General and Special Evidence for Intelligent Design in Biology
The general evidence for intelligent design in biological systems is evidence that can be used to support both unintelligent causation (e.g., Darwinism) and intelligent causation (i.e., intelligent design theory). Thus, the general evidence for intelligent design is the same evidence that evolutionists, particularly Darwinists, use to support theories of unintelligent causation. However, an objective approach shows that Darwinism is only one interpretation of the evidence. As with any evidentiary question in which present day evidence is used to determine a past historical event (as in crime solving), it's the interpretation of the evidence against competing explanatory theories that permits one to converge on a best explanation. In the case of origins science the present day evidence in nature can be viewed in light of alternative explanatory causes. To a priori rule out intelligent causation and mandate only explanations involving unintelligent causes removes the inquiry from the realm of science. Insisting that science can only consider unintelligent causation converts origins science into unchallengeable dogma. Science should be tentative, considering all reasonable causal inferences based on observed material data.
The fact of speciation, that is, that we observe distinct species of plants and animals in nature, is strong evidence of intelligent design.
Darwin attempted to explain how unguided, purposeless processes could create new species. Darwin analogized to intelligent breeding, which involves intelligent selection among variant offspring to produce differences in future generations of a given animal or plant line. Darwin theorized that if intelligent agents could produce variations in physical characteristics in pigeons, for example, perhaps nature, via natural selection, over time could produce all the variety of species we observe.
Modern science calls Darwin's theory into question for at least two reasons. First, regardless of whether "selection" is unintelligent (by nature alone) or intelligent (by breeding), the selection process can only be effective once there is a favorable variation in the base species from which to "select". What this means is that regardless the efficacy of "natural selection", there is nothing to select until some beneficial feature or characteristic is created in the first place. Current scientific data shows that variations in the genome, i.e., random mutations, are rarely, if ever, beneficial in an organism. Most mutations are either neutral in effect, or harmful. Therefore, the idea that "selection" can be made in an unguided, unintelligent manner among largely harmful mutations to result in long term beneficial speciation is not supported by the evidence. Second, even when intelligent selection is utilized, such as in the breeding of dogs, cows, or fruit flies, the evidence shows that regardless the extent of selection, the respective species remain intact. No amount of intelligent selection, as in breeding, has ever produced any new, beneficial features, like new organs, new eyes, new wings, etc.
Therefore, the scientific question with respect to speciation is this: What evidence is there that unintelligent processes can create new, beneficial variations, such as genetic mutations, that can then be selected to propogate to future generations?
Darwin's 19th century theory was bolstered with the advent of modern genetics, microbiology, and other science disciplines, from which neo-Darwinism was born. Neo-Darwinism holds that the variation necessary for creating new features and benefits arises due primarily to the random mutations that occur in the genome of a living organism.
But can the random variation produced by chance mutations in the genome produce any beneficial change, and especially enough long-term, directional change in major features and body plans to create a new species? To date there is no evidence to suggest that such unintelligent variation can cause speciation. Just as intelligent selection can produce only different versions of an existing species, it appears from the evidence that unintelligent variation (i.e., random mutations) is likewise limited to change only within the bounds of a species. Even the intelligent manipulation of existing species such as the fruit fly has produced only more and different fruit flies.
There is simply no evidence to suggest that the random action of chance mutations can create beneficial changes from which natural selection can "select" sufficient to produce new body plans evident in even closely related species. In fact, random mutations are almost universally neutral in effect, but when of a magnitude to affect the organism are likewise almost universally detrimental to the health of the organism. In most cases such mutations result in what are called birth defects.
For this reason, the fact of different species, each being bounded by a genomic limit with respect to change, is evidence for intelligent design. An intelligent cause can create with a purpose. An intelligent cause can be forward looking to produce changes that are beneficial. An intelligent cause can create information-bearing genetic instructions, where unintelligent causes can simply shuffle genetic information in random ways, usually harming the organism.
Fossils offer both positive evidence for design, and negative evidence for Darwinian gradualism.
Positive Evidence for Design
Fossils exhibit features that appear designed, much like living organisms. The scientific question presented is, "is the design exhibited by fossils the result of unintelligent causes, or intelligent causes?"
The assumption of those steeped only in Darwinism, of course, is that fossils are solely the result of unintelligent causes, specifically Darwin's "descent with modification" in which each fossil is the unintelligently modified version of an ancestor in a gradual chain of cause and effect occurrences. The unintelligent operations of physics and chemistry alone are believed to have produced the specified complexity observed in fossils, and in ever-increasing specification and complexity over time.
