1

"Intelligent Design": Defending I.D in Molecular

Biology from the 'CFI's' "Extraordinary Claims Require Extraordinary Evidence" Campaign":

As most of you have probably heard, the 'Center For Inquiry' (CFI) in late 2010 rolled out their bus ads in Vancouver attacking religion, and they have one particular web-page that attempts to refute the theory of Intelligent Design in molecular biology. Their one-page manifesto on Intelligent Design totally fails, and I will examine it in detail, and show how I.D can easily withstand all of their criticisms.

Here is their anti-I.D web-page for their 'Extraordinary Claims' internet campaign (first posted online on September 21st 2010): http://extraordinarybus.wordpress.com/2010/09/21/intelligent-design/. I will quickly sum up the theory of 'Intelligent Design' in biology before showing their manifesto. So what does the 'Design Inference' say in the realm of molecular biology?: that DNA and certain I.C Molecular Machines could only have ever arisen via an "Intelligence. To keep it a scientific theory though, we cannot say that "God did it"- only that "we have detected Design" (so, it could be aliens). However, "Design" at Life's fundamental basis (DNA) would destroy the Materialist/ Naturalist theory which says that undirected chemical evo. made the first Life on Earth. The question of the origin of biological information dismantles Darwinism, as Darwinism is Materialism incarnate, but material processes alone could never (even given favourable conditions & all the time since the Big Bang) have created highly-specified codes of information (within every cell upon Earth). DNA is digital information, and it employs multiple codes for storing and transmitting that info- so where did that info. come from? In fact, we only have 3 choices: 1: by Chance: from chance processes of chemicals 2: by Necessity: via some Law of Nature, like a Law of Chemistry or Physics, or 3: by Design: caused by some kind of an 'Intelligence'. Darwinism is dead, and Stephen Meyer's 2009 ground-breaking'Signature in the Cell' put the final nail in the coffin.

Here's Their 4-Paragraph-Anti-I.D-Manifesto:

"The Claims:
"Intelligent design (ID) is the proposition that some features of life on Earth were created abruptly by an intelligent and powerful being rather than being the result of the undirected natural processes of evolution. The proponents of ID claim that it is a legitimate alternative to evolutionary biology and that it deserves equal time in public schools. ID proponents hold that evolution can account only for small changes within species, not for the diversity of biological species on Earth. Some features of biological organisms are considered to be too complex to have evolved through variation, heredity and natural selection. ID proponents claim that organs such as the human eye or the bacterial flagellum (a tiny propeller that allows bacteria to move around) illustrate a kind of complexity that is simply unexplainable through natural causes (a concept called irreducible complexity). They have argued that such complex organs cannot function if a single part is malfunctioning or missing, so they could not have evolved gradually: they must have been created as fully functional wholes.

The Evidence:
Claims of irreducible complexity have been shown to be false. Studies in molecular biology have shown that the bacterial flagellum could function without some of its parts - not as a locomotion tool, but as a sort of syringe through which the bacterium injects toxins into its host. These studies have classified the bacterial flagellum as an evolved type III secretory apparatus (McNab 1999, Aizawa 2001). Molecular genetics has allowed the genomes of plants and animals to be mapped, and the genetic similarities and differences between species to be observed. The evidence for evolutionary biology (and against ID) is overwhelming. The facts clearly demonstrate that all forms of life on Earth form a tree of life with three big branches (bacteria, archaea and eucarya) and many splitting sub-branches. ID rejects the branching tree model, holding instead that species have no historical connection to each other (known as the parallel grass blades model). ID postulates the existence of an intelligent designer, not considered part of the natural world, which is responsible for the origin of species on Earth. Since the designer is said to be beyond the realm of the observable, claims about its existence can be neither supported nor undermined by observation or experiment. Therefore ID does not follow the scientific method of systematic observation and experiment, and fails as a scientific hypothesis. If, however, the Intelligent Designer is considered part of the natural world, it is a form of life. In this case, ID has created a problem bigger than the one it attempts to solve: life on Earth is explained by assuming the existing of a being far more complex and powerful, with no attempt to account for its origins.

Conclusion:
Up until today (September 2010), the ID movement has not published a single peerreviewed article in a recognized scientific journal. ID is religious in nature, being a modern form of Creationism, which is itself derived from a literal and fundamentalist interpretation of the biblical book of Genesis. However, unlike standard Creationists, the supporters of ID may not necessarily agree with the Young Earth hypothesis. Links: Wikipedia Entry on Intelligent Design; Skeptics Dictionary Entry on Intelligent Design; The Flagellum Unspun: The Collapse of Irreducible Complexity Miller, K. 2004; Bacterial Flagella and Type III Secretion Systems Aizawa, S.-I., 2001; The Bacterial Flagellum: Reversible Rotary Propellor and Type III Export Apparatus McNab, R. M., 1999; Stanford Encyclopedia of Philosophy Entry on Creationism .

"

Note that in their sources and references section at the bottom of the web-page, their most recent source was an article via biologist Ken Miller (2004), who was prominent in the 'Dover debacle' (2005)- and I will deal with him specifically up ahead and show that his argument against ID has been soundly debunked- but first, their new slogan goes, "Extraordinary Claims Require Extraordinary Evidence". Without a doubt, DNA's Digital Code is the "Extraordinary Evidence" that they should be acknowledging! To familiarize oneself with the latest DNA developments, these 2 papers are key. It seems the CFI is oblivious to the fact that DNA is Extraordinary! 1) 'The Digital Code of DNA' - 'Nature' 2003: http://www.ncbi.nlm.nih.gov/pubmed/12540920). 2) 'Deciphering the Splicing Code' - 'Nature' 2010: http://www.nature.com/news/2010/100505/full/465016a.html).

4 The theory of Intelligent Design via biology has positive empirical evidence to back up its inference to Design at the molecular level, and the critics are hurling everything they got at the notion of being able to infer it ('Design')- specifically: that Science can aid and allow this enterprise. But the Design-Inference easily holds, as Science already uses it for many fields in the Historical Sciences! The biological case for Design concerns the origin of the Digital Code(s) found in DNA, and also, how certain Irreducibly Complex molecular machines could have come together under an undirected process with no end-goal in sight (when they in fact need all of their parts arranged together in a specific temporal sequence to even work at all!). But again, I must stress that ID can only say that "we have detected Design"- much like archaeologists, forensic scientists, cryptographers, or scientists working on SETI doID is not against the process of Evolution at all, just the notion that it could have happened through an Undirected Process. Instead, ID maintains that if it did happen, it would have had to have been via a Directed Process (and this is easily evident from the reams of digital codes which constitute the very basis of Life itself).

