wedge Document": "So What?"". Available on www.discovery.org. this article is the Discovery Institute’s attempt to explain away the Wedge Document, and includes text of the actual document.
Eldredge, N., Fossils: The Evolution and Extinction of Species. Harry N. Abrams, Inc., NY, 1991. One of the best general guides to fossils and evolutionary theory ever published in my opinion. Outstanding images of fossils from the American Museum of Natural History accent a beautifully written book.
Gould, SJ. Dinosaur in a Haystack Three Rivers Press, NY, 1995. Article "Hooking Leviathan by its Past" on whale transitional forms present in this work
Humes, E. Monkey Girl: Evolution, Education, Religion, and the Battle for America’s Soul. HarperCollins NY, 2007. First Edition. Discussion of the recent Dover trial.
Johnson, PE. Darwin on Trial. InterVarsity Press, Downers Grove, 1993. One of the books credited with kicking off the Intelligent Design movement.
National Center for Science Education. "Icons of Evolution? Why Much of What Jonathan Wells Writes About Evolution is Wrong". www.natcenscied.org/icons.html
this page explains nicely the errors in reasoning of Well’s book Icons of Evolution.
Shermer, M. Why Darwin Matters: The Case Against Intelligent Design. Times Books, NY, 2006. A stinging rebuttal of Intelligent Design that shows its inherent existence outside the realm of science
Wells, J. The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc, Washington DC, 2006. a guide to intelligent design published by Discovery Institute. Read with caution; the work is massively biased.
Wells, J. Icons of Evolution, Science or Myth?: Why Much of What we Teach About Evolution is Wrong. Regnery Publishing, Inc, Washington DC, 2000. Wells’ first major work attempting to disprove some evidence for evolution presented in classrooms.