The true cause of fossils can only be determined by testing known causal agents to see if they can produce the specified complexity evident in the design of fossils. Unintelligent causes such as the random variation of mutations or the deterministic law of natural selection have not been shown to be capable of producing specified complexity, much less new and more specified complexity. Specifically, natural selection (which can only select what is already created) has no creative power. The only things that can be "selected" are things already in existence. Therefore, in Darwinism any "creating" of new DNA information coding for new body designs as evidenced in fossils must be produced by unintelligent deterministic physics. Each random mutation of the genome of an existing body plan must be directionally beneficial in producing a new, beneficial body plan. But, as discussed above, no unintelligent natural process has been shown to produce new, beneficial morphology, or new, beneficial information content in the genome, or new species. Therefore, the ability of Darwinian processes to produce the specified complexity evident in fossils is called into serious question.
Negative Evidence of Darwinian Gradualism
Charles Darwin himself recognized in his book On the Origin of Species that the fossil record does not support his theory. Beginning in Chapter 6, entitled, "Difficulties on Theory", Darwin himself noted that among the "crowd of difficulties" with Darwinism, the foremost difficulty is that the fossil record does not support his theory of gradual descent with modification. Darwin himself asked: "why, if species have descended from other species by fine gradations, do we not everywhere see innumerable transitional forms?"
There are no unambiguous transitional forms, and few purported forms in a fossil record that should be teeming with millions upon millions of such creatures. Such knowledge is common among educated scientists and paleontologists, but virtually unknown among members of the public, including students. In fact, evolutionist Stephen J. Gould described the rarity of transitional fossils as the "'trade secret' of paleontologists" in his book, The Panda's Thumb (see further, below).
Note the surprising conventional wisdom that fossils are not only evidence, but proof of "evolution". Rather than being proof for Darwinism, however, an honest assessment of the evidence shows fossils to be stronger evidence of true design than unguided, purposeless evolution. Consider, for example, the preeminent Darwinist Ernst Mayr, known as "the Darwin of the 20th century." In his 2001 book entitled What Evolution Is Mayr discusses the evidence for evolution in Chapter 2, in a section headed "What evidence does the evolutionist have?" Predictably, he first discusses the fossil evidence. Specifically, on page 14 of the paperback Basic Books edition, he states:
Given the fact of evolution, one would expect the fossils to document a gradual steady change from ancestral forms to the descendants. But this is not what the paleontologist finds. 
Mayr goes on to make clear that the fossil record does not support Darwinian gradualism (as noted above, a fact Darwin himself recognized, but believed future fossil finds would fill in the gaps). Then Mayr asks a revealingly honest question:
This raises a puzzling question: Why does the fossil record fail to reflect the gradual change one would expect from evolution?
The fact is that the fossil evidence does not support Darwinian gradualism. It never has and likely never will. Evolutionists such as Stephen Jay Gould were forced to propose theories such as "punctuated equilibrium" to "save the phenomena," i.e., explain the evidence in a coherent fashion." Stephen J. Gould refers to the rarity of transitional fossils as the "'trade secret' of paleontologists". Gould states:
"The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils. Yet Darwin was so wedded to gradualism that he wagered his entire theory on a denial of this literal record: ". . . He who rejects these views on the nature of the geological record, will rightly reject my whole theory." 
Comparative anatomy of many living beings shows similarity in morphology, i.e., in body parts and structure. Sometimes referred to as an organism's Bauplan, which is a German word coined to refer to the "building plan" or "blueprint" of the organism, common or "homologous" morphological features such as skeletal frameworks point to a common intelligent designer. Just as modern architects use blueprints having common building features and engineers use common parts in different models of machines, it is not surprising that an intelligent designer of living beings would use common structure across various "models" of animals. In fact, it would be surprising if that were not the case.