The CFI Article: Some features of biological organisms are

considered to be too complex to have evolved through variation, heredity and natural selection. ID proponents claim that organs such as the human eye or the bacterial flagellum (a tiny propeller that allows bacteria to move around) illustrate a kind of complexity that is simply unexplainable through natural causes (a concept called irreducible complexity). They have argued that such complex organs cannot function if a single part is malfunctioning or missing, so they could not have evolved gradually they must have been created as fully functional wholes.

My Response:
The CFI's anti-ID-page is focused solely on Mike Behe's work regarding molecular machinery found in the cell: specifically, the bacterial flagellum; however, astonishingly it says nothing at all about Stephen Meyer's 2009 book 'Signature in The Cell', which makes a rigorous philosophical case for inferring Design based on the digital information found within the DNA molecule (Complex Specified Information that could only have ever arisen via an 'Intelligent Cause' of some kind): http://www.signatureinthecell.com/.

Meyer's ideas first went public in 2004, when he wrote that no materialistic theory can account for the origin of the biological information needed to build new and novel animal forms (and this article appeared in the peer-reviewed 'Proceedings of the Biological Society of Washington': http://www.discovery.org/a/2177). But in his 2009 ground-breaking 'Signature in the Cell', Meyer rigorously assesses all of the various scientific theories that have tried to account for the origin of the digital code needed to build the 1st working bio-informatic molecule, let alone the 1st Cell (and to construct a cell with all of its constituent protein parts, massive amounts of digital code are needed). So where did this biological information come from? Using a form of Abductive Reasoning, like Darwinism and the rest of the Historical Sciences, Meyer argues that Information can only ever come into existence via an Intelligent source of some kind (he isnt saying "God made DNA"- that would be going above what the evidence warrants). He painstakingly tries to show in the book how alternate theories offered by the Darwinists cannot work, namely, Chance-Based Theories or Necessity-Based Theories regarding the origin of DNA, and to disprove the contention that DNA could only have come from an Intelligent Source, we need to see proof that Information can arise on its own through Chance or Necessity-Based Natural Processes- but that has never been demonstrated. On the other hand, our present experience of causal reality constantly confirms that Information (be it a software code, languages, or sheet music etc.) can only ever come from a Mind/Intelligence (not natural processes of Matter and Energy). Information never comes from Nature, but rather from Minds. Information is an entity entirely different from physical forces of Matter and Energy (i.e - Information is not the ink). This is the insurmountable problem for Naturalism/Materialism: Matter and Energy by itself can never cause Information (esp. highly-specified codes) to come into existence, only an Intelligence/Mind can. If one maintains otherwise, that Information can arise from just Matter & Energy alone (without an Intelligence being involved), then they're basing that solely on Faith, not on Causality. If the critics are to ever beat ID, then this is the argument that they must contend with; it is empirically-derived/Inductively-based, and I didn't see it addressed anywhere whatsoever on the CFI's anti-ID-page! How come? It appears that they are far behind the current advances going on in the field of Micro-biology, and have perhaps never even heard of the new field of 'Bio-Informatics'? (which is all about 'Information').

The DNA-Is-Digital-Information-Argument:
Premise 1: DNA is Complex Specified Information (digital too). Premise 2: All Complex Specified Information comes from an Intelligent source of some kind, and not natural/physical processes of Matter & Energy alone.

6 Conclusion: therefore, DNA was made by some kind of an 'Intelligence'.

Chance-Based or even Necessity-Based Processes of Matter and Energy alone could never have produced Complex Specified Information. Necessity-Based Law-like forces produce patterns and redundancy, not complex specificity & irregularity (what DNA entails). It is sound to infer that an Intelligence has played a part in the origin of DNA's digital code(s) as our repeated and uniform experience of causal reality shows that only it (an Intelligence/Mind) can create highly-specified codes of digital information. If one doubts that, refer oneself to Craig Venter's 2010 experiment: after months of delays and errors, his 'DNA spell-checker program' finally saved the day by spotting one little 'spelling' mistake out of the millions of other A/C/G/T amino acids within the mind-boggling huge nucleotide sequence, and that shows without a doubt that DNA is a kind of 'Complex Specified Information'. Remember, DNA is digital instructions for building every known celluar nanoprotein machine on Earth, and Instructions/blue-prints = Information. Matter & Energy alone can never cause Information to come into existence, only a Mind/Intelligence can! How come the CFI refuses to even mention Digital DNA?! This is not an 'Argument from Ignorance', where we're authenticating I.D solely because Materialism cannot explain the origin of biological information, like, Premise 1: Materialism cannot explain the origin of biological Info. Conclusion: Therefore, an Intelligence/Mind caused the origin of biological Info. Indeed, that's an 'Argument from Ignorance' because it omits a premise citing positive evidence. In other words: "your cause is inadequate, therefore, mine is adequate". But this new and powerful argument regarding the origin of biological information does not commit that error as it is an "Inference to the Best Explanation", employing the scientific methodology of 'Multiple Competing Hypotheses' (whereby we study all contending hypotheses, and then choose the one with the most causal adequacy, which best explains the origin of the Effect in question). So we compare the Design Hypothesis with material theories based on 'Chance', and 'Necessity' (either internal or external self-organizational models), as well as a combination of both, Chance-+Necessity. The hypothesis with the most causal adequacy is then chosen as the Best Explanation concerning the origin of the digital information within DNA and the cell's information-processing system. So I.D's Digital-DNA-Argument goes:

Premise 1: Despite a thorough search, no material causes have been discovered

that demonstrate the ability to produce Complex Specified Information. Premise 2: Intelligent Causes have demonstrated the power to produce large amounts of Complex Specified Information. Conclusion: therefore, I.D constitutes the best, most causally adequate explanation regarding the origin of DNA's digital code. That cannot be an 'Argument from Ignorance', it is an Inference to the Best Explanation- a mode of argumentation used by all of the Historical Sciences.

The CFI Article: Claims of irreducible complexity have been

shown to be false. Studies in molecular biology have shown that the bacterial flagellum could function without some of its parts - not as a locomotion tool, but as a sort of syringe through which the bacterium injects toxins into its host. These studies have classified the bacterial flagellum as an evolved type III secretory apparatus (McNab 1999, Aizawa 2001).

Me:
First: they totally misrepresent the concept of Irreducible Complexity (also what Ken Miller does) as they claim that the Bacterial flagellum (with its 30-part rotary engine) "can still function without some of its parts"- but sorry, that is simply not true: for if even one single part is removed from that 30+-part rotaryengine, over-all function in that system becomes impossible (just like if you were to remove a single piece from a mouse-trap; then the whole thing would cease to work). Then the CFI goes on to say that studies have shown that without some of its parts, the "bacterial flagellum" could still function, "not as a locomotion tool, but as a sort of syringe". Whoa! Stop right there! that does not make any sense! If the bacterial flagellum lost some of its parts (which would necessarily destroy over-all function in its rotary-engine)- and then some elements of that formerly operational system became able to function "as a sort of syringe"- then 1) it would no longer be a bacterial flagellum in the slightest! and 2) that still does nothing to refute the Inference to Design based on I. C within the flagellum's 30+-part-rotary-engine.

8 Bio-Chemist Dr. Michael Behe first came up with the concept of Irreducible Complexity in molecular biology, and he introduced it to the public in the university press peer-reviewed book 'Darwin's Black Box: the Biochemical Challenge to Evolution' in 1996. It's been almost over 15 years since then, and so far, the critics' only counter-explanation for these Irreducibly Complex Nano-Molecular Machines found within the Cell is (to paraphrase): "through Natural Selection, these Irreducibly Complex Nano-Molecular Machines were built up from smaller subsystems" (the Neo-Darwinists refer to this process as "co-opting"). Now, I want to delve into I.C in biology and Ken Miller in more detail, as Miller is their most recent source (2004). Remarkably, in the CFI's anti-ID-manifesto, they only devote 3 sentences to refute the Design Inference in biological systems based on Irreducible Complexity within the flagellum's rotary-engine, and they only use Ken Miller's 2004 paper. But 2004? It's now 2011, where have they been????????????????

Commonly-Touted 'Ken-Miller-Bacterial-Flagellum-Criticism':
Ken Miller of Brown University has suggested that the flagellar motor might have arisen from the functional parts of other simpler systems, and his purported smokinggun is the 'Type-Three Secretory System' (T3SS). The T3SS is a little molecular syringe/pump, and it's made up of about 10 proteins that are found within the bacterial flagellum. For Miller, the key thing is that the T3SS is usually found inside other bacterium, so he therefore assumes that the T3SS is an ancestor or precursorsystem to the bacterial flagellum. So in short: Miller's criticism says that 'the bacterial flagellum arose from the smaller molecular pump T3SS' (Miller, K. (2004): 'The Bacterial Flagellum Unspun'- in W.A Dembski's and Michael Ruse's edition of 'Debating Design: From Darwin to DNA' Cambridge: pg: 81-97).

"STILL SPINNING JUST FINE: A RESPONSE TO KEN MILLERBy Dr. William A. Dembski, 2.17.03, v.1" (2004):
http://www.designinference.com/documents/2003.02.Miller_Response.htm.

Ken Miller Is Missing 3 Key Things 1) he doesn't mention the mysterious composition of the bacterial flagellum: it has
over 20 other unaccounted for protein parts.

2) If using Natural Selection, Miller fails to recognize how all of the rotaryengine's protein-parts would have needed to have been assembled in the right temporal sequence (if to attain over-all function).

3) he 'Begs the Question' (specifically: he forgets that every time we observe these
little nano-protein-machines getting assembled inside the Cell, like cars on a factory floor- it is solely thanks to DNA's digital information). Let's assess Miller's theory of 'co-option' in light of those three points; then, I will address Miller's well-known objection to the concept of Irreducible Complexity.

#1) The Other Proteins Within the Bacterial Flagellum:

Miller doesn't tell us that the other twenty or so protein-parts that comprise the bacterial flagellum are found in no other bacterium on Earth! This then raises an even more important question if we follow Miller's reasoning: from where were these other protein parts 'co-opted' from? The fact that we cannot find these 20+ other proteins inside any other bacterium on this planet poses a huge problem; and Miller's claim that "we've found 10 of the flagellum's protein-parts inside other bacterium"- does not address how the flagellum's 30+-part rotary-engine originated!

#2) The Assemblage Problem:

DNA easily solves this problem as it supplies the precise digital instructions to all of the proteins for assembling and building every known protein component within the

10 Cell, but let's examine how Co-Option through Natural Selection could have made some of these Irreducibly Complex Molecular Machines. Microbiologist Scott Minnich of the university of Idaho has pointed out that even if all of the protein parts to make the bacterial flagellar motor were somehow available during the evolution of life, all of the parts would then still need to be assembled in a SPECIFIC TEMPORAL SEQUENCE (similar to the way an automobile is assembled in a factory, or setting up a mouse-trap)- and that simply cannot happen with Natural Selection under Neo-Darwinism. And why not? Because Natural Selection is only supposed to develop and pass on things that have FUNCTION; but for the flagellar motor to attain Overall-Function, its parts must be assembled in the right order, but pertinently, before its assemblage into Overall-Function, it would have been carrying around some functionless parts, and adding new ones, saving them also, until, finally it acquired the last one- and then attained Overall-Function. Sorry, under Natural Selection, which has no Fore-sight, that kind of process is impossible. Natural Selection under NeoDarwinism is supposed to be a blind and undirected process having no 'end-goal-in-sight'; it can only develop new adaptations that function and benefit the organism immediately. It cannot 'save' non-functional things for down the road; surely, that bespeaks of Foresight & Purpose, not of an 'Un-Directed Process'.