Without a "rule" that prohibits a scientific inference of intelligent causation, common homology among various organisms would be plainly and simply clear evidence of intelligent design. As Jonathan Wells and Paul Nelson explain in their essay, Homology, a Concept in Crisis, "Before Darwin, homology was defined morphologically and explained by reference to ideal archetypes -- that is, to intelligent design." It is only when unintelligent causes are mandated that common morphological features are "proof" of unintelligent Darwinian descent with modification. Wells and Nelson continue:
Darwin reformulated biology in naturalistic* rather than teleological terms, and explained homology as the result of descent with modification from a common ancestor. Descent with modification, however, renders design unnecessary only if it is due entirely to naturalistic mechanisms. Two such mechanisms have been proposed, genetic programs and developmental pathways, but neither one fits the evidence. Without an empirically demonstrated naturalistic mechanism to account for homology, design remains a possibility which can only be excluded on the basis of questionable philosophical assumptions.
*In this article, "naturalism" and "naturalistic" refer to the philosophical doctrine that nature is the whole of reality, and that intelligent causation does not qualify as a scientific explanation.
Wells and Nelson continue:
Diverse organisms possess homologous features. Homology in some cases may or may not be due to inheritance from a common ancestor, but it is definitely not due to similarity of genes or similarity of developmental pathways. In 1971, Gavin de Beer wrote: "What mechanism can it be that results in the production of homologous organs, the same 'patterns', in spite of their not being controlled by the same genes? I asked this question in 1938, and it has not been answered." (de Beer, 1971, p.16) Twenty-six years later, the question still has not been answered.
Without a naturalistic mechanism to account for homology, however, Darwinian evolution cannot claim to have demonstrated scientifically that living things are undesigned, and the possibility remains that homologies are patterned after non-material archetypes. Without a demonstrated mechanism, naturalistic biologists are left with only one alternative: exclude design a priori, on philosophical grounds.
This exclusion could be taken as a statement that intelligent design does not exist, or it could be taken as a statement that intelligent design is beyond the reach of empirical science. The first is a philosophical or theological statement, and warrants the same response. The second is a methodological limitation which cannot be logically extrapolated to a limitation on reality. In other words, a scientist who makes the first move is engaging in metaphysical disputation, while a scientist who makes the second is declining to investigate a possible aspect of reality.
Unfortunately, many biologists make both moves, but fail to distinguish logically between them. While justifying their exclusion of intelligent design on methodological grounds, they act as though science has disproved its existence by providing a naturalistic explanation for homology. When confronted with the fact that science has failed in this regard, they reaffirm their methodological commitment and express faith that a naturalistic mechanism will someday be discovered.
In the end, Wells and Nelson contend that genetics and developmental pathways are insufficient unintelligent causal agents to account for common morphology.
Further information from a creationist perspective can be found at The Parent Company in an essay entitled Do Similarities Prove Evolution from a Common Ancestor?
Special Evidence for Intelligent Design in Biology
The special evidence for intelligent design in biological systems is material evidence for which there is no known naturalistic explanation. Such evidence can only reasonably be considered to support an inference of intelligent causation (i.e., Intelligent design theory).
Origin of Life
To date there are no known naturalistic (involving only unintelligent processes) causes known that can explain the occurrence of life from non-life. Of all the proposed explanations for first life, only intelligent causation is tenable.
Darwin did not (and did not purport to) provide any explanation for the origin of the first replicating life form necessary for his theory of origin of species to work. That is, Darwinism is a naturalistic explanation for the origin of species that assumes a replicating life form to start the process.
Origin of life from non-living sources is termed abiogenesis or chemical evolution and scientific hypotheses that seek explanations for a first replicating life form suitable for Darwinian processes must postulate at least an unintelligent, deterministic physical cause for the first complex strand of DNA or other biologically active material.
Atheists, evolutionists and Darwinists who seek to provide an explanation for abiogenesis face the problem of proposing how the extremely unlikely occurrence of life could appear or evolve from purely unintelligent physical causes. By any account, the probability of such an occurrence by any known natural causes over any postulated time period is so low as to make the occurrence practically impossible.
By way of example of the probabilistically impossible odds of abiogenesis, consider the May 31, 2007 paper published by Eugene V. Koonin of the National Center for Biotechnology Information. Peer reviewed and published in Biology Today , Koonin calculated the probability of the most simple life form arising by natural processes, with the following conclusion:
The requirements for the emergence of a primitive, coupled replication-translation system, which is considered a candidate for the breakthrough stage in this paper, are much greater. At a minimum, spontaneous formation of:
- two rRNAs with a total size of at least 1000 nucleotides
- ~10 primitive adapters of ~30 nucleotides each, in total, ~300 nucleotides
- at least one RNA encoding a replicase, ~500 nucleotides (low bound) is required. In the above notation, n = 1800, resulting in E <10-1018.