#3) Back To Digital DNA:

Yet in order to choreograph the assembly of the flagellar motor, present-day bacteria need an elaborate system of genetic instructions, as well as an array of protein machines (which are assembled inside the cell along little 'nano-assembly-lines' reminiscent of a high-tech factory). But arguably, the Cell's fundamental system of DNA-RNA-Protein-Reciprocity is itself Irreducibly Complex! On a side note, this is what is known as the massive

11 'chicken-and-the-egg-problem' of modern molecular biology: for without proteins, there can be no assemblage, but without DNA, there can be no proteins- so which one came first? The 'RNA World Hypothesis' has attempted to solve this paradox because RNA acts as a 'go-between', but this theory still does nothing to explain the origin of the biological information in RNA (it only Begs the Question and assumes the existence of Complex Specified Information). For how did the RNA molecule's amino acids of A, T, C, and U become arranged into complex-information-rich sequences? In fact, at bottom, but under Miller's assumed gaze, 'Co-option' theories only explain Irreducible Complexity by assuming Irreducible Complexity! What I mean is that Miller takes for granted the fundamental DNA-RNA-ProteinReciprocal-System that makes and directs all activities within the Cell; it is itself Irreducibly Complex! That reciprocal system makes his Neo-Darwinistic mechanism possible (as DNA records changes, and then allows them to be passed on).

2004 Genetic Analysis Has Shown That The Bacterial Flagellum Could Not Have Evolved From The T3SS:
To put to rest the notion that the bacterial flagellum evolved from the T3SS molecular-pump, refer yourself to this 2004 paper: Saier, M.H. (2004): 'Evolution of the Bacterial Type 3 Protein Secretion Systems' - in 'Trends in Microbiology' Feb 2004 #12 pg: 113-115 (http://www.sciencedirect.com/science/article/pii/S0966842X04000174). This peer-reviewed paper says that analysis of the gene sequences of the 2 systems ('the Bacterial Flagellum motor' and the 'Type-3 Secretory System'/Molecular Syringe/Pump) has revealed that the flagellum arose first, and then the T3SS came later. The pump evolved from the motor, not vice-versa! M. Behe now stands verified.

12

Miller's Objection to Irreducible Complexity Totally Fails

Ken Miller insists that the T3SS refutes Behe's claim that the flagellar motor is Irreducibly Complex because he thinks that I.C entails that no part of an I.C System can have another function outside of that System. That's why he points to the T3SS, and says (paraphrasing): "look, it's from the flagellar motor, and it can work outside of that system, and have another function! Therefore, the Bacterial Flagellum is not irreducibly complex!" Sorry Miller, all Behe is saying is that (and this is the strict concept of I.C) (paraphrasing again): "if you remove one part from an Irreducibly Complex system, you will lose function IN THAT SYSTEM, nothing more". Miller's objection/refutation totally misrepresents the strict concept of I.C.

In Conclusion Regarding Behe and 'Irreducible Complexity':

The critics' theory of 'co-option' under Neo-Darwinism, which is an Undirected Process, does not provide a better CAUSALLY ADEQUATE EXPLANATION for the origin of the flagellum's rotary-engine than does M. Behe's 'Design Hypothesis'.

"Michael Behe Hasn't Been Refuted on the Flagellum (March 2011)":

http://www.evolutionnews.org/2011/03/michael_behe_hasnt_been_refute044801.html

"Molecular Machines in the Cell (2010)":

http://www.discovery.org/a/14791

13

Some 'Facebook-Bacterial Flagellum-Criticism'

Critic:
"Irreducible Complexity is always an Argument from Ignorance. Just because we don't see the way that it is broken down, does not mean that it can be Irreducibly Complex. It's supreme arrogance to say otherwise".

Me:
"It is not an Argument from Ignorance. An Argument from Ignorance is all about validating one idea simply based off the casual inefficacy of another idea, yet without citing any Positive Evidence to support your own idea. In fact, certain molecular protein-machines being I.C is based on what we know, not what we do not know, and we were never able to map and see every single part of protein-machines until relatively recently (and by using X-ray crystallography). Is a mouse-trap Irreducibly Complex? Yes it is, and the same with the bacterial flagellum; and just like with a mouse-trap, to attain over-all function, all of the parts to the flagellar motor must be assembled in the right temporal sequence. I.C denotes that if you were to remove any one of the Mouse Trap's parts, or the Bacterial Flagellum's 30+ protein parts that encompass its rotary-engine- it would cease to function. But if to attain over-all function, all of its parts must be assembled in the right temporal sequence, then how could it have attained over-all function through Neo-Darwinism? which is supposed to be a process that only uses changes that benefit the organism immediately? having no Foresight? incapable of saving useless parts until attaining over-all function at the end? (which some of its parts would have been). Micro-biologists have now mapped out all of the bacterial flagellum's parts, as well as seen how all of them interact with each other, so when it comes to explaining the origin/assemblage of the flagellum's 30+-part rotary-engine- the Design Inference has far greater Causal Adequacy".

Critic:
"People used to think that all the organs were all there was, and then we discovered cells, then we discovered DNA/RNA, etc, etc. Or in physics we used to think it was molecules, then atoms, then protons/electrons, then quarks, etc. There is always something more basic".

Me:
"True, but irrelevant. The question is not if something is more basic than the Flagellum (of course DNA is as it embodies the Bacterial Flagellum's Instructions)-

14 but the question becomes rather: "how could something I.C which must have all of its component parts assembled together in the right temporal order have come together under a process that is supposed to be Blind/Un-Directed? (thus having no over-all End-Goal in sight). It is not about going to another more fundamental level to explain a level that is I.C, but rather it is all about how that particular I.C level could have come together. For example, the question isn't if an out-board-motor type-unit is composed of smaller and more reducible parts (it obviously is)- but rather, how did the motor come together and attain functionality? (period). Sure, the smaller and more reducible level of DNA does tell us how the level of cellular nano-machinery came together, for it supplies the precise digital instructions that tell other proteins how to assemble themselves- but then the question still becomes: 'how did DNA's digital instructions arise'? Can one go more fundamental? Reducible? Can going to a smaller level explain the origin of that level? the level of 'Bio-Informatic Molecules'? the level of biological information? Could the level of atoms and sub-atomic particles help here? (like quarks etc.). No. "Information is information, neither matter nor energy" Dr. Hebert Weiner - the Father of Cybernetics

The CFI: Molecular genetics has allowed the genomes of plants

and animals to be mapped, and the genetic similarities and differences between species to be observed. The evidence for evolutionary biology (and against ID) is overwhelming.

Me:
Similarities dont do anything to address the origin of the Digital Code found within DNA! So they're simply Begging the Question by claiming that similarities between various organisms' DNA-Sequence prove that Darwinian Evo. is true, and ID, false.

15

Truly, when it comes to explaining the formation of DNA and how its astronomicallylong chain of amino acids could have come together (the smallest bacterium on Earth have chains of 500,000 amino acids)- one cannot appeal to Natural Selection. Without a doubt, Natural Selection cannot even kick-in until DNA is already functioning; when that huge nucleotide strand has hit that right Sequencing and has attained Function (aka. the ability to Replicate/Copy itself). Natural Selection could only have ever emerged onto the scene after DNA first became Functional; only then would the DNA molecule have been able to record and pass on any changes, thus allowing Darwinian Evo. by the mechanism of Natural Selection, to have begun. Because Natural Selection cannot be invoked when it comes to explaining the formation of the 1st replicator, the 1st functioning bio-informatic molecule, the origin of Life (in other words)- Neo-Darwinists/Naturalists/Materialists can only appeal to either 'Necessity-Based Theories' or 'Chance-Based Theories'. The most classic Necessity-Based Theory is the 'Chemical-Organizational-Theory-of-DNA' , which came via Dr. Dean Kenyon in the 1970s: he said that DNA's amino-acid-sequence had come together into a sequential arrangement due to some attractive forces present within the amino acids themselves- but after more information began to come in concerning the specificity and aperiodicity of the DNA molecule (which has phosphate bonds that allow for any arrangement of the amino acids A, T, C, Gnever preferring one over the other)- Kenyon then recanted and pronounced his old findings false! He now affirms that Design "Best Explains" the origin of the Info. found in DNA. Dean Kenyon, a world-class researcher since 1968, is now an ID'er.

Because DNA's information-bearing-amino-acid-sequences are highly specified and irregular, 'Necessity-Based Theories' and 'Chance-Based Theories' cannot give an adequate causal account of their origin. Necessity-Based/Law-like Forces only produce patterns (as they ensure that the same Effect is repeated if given the same

16 conditions) - so one should see mostly redundancy and repetition characterizing DNA's amino-acid sequence if Necessity-Based Forces Caused it to form. However, Chance-Based Forces produce Effects that are random, which means that the Effects are not supposed to attain some specific purpose or arrangement. Indeed, Chance is antithetical to Specified Information for Specified Information implies that its constituent elements have been deliberately arranged (the polar opposite of Chance). Only an Intelligence/Mind could have come up with the Complex Specified Information in DNA; come up with its Logic that determines what 3 triplets will encode for one of the 20 amino acids to be used in protein construction. Remember what they said? Molecular genetics has allowed the genomes of

plants and animals to be mapped, and the genetic similarities and differences between species to be observed. The evidence for evolutionary biology (and against ID) is overwhelming.
Is that true? Not at all! they are just assuming the existence of DNA without first addressing the origin of it! and without first contemplating its origin, they are failing to see that similarities at the genetic level could mean the reverse of what they're assuming it means: namely, that if an Intelligent Designer designed the whole program of Life/DNA, apparent similarities at the physical and genetic levels between species are to be expected (after all, aren't we made of the same stuff? (DNA?). Along these lines, but appealing to genetics for Darwinian Evolution, Dawkins cited in his most recent book ('the Greatest Show on Earth') the "Near Universality of the Genetic Code inside all Life" as proof of Darwinian Evo. But is there Universality?

The fact that we have now found over 17 Variant Genetic Codes inside the DNA of various organisms on this planet shatters that idea! Those Variant Codes all employ different sequential logic! so to give a hypothetical example, in a sheep, the sequential arrangement of the amino acids ACC will code for the amino acid leucine, but in a butterfly, TGC will code for it. But if Darwinism is true (Universal Common Descent via N.S acted on by random mutations)- then we should expect to see one Universal Code throughout all organisms on the planet, not Variants! So where did all of that Info./Logic that dictates those Variant Coding Conventions derive from?!

17

In 2011, world-class DNA-researcher Craig Venter mentioned the fact of these Variant Coding Conventions at a major Evolution Conference where Dawkins was present, and what he said obviously burst Dawkins' bubble (as it went against Dawkin's centerpiece of proof in his new book for Universal Common Descent and the Tree of Life). Venter then made it clear in no uncertain terms that there is no Tree of Life which demonstrates Universal Common Descent (the Darwinian idea that all Life evolved from a single ancestor gradually over vast epochs of time). The Universality of the Genetic Code in all life-forms would certainly back up that nucleic Darwinian idea, but that hope has been forever derailed with the discovery of 17 other Variant Codes present in the DNA of various organisms on Earth. Predictably, Dawkins appeared shocked, and he replied in his usual arrogant and incredulous form. From 'The

Greatest Show On Earth' (2009), pg. 409: "...the genetic code

is universal, all but identical across animals, plants, fungi, bacteria, archaea and viruses. The 64-word dictionary, by which three letter DNA words are translated into 20 amino acids and one punctuation mark, which means 'start reading here' or 'stop reading here,' is the same 64-word dictionary wherever you look in the living kingdoms (with one or two exceptions too minor to undermine the generalization)".
In his new book, Dawkins said that all throughout the "living kingdom" we will find "the same 64-word dictionary"- but that is patently false, and it appears as if Dawkins is not even abreast of what is going on these days. All of the currently known Codes, both Nuclear and Mitochondrial, are listed here: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#564. So far, there are 17 Variant Codes, which = 17 different "64-word dictionaries", but each employing a different Language! (aka. Logic). No more appealing to the supposed "Universality" of the Genetic Code to prove Universal Common Descent!

"Venter vs. Dawkins on the Tree of Life - and Another Dawkins Whopper":
http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html

"Craig Venter Denies Common Descent - Dawkins Incredulous":

http://www.uncommondescent.com/evolution/craig-venter-denies-commondescent-dawkins-incredulous/.