That is, the chance of life occurring by natural processes is 1 in 10 followed by 1018 zeros. Koonin's intent was to show that short of postulating a multiverse of an infinite number of universes, the chance of life occurring on earth is vanishingly small, and we can understand the practical import to be that life by natural processes in a universe such as ours to be impossible.
Other prominent evolutionists agree that naturally occurring life from non-life is impossible. Evolutionist and theoretical physicist Paul Davies, for example, considers random self-assembly of proteins to be “a nonstarter”. Davies recognizes that life as we know it requires hundreds of thousands of specialist proteins, not to mention the nucleic acids; the number of amino acids sequenced in a small protein is 10^130 (written as one followed by 130 zeros). According to Davies, such an improbable sequence that is best explained by unconventional theories such as life has always existed. That is, there was no origin of life, because life is eternal, “spread around the universe … without having originated anywhere in particular”.
Davies also argues for a yet-to-be-discovered natural law, one that could be capable of abiogenesis:
[E]mergent laws of complexity offer reasonable hope for a better understanding not only of biogenesis, but of biological evolution too. Such laws might differ from the familiar laws of physics in a fundamental and important respect. Whereas the laws of physics merely shuffle information around, a complexity law might actually create information, or at least wrest it from the environment and etch it onto a material structure.
With respect to problems presented regarding the chance origin of life, and his proposed explanations, Davies concluded, “If you have found the foregoing argument persuasive, you could be forgiven for concluding that a genome really is a miraculous object. However, most of the problems I have outlined above apply with equal force to the evolution of the genome over time” 
Likewise, Nobel Prize winner Francis Crick (who along with James Watson, determined DNA’s molecular structure), considered the chance synthesis of even a small protein of 200 amino acids so improbable that he concluded that “the great majority of sequences can never have been synthesized at all, at any time.” 
Finally, consider Sir Fred Hoyle, an atheist astronomer who nevertheless reached the conclusion that the universe is governed by a greater intelligence. In 1978, Hoyle described Charles Darwin's theory of evolution as wrong and claimed that the belief that the first living cell was created in the "sea of life" was just as erroneous. Together with Chandra Wickramasinghe, Hoyle stated:
Precious little in the way of biochemical evolution could have happened on the Earth. It is easy to show that the two thousand or so enzymes that span the whole of life could not have evolved on the Earth. If one counts the number of trial assemblies of amino acids that are needed to give rise to the enzymes, the probability of their discovery by random shufflings turns out to be less than 1 in 10 to the power of 40,000.
Clearly, then, to an objective observer of the material evidence, the fact of life's existence, knowing that it must have a genesis, or a beginning, holds little in the way of evidence for naturalistic, unguided, unintelligent processes of nature.
Origin of life, therefore, is prima facie evidence of intelligent agency, and is at minimum sufficient observational evidence to support a reasonable scientific inference of intelligent design.
Specified Complex Information
Specified Complex Information (SCI) is noted by William Dembski as strong evidence of intelligent agency in biological systems. Based on the probability of certain arrangements or components of a whole, Dembski explains his idea in an essay entitled Explaining Specified Complexity
Briefly, Dembski states:
Life is both complex and specified. The basic intuition here is straightforward. A single letter of the alphabet is specified without being complex (i.e., it conforms to an independently given pattern but is simple). A long sequence of random letters is complex without being specified (i.e., it requires a complicated instruction-set to characterize but conforms to no independently given pattern). A Shakespearean sonnet is both complex and specified.
“Information” is the intangible property of an arrangement of elements that imparts a message or conveys meaning. Just as a book is more than paper and ink, the message formed by the specific, non-random combination of letters and spaces you are now reading reflects the purposeful character of this sentence. Living organisms exhibit vast amounts of information content similar to that in a computer program. In fact, information is defined as “the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects." The idea that the information in a computer program or in DNA could possibly be formed in an unspecified manner by unintelligent causes is a matter for mathematicians and statisticians, all of whom report back numbers that, in the time available in our universe, make such an occurrence by unguided processes effectively impossible.
DNA is one example of specified complex information in living organisms, reflecting a purposefulness that cannot be reduced to matter alone. As intelligent design theorist Phillip E. Johnson explains:
The important thing about DNA is not the chemicals but the information in the software, just as the important thing about a computer program or a book is the information content and not the physical medium in which that information is recorded.