18

At this 2011 Conference at Arizona State University, with a panel including Dawkins, Venter, Physicists Paul Davies and Lawrence Krauss, to name a few- the topic was "What is Life?"- watch it here: http://thesciencenetwork.org/programs/thegreat-debate-what-is-life/what-is-life-panel- and most of the panel started off by saying that all Life on Earth was of the same kind (descending from a Last Universal Common Ancestor (LUCA)). But around 9 minutes in, Venter starts to remarkably disagree with the other panelists, especially Dawkins. More people need to know this:

Venter: "I'm not so sanguine as some of my colleagues here," "that there's only one
life form on this planet. We have a lot of different types of metabolism, different organisms. I wouldn't call you (turning to Davies) the same life form as the one we have that lives in pH 12 base, that would dissolve your skin if we dropped you in it."

Davies: "Well, I've got the same genetic code," "We'll have a common ancestor." Venter: "You don't have the same genetic code". "In fact, the Mycoplasmas use a
different genetic code that would not work in your cells. So there are a lot of variations on the theme..."

Davies: "But you're not saying it belongs to a different tree of life from me, are
you?"

Venter: "Well, I think the tree of life is an artifact of some early scientific studies
that aren't really holding up...So, the tree, ya' know... there may be a bush of life(laughter from audience)So, there is not a tree of life". Then he ends by stressing the "diversity present in the DNA world" (the Variant Coding Conventions)- then Dawkins:

Dawkins: "I'm intrigued, at Craig saying that the tree of life is a fiction. I mean...the
DNA code of all creatures that have ever been looked at is all but identical". "Surely that means that they're all related? Doesn't it?"

Venter: (just smiles). (probably thinking: "did you even hear what I said?")
So there was Venter, telling the panel about the Variant Coding Conventions found within various organisms' DNA, and then Dawkins, a few minutes later, hilariously acting as if he wasn't listening to one of the greatest authorities on DNA/ Genetics.

19

The CFI: "The facts clearly demonstrate that all forms of life on
Earth form a tree of life with three big branches (bacteria, archaea and eucarya) and many splitting sub-branches. ID rejects the branching tree model, holding instead that species have no historical connection to each other (known as the parallel grass blades models)".

Me:
"Contrary to what the CFI claims, the "facts" do not show that "all forms of Life on Earth form a Tree-of-Life". What a whopper! the tree of Life does not exist (see Venter's remark to Dawkins). Our very complete planetary fossil record does not show a gradual tree of life model (whereby the simplest life-forms evolved into more complex ones while branching away from each other)- thus demonstrating Universal Common Descent via an Undirected Process. The Earth's fossil record rather shows a sudden and abrupt Top-Down Appearance starting amidst the mysterious Cambrian Explosion (which happened around 530 million years ago). The Tree of Life has never been corroborated by the very complete planetary fossil record. Importantly, ID never "rejects the branching tree model, holding

instead that species have no historical connection to each other (known as the parallel grass blades models"- instead, ID knows that all Life
fundamentally shares a "historical connection" as it all uses biological information. It is the CFI and other critics who choose to ignore the true "historical connection" when they refuse to mention the biological information at the heart of all Life. Instead, they just assume its existence, and then conjure up a Tree of Life based on it. If people find blasphemous the notion that the fossil record does not show Darwin's predicted 'Gradually-Branching-Away-From-Each-Other-Tree-Of-Life-Model', then recall the famous late & great Harvard Neo-Darwinist Stephen J. Gould (who formulated the theory of "Punctuated Equilibrium"). P.E is all about Rapid-change,

20 going against Darwin's nucleic theory of Gradual-Change, but Gould was spurred into thinking this by the 'Very Complete Planetary Fossil Record', and he was trying to account for its huge gaps (thanks to no major transitional forms ever being found, as well as the puzzling and mysterious Cambrian Explosion). In fact, the pattern of fossil appearance in the Cambrian contradicts the predictions of NeoDarwinian and Punctuationalist evolutionary theory, and it soundly refutes the mythical Tree of Life: for in it, we find complex new phyla (body plans) emerging without any proper pre-cursor ancestors, and those new phyla/body plans require massive infusions of new biological information into the genome and bio-sphere. "The Cambrian Explosion was the most remarkable and puzzling event in the history of life" - Stephen J. Gould - Harvard Neo-Darwinist / Paleontologist. Check out this peer-reviewed paper: 'The Cambrian Explosion: Biology's Big Bang' - by Dr. P. Chien, Dr. M Ross, Dr. P. Nelson, and Dr. Stephen Meyer in 'Darwinism, Design, and Public Education' - Michigan State University Press 2003 pg: 323-402): http://www.discovery.org/scripts/viewDB/filesDBdownload.php?command=download&id=639).

The CFI: ID postulates the existence of an intelligent designer, not

considered part of the natural world, which is responsible for the origin of species on Earth. Since the designer is said to be beyond the realm of the observable, claims about its existence can be neither supported nor undermined by observation or experiment. Therefore ID does not follow the scientific method of systematic observation and experiment, and fails as a scientific hypothesis".

Me:
In the realm of biology, we are only inferring an Intelligent Cause to these specific kinds of Effects: 1) DNA's Digital Info., and 2) certain Irreducibly Complex Protein-Nano-Machinery. DNA is observable as well as all of the molecular machines, so why can't we infer Design? In fact, we dont need to show evidence of the Designer to infer Design; rather, only evidence of Design. It is just that simple.

21

Dawkins' common retort goes, "well, Who Designed the Designer Then?!" But that is easily refutable. If we found Pyramids on the Moon, we would be justified in INFERRING that they were the products of some kind of an Intelligence even if we didn't know anything about who made them or where its builders came from. Even if we couldn't answer who made those Lunar Pyramids, we'd still be allowed to infer that some kind of an 'Intelligence' had caused them to come into existence (and not natural processes alone). When making an 'Inference to Design', what many Historical Sciences do, such as Archaeology, Forensics, Cryptography, and SETI, one doesn't then need to come up with an 'explanation of the explanation' (in other words, an explanation of the Design Inference itself). So, to justify our inference that the Pyramids were intelligently designed, we wouldnt then need to come up with another explanation that told us about the beings that made them, where they came from etc.- and if we demanded an "explanation for an explanation" in this kind of enterprise, it would have disastrous consequences upon the Science that Dawkins holds so dear. Science would be cursed with an infinite regress problem, whereby every explanation would then need to be qualified by a further explanation, and that explanation by a further explanation, and so on, and so on, into absurdity. With that kind of methodology taken to heart, Science would surely be destroyed. So ID does not have to answer the "Who Designed the Designer Question"- it only needs sound physical evidence to make its Inference to Design valid. (just like if you found a computer software-program in the ground, you would be sound if you inferred that the program had come into being by some kind of an Intelligence, and not through natural processes alone (acted upon by either Law-like or Chance-Based Forces). Someone is sorely blind if they then demanded that you cannot infer that the program was Designed unless you can 1st explain the Being/s that made that program!

(But if one really wants to know "Who Designed God" (if they have Him in mind
when they hear "Designer")- then that question cannot be fully answered by Science; only by Philosophy (and easily enough): "God" is a necessarily-existing UnCaused/Un-Created Being, therefore, He has no "Designer" to Himself; rather, He is the Designer of Everything exterior to Himself; of all Existential Reality; all SpatioTemporal Existence. God made Time, so He must be Timeless Himself. Think about it from our perspective: because Time began Absolutely, there must necessarily exist an Eternal/Timeless Prime Reality that gave rise to It (Time/the 1st Event). That Timeless Prime Reality is the reason why Anything exists rather than Nothing).

22

The CFI: Since the designer is said to be beyond the realm of the
observable, claims about its existence can be neither supported nor undermined by observation or experiment. Therefore ID does not follow the scientific method of systematic observation and experiment, and fails as a scientific hypothesis.

Me:
So is ID's Design Inference sound? ID's main biological evidence is DNA's Digital Code embedded along every cell's nucleus, as well as certain completely-mapped-out molecular-machines found within the cell- and ID contends that an Intelligence of some sort can Best Causally Explain the origin of those Effects in question (and not Materialistic/Naturalistic Theories, either Necessity or Chance-Based). If the Design Inference "fails as a scientific hypothesis" then why does it use objectively verifiable data? (Digital DNA & Irreducibly Complex Nano-Molecular Machines) and a form of Abductive Reasoning like the rest of the Historical Sciences? If ID is not scientific, than neither is Darwinism, as Darwinism uses the same form of Abductive Reasoning: it uses empirical data (Presently-GivenEffects) to make inferences toward Past Un-Observable Causes. Also, if ID is not science, then it wouldn't be falsifiable, and most importantly, it wouldnt be able to make predictions, but it can, and it has made some astounding ones that have just recently been confirmed: ID says that by necessity most of the DNA sequence should have 'function', whereas Darwinists have said that much of it should be interspersed with useless 'junk-DNA' segments (if the result of a process of gradual random evolution). But new research has actually confirmed that those purported Junk-DNA regions are not in fact 'junk', but in fact perform crucial higher-order functions. http://www.evolutionnews.org/2010/07/junk_rna_found_to_encode_pepti036961.htm l. Dawkins' 2009 book, 'The Greatest Show on Earth', also incorrectly claimed that Junk DNA has proven Darwinism to be correct. Oh boy, what a mess he has gotten himself into. I wonder if he'll edit that out of his next edition? This prediction that "Junk-DNA is not in fact junk" was made by ID over 15 years ago, and in the end, they turned out to be right, and not the Darwinists (and validated thanks to physical evidence). How can ID not be a scientific theory regarding Junk DNA? Concerning Junk-DNA, ID showed that it could make verifiable observations and predictions that were then testable (hence, falsifiable)- and all thanks to rigorous experimentation.

The CFI: If, however, the Intelligent Designer is considered part of

the natural world, it is a form of life. In this case, ID has created a

23

problem bigger than the one it attempts to solve: life on Earth is explained by assuming the existing of a being far more complex and powerful, with no attempt to account for its origins.

Me:
Notice what they say at the end there? how ID assumes the existence of a being " far more complex and powerful, with no attempt to account for its origins"so thus it is not a proper theory? This is pure Dawkinism, taken out of the annals of the God Delusion (2006). Once again, a scientist making an Inference to Design with physical data to go off from does not need a further explanation for his explanation (another explanation that explains the Design Inference). If scientists working on the SETI project received radio-signals from deep space, and we asked them what 'Caused' them to arise, they could answer it 3 ways: by Chance, by Necessity, or by Design. After ascertaining that other Material-Based Hypotheses do not have the Causal Adequacy to generate the Information present in the signals, and after ruling out other natural factors like pulses from quasars, the scientists then make a Design Inference: saying, "the Best Explanation of those received deepspace signals is Intelligent Design". But then Dawkins and his CFI disciples enter and say, "no, you cannot Infer Design until you have given us an explanation on whomever sent those signals, and where they came from and how they arose in the Universe etc". The SETI scientists would then say, "no, I do not have to do that when inferring Intelligent Design! I know my job, so take a hike". Many critics of 'ID applied to molecular biology' say that one cannot infer that an outside 'Intelligence' made DNA because we have no proof of any other kind of Being/Intelligence that could do such a thing other than us humans. But that kind of logic would shut down SETI. The case for ID in biology concerns physical phenomenon (DNA & Molecular Machines) which were perhaps created by some kind of an Intelligence greater than human beings (could be aliens), but despite the fact that up until now Science has never confirmed the existence of any Intelligence higher than humankind- one can still justifiably infer that DNA was brought into existence by some kind of Intelligent Cause superior to humans- much how like SETI scientists would be warranted in inferring the existence of some Intelligence as being the Cause of some presentlygiven Effect (i.e radio-signals containing embedded information) even if they had no knowledge up until then of any other kind of Intelligence in the Universe superior to that of humans. To conclude: even though the "Designer of DNA" is something that we've obviously never before seen, and cannot be human, but something far greater- we can still nevertheless infer that DNA & certain I.C Molecular Machines were "Designed".

24

The CFI: "ID has created a problem bigger than the one it attempts
to solve: life on Earth is explained by assuming the existing of a being far more complex and powerful, with no attempt to account for its origins.