Very simply, there is no known unguided, purposeless process (including Darwinism) that can make non-repetitive, specified sequences of matter, particularly the long, detailed sequences of DNA, comparable in quantity and quality to an entire set of encyclopedias. 
The information content of DNA is many, many times more complex and specified than a Shakespearean sonnet. Just as no scientist would suggest that Shakespearean sonnets were the work of unintelligent causes (even if the author were unknown), the presence of specified, complex information in DNA is equally dispositive of intelligent causes in living systems. The question of the cause of Specified Complex Information is critical to the origins science debate. If “evolution” means “change over time,” then there is no controversy. However, if “evolution” is defined as “a natural, unguided, information-producing process capable of creating Specified Complex Information,” then virtually no one would be an evolutionist based on the evidence. The evidence overwhelmingly suggests an intelligent cause. However, the question of the source of Complex Specified Information is secondary, and not necessarily a scientific question. But to rule out intelligent causes for Specified Complex Information based on the supposed inability for science to detect the source (e.g., as due to a conflict between "science" and "religion") is to make a category mistake. As Dembski states, “The proper contrast is between natural causes on the one hand and intelligent causes on the other.” Dembski elaborates:
Intelligent causes can do things that natural causes cannot. Natural causes can throw scrabble pieces on a board but cannot arrange the pieces to form meaningful words or sentences. To obtain a meaningful arrangement requires an intelligent cause. Whether an intelligent cause operates within or outside nature (i.e., is respectively natural or supernatural) is a separate question entirely from whether an intelligent cause has operated.
For more on the importance of biological information, see, Stephen C. Meyer, The Origin of Biological Information and the Higher Taxonomic Categories, Proceedings of the Biological Society of Washington,. Meyer argues, citing numerous studies by other scientists, that no current materialistic theory of evolution can account for the origin of the information necessary to build novel animal forms. Proposing intelligent design as an alternative explanation, arguing that new life forms such as those exhibited in the Cambrian explosion can only be attributed to a “remarkable jump” in complex specified information. No known material cause exists for such a jump.
Irreducible ComplexityMichael Behe, Professor of Biological Sciences at Lehigh University, argues that the most convincing evidence for design is not to be found in the stars or the fossils, but in biochemical systems. Author of Darwin's Black Box: The Biochemical Challenge to Evolution, and The Edge of Evolution: The Search for the Limits of Darwinism, Behe has posed a scientific response to Charles Darwin's challenge in Origin of Species:
If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.
Michale Behe claims to have shown exactly what Darwin claimed would destroy the theory of evolution, through a concept he calls irreducible complexity. As explained by the Intelligent Design and Evolution Awareness Center (IDEA), "In simple terms, this idea applies to any system of interacting parts in which the removal of any one part destroys the function of the entire system. An irreducibly complex system, then, requires each and every component to be in place before it will function."
The IDEA Center continues:
Since the publication of Darwin’s Black Box, Behe has refined the definition of irreducible complexity. In 1996 he wrote that “any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.”. By defining irreducible complexity in terms of “nonfunctionality,” Behe casts light on the fundamental problem with evolutionary theory: evolution cannot produce something where there would be a non-functional intermediate. Natural selection only preserves or “selects” those structures which are functional. If it is not functional, it cannot be naturally selected. Thus, Behe’s latest definition of irreducible complexity is as follows:
“An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.” (A Response to Critics of Darwin’s Black Box, by Michael Behe, PCID, Volume 1.1, January February March, 2002; iscid.org/)
Evolution simply cannot produce complex structures in a single generation as would be required for the formation of irreducibly complex systems. To imagine that a chance set of mutations would produce all 200 proteins required for cilia function in a single generation stretches the imagination beyond the breaking point. And yet, producing one or a few of these proteins at a time, in standard Darwinian fashion, would convey no survival advantage because those few proteins would have no function-indeed, they would constitute a waste of energy for the cell to even produce. Darwin recognized this as a potent threat to his theory of evolution-the issue that could completely disprove his idea. So the question must be raised: Has Darwin's theory of evolution "absolutely broken down?" According to Michael Behe, the answer is a resounding "yes."
For a good description of irreducible complexity, including examples, see the entire article at the IDEA Center website. Michael Behe's concept of irreducible complexity is further explained by the International Society for Complexity, Information and Design (ISCID) in their Encyclopedia of Science and Philosophy:
Michael Behe's Original Definition:
A single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning. (Darwin's Black Box: The Biochemical Challenge to Evolution, p. 39)
William Dembski's Enhanced Definition:
A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system. (No Free Lunch: Why Specified Complexity Cannot be Purchased Without Intelligence,p. 285)
Michael Behe's "Evolutionary" Definition:
An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.
Behe first introduced the concept of irreducible complexity in his book Darwin's Black Box: The Biochemical Challenge to Evolution. He has since expanded on the concept in his book The Edge of Evolution: The Search for the Limits of Darwinism. In Edge of Evolution he extends his analysis to define what evolution is capable of doing and what is beyond its scope.
In Darwin's Black Box Behe used the illustration of a mousetrap as an example of an irreducibly complex system. See here. A simple mousetrap includes: (1) a flat wooden platform to act as a base; (2) a metal hammer, which does the actual job of crushing the little mouse; (3) a wire spring with extended ends to press against the platform and the hammer when the trap is charged; (4) a sensitive catch which releases when slight pressure is applied; and (5) a metal bar which holds the hammer back when the trap is charged and connects to the catch. There are also assorted staples and screws to hold the system together.
If any one of the components of the mousetrap (the base, hammer, spring, catch, or holding bar) is removed, then the trap does not function. In other words, the simple little mousetrap has no ability to trap a mouse until several separate parts are all assembled, i.e., all the parts arrive in functional order and are assembled at the same time. Because the mousetrap is necessarily composed of several parts, it is irreducibly complex. Thus, irreducibly complex systems exist.
Behe then asks: Now, are any biochemical systems irreducibly complex? Yes, it turns out that many are. In many biological structures proteins are simply components of larger molecular machines. Like the picture tube, wires, metal bolts and screws that comprise a television set, many proteins are part of structures that only function when virtually all of the components have been assembled. A good example of this is a cilium. The components of cilia are single molecules. This means that there are no more black boxes to invoke; the complexity of the cilium is final, fundamental. And just as scientists, when they began to learn the complexities of the cell, realized how silly it was to think that life arose spontaneously in a single step or a few steps from ocean mud, so too we now realize that the complex cilium can not be reached in a single step or a few steps. But since the complexity of the cilium is irreducible, then it can not have functional precursors. Since the irreducibly complex cilium can not have functional precursors it can not be produced by natural selection, which requires a continuum of function to work. Natural selection is powerless when there is no function to select. We can go further and say that, if the cilium can not be produced by natural selection, then the cilium was designed.
Another example is the bacterial flagellum. As quoted at Access Research Network, Behe explains: "Because the bacterial flagellum is necessarily composed of at least three parts -- a paddle,a rotor, and a motor -- it is irreducibly complex. Gradual evolution of the flagellum, like the cilium, therefore faces mammoth hurdles." The bacterial flagellum is just one of virtually innumerable biological structures, that, once understood in detail, have no naturalistic causal explanation. Many evolutionists have attempted to deny Behe's contention that the flagellum is irreducibly complex, but every attempt fails to show how the flagellum actually could have been formed by Darwinian gradualism. Rather, all denials by evolutionists of irreducible complexity rely on non-confirmable, non-falsifiable, non-experimental assumptions to justify belief in unguided processes to produce such structures.
- Indeed, one characteristic of religion is the presence of dogmatic views. The mark of true science is tentativeness in holding to theories. Ironically, once a theory like Darwinism becomes unchallengeable based on the supposed religious implications of a competing theory, Darwinism itself is converted from science to religion.
- The term "species" is used in its ordinary and usual sense. Although the term can be defined in different ways, at least the term refers to organisms differentiated by reproductive compatibility and/or morphological dissimilarity, each of which involves the presence of differences in the coding of the information in the organism's genome.
- The term "species" is itself malleable, and is often stretched to a meaningless status by those who wish to show that "natural selection" has produced a "new" species. In any event, the selection usually referred to is not "natural", but is performed by intelligent beings in a lab, and the "species" exhibits no new, beneficial features that might yield a reproductive advantage. Usually, like in the intelligently designed "four-winged fruit fly" the new features are not beneficial, but detrimental to survival.
- When any new features do appear, such as on the intelligently designed "four winged fruit fly", the features are actually harmful to the organism's survival. Such organisms are referred to as "freaks". (For more information on the four-winged fruit fly, see http://www.idthefuture.com/2005/12/icons_of_evolution_a_response_4.html)
- Online at http://darwin-online.org.uk/content/frameset?itemID=F391&viewtype=text&pageseq=1
- See online at http://darwin-online.org.uk/content/frameset?itemID=F391&viewtype=text&pageseq=1, p. 133.
- Ernst Mayr, What Evolution Is, (New York: Basic Books, 2001), back cover.
- Ernst Mayr, What Evolution Is, (New York: Basic Books, 2001).
- Ernst Mayr, What Evolution Is, (New York: Basic Books, 2001), p. 14.(emphasis added).
- Ernst Mayr, What Evolution Is, (New York: Basic Books, 2001), p. 14.
- The Panda's Thumb, (New York: W.W. Norton & Company, Inc., 1980), p. 181.
- Intelligent design's opponents rely on a hidden assumption to remove intelligent design as a challenge to Darwinism. The assumption is that materialism is effectively true, meaning that only unintelligent causes can be considered to explain the cosmos, including life. The "rule" effectively re-defines “science” and serves to block all but unintelligent natural forces as potential causes for life and its diversity. The assumption operates as a rule—the “unwritten rule” of science, as described in a book by popular science writer Robert Wright. In his book, Wright explains that certain assumptions in science result in “unwritten rules of scientific conduct” that require adherents “to scrupulously avoid even the faintest teleological [i.e., design] overtones. (See, Robert Wright, Three Scientists and Their Gods (New York: Times Books, 1988), 70-71.)
- Jonathan Wells is a Senior Fellow at the Discovery Institute. Jonathan Wells has received two Ph.D.s, one in Molecular and Cell Biology from the University of California at Berkeley, and one in Religious Studies from Yale University. He has worked as a postdoctoral research biologist at the University of California at Berkeley and the supervisor of a medical laboratory in Fairfield, California, and he has taught biology at California State University in Hayward. Dr. Wells has published articles in Development, Proceedings of the National Academy of Sciences USA, BioSystems, The Scientist and The American Biology Teacher. He is also author of Charles Hodge's Critique of Darwinism (Edwin Mellen Press, 1988) and Icons of Evolution: Why much of what we teach about evolution is wrong. Most recently Dr. Wells authored, The Politically Incorrect Guide to Darwinism and Intelligent Design.
- Paul A. Nelson, Fellow of the Discovery Institute, received his Ph.D. from the University of Chicago in Philosophy (1998). He is a philosopher of biology, specializing in evo-devo and developmental biology. He has published articles in such journals as Biology & Philosophy, Zygon, Rhetoric and Public Affairs, and Touchstone, and chapters in the anthologies Mere Creation, Signs of Intelligence, and 'Intelligent Design Creationism and Its Critics. Nelson is also a fellow of the International Society for Complexity, Information and Design.
- Chemical Evolution: the hypothesis that the appearance of life from non-living materials occurred via Material Causes alone.
- The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life 
- Paul Davies, The Fifth Miracle, The Search for the Origin of Life (New York: Simon & Schuster, 1999), p. 91).
- Ibid., pp. 247-49).
- Ibid., p. 259.
- Ibid., p. 120.
- Francis Crick, Life Itself: Its Origin and Nature (New York: Simon & Schuster, 1981) p. 51-2).
- Sir Fred Hoyle and Chandra Wickramasinghe, Where Microbes Boldly Went, New Scientist, vol. 91 (August 13, 1991), p. 415
- William Dembski, The Design Inference, (Cambridge: Cambridge University Press, 1998), sec. 6.5.
- Merriam-Webster’s Collegiate Dictionary, Tenth Edition: 1996 (Springfield, MA: Merriam-Webster. Inc.)
- Johnson, Wedge of Truth, p. 53.
- Atheist and Darwinist Richard Dawkins states that each nucleus of plant or animal cells contains a digitally coded database larger, in information content, than all 30 volumes of the Encyclopedia Britannica put together." Richard Dawkins, The Blind Watchmaker, (New York: W.W. Norton & Co. 1996) p. 17-18, (emphasis added).
- Dembski, Intelligent Design, p. 106.
- Behe, M, 1996. Evidence for Intelligent Design from Biochemistry, a speech given at the Discovery Institute's God & Culture Conference, August 10, 1996 Seattle, WA. http://www.arn.org/docs/behe/mb_idfrombiochemistry.htm