Me:
To say it another way: ID is a strict scientific theory, so therefore, it can only ever say, "we have detected Design". For example, if archaeologists found arrow-heads and pottery-shards in the ground, they could justifiably infer that they were the products of "Intelligent Design" after first assessing that Design Inference against other 'Natural Explanations' (i.e whether or not natural forces of erosion or other factors could have formed them). Using the principle of Multiple Competing Hypotheses, those archaeologists could show that the Design Inference has greater Causal Adequacy and can Best Explain the Presently-Given-Effects (the arrowheads and pottery shards). The archaeologists wouldn't then need to come up with another explanation for Dawkins, telling him about the beings that made them and left them there in the ground etc. To demand that, makes Dawkins sound childish: try and imagine someone in a high place of authority, making scientific decisions, with that kind of mind-set: "Uh, sir, we found a pile of old machinery on the back-side of the Moon". "Oh really, but why?" "Uh, I don't know why sir, but we've found some all the same". "But why?". "Uh, I don't know sir, I got to run; thought you'd be interested". Dawkins' supposedly-deadly "Who Designed the Designer?" mantra reveals him to be utterly oblivious to some key things elucidated in the Philosophy of Science: specifically, one does not need to "give an explanation of an explanation" when making an Inference to Design. So to end: if we asked for origins concerning the It/Thing that created DNA's Digital Code, how could we answer that? We only have physical evidence of DNA's Digital Code exhibiting Design, and though we wish it could, it cannot point us towards its Designer. Still, Design within DNA is antithetical to Darwinian Evolution; Darwinism is dead.

"ID has created a problem bigger than the one it attempts to solve: life
on Earth is explained by assuming the existing of a being far more complex and powerful, with no attempt to account for its origins

Me:
Dawkins popularized this idea in the 'God Delusion', and critics always bring it up: they say (to paraphrase): "the idea of God making all of complex Material Reality does not make sense because then God would need to be as complex & variegated as the Material Reality that He Created; so therefore, saying that "God Caused it" is meaningless and answers nothing". Now, let's stress that this Dawkin-ish retort is

25 aimed at those that invoke an Intelligence as being the Cause of apparent cosmological Design (the Cause of the Universe and its Fine-Tuning, which would have to be God as aliens couldnt do that)- but when it comes to invoking an Intelligence as being the Cause of DNA and Irreducibly Complex Molecular Machines, Dawkins' reasoning cannot apply. The critics cannot say, "DNA must have a creator that is as complex as DNA itself, so therefore, it is meaningless to ask if DNA was Designed". That sounds dumb, entirely; and indeed that kind of logic would shut down SETI. Obviously, if other Beings created our DNA, then they would have to be even more complex than us humans- so rather, this kind of criticism is usually launched against the idea of God being the Cosmic Designer. But that displays an un-appreciation of the Big Bang Model, and of the consensus now reached in current cosmology and astro-physics regarding it. When one tries to account for the Absolute Origin of all Space/Time/Matter/Energy somewhere in the finite past, then it becomes reasonably manifest what properties God would have to necessarily possess if He was the Cause of that (if He was the ultimate source of all Space/Time/Matter/Energy).

But now we're out of ID's territory, and into the realm of Theology and MetaPhysics (using philosophy conjoined with the latest advances in Big Bang Cosmology)- but this is a question that needs to be answered thoughApplying a 1st Cause to the Big Bang Singularity, or even a 1st Cause to the Multi-Verse (if one wants to presume that there was perhaps an even earlier stage to Reality, before our Big Bang)- reveals that 1st Cause to be a simple kind of Entity. Critics like Dawkins think that God must be ultra-complex, when strangely and loudly enough, the early church fathers and theologians always conceived of Him as being a very Simple Being. Why? Here's how to answer: God is an Immaterial Entity; He is the 1st Cause of all Space and Time, so therefore, He is Non-Spatial/Non-Physical and Timeless. That would make Him Changeless, as well as not made out of Matter and Energy (which always undergo physical change). God has Freedom of the Will, for He freely created Everything out of Nothing (and not out of Himself, for He is not Physical). This all makes God more like an Un-Embodied Mind of sorts, and a Mind is a simple thing: it is an un-extended, non-spatial substance, and it has no 'parts'. So God can be Simple yet create a Complex Material Reality; in fact, Material Reality demands a simple Source/Cause of it: the Absolute Origin of Everything/the Beginning of all Material Reality/of all Time & Space & Matter & Energy- requires a Prime Reality that Caused it to arise into existence that is Itself Timeless, Un-Caused, Non-Physical/Non-Spatial, Immaterial, and Changeless. That Prime Reality is in a way less complex and simpler than the Material Reality that existentially issued forth from it (sometime in the finite past). This analogy via Dr. William Lane Craig will help illuminate how God can be Simple and yet the Universe be Complex: for example, start thinking about calculus and infinite set-theory in your Mind: you may be thinking about something very complex, but the Mind itself thinking about it is still simple. Thus, the Ultimate 1st Cause of the Cosmos is plausibly a Simple Entity.

26

The CFI: "Since the designer is said to be beyond the realm of the
observable, claims about its existence can be neither supported nor undermined by observation or experiment. Therefore ID does not follow the scientific method of systematic observation and experiment, and fails as a scientific hypothesis".

Me:
The CFI said (to paraphrase them): "Because the Cause of this Presently-GivenEffect (DNA) is "beyond the realm of the observable", this means that any claims made about DNA's "Unobservable Cause" being an Intelligence will always be impossible to verify through "observation and experiment"- and thus, will never be Science" (in other words: "the Design Inference in molecular biology will never be a valid scientific hypothesis"). But this is an insane assertion! and shows clearly a lack of background philosophical knowledge of the Sciences, and what its various fields entail and aim for. ..First of all, I must stress that philosophers of Science, the people who in a way study Science better than the scientists themselves, incessantly stress how difficult it is to define what Science is. It has many different sub-fields contained within itself, and some employ very different aims and methodologies. Finding out the aims and criteria of Science thrusts one upon "the Demarcation Problem": whereby it becomes difficult to define what Science is if one is looking for an all-encompassing generalization as some of its sub-fields hold to different aims & forms of reasoning.

For example, some fields such as Physics and Chemistry seek out Natural Laws that describe processes in reality; however, in a much different pursuit, the Historical Sciences seek out Past Causes to Presently-Given-Effects, and those Past Causes are of course, Un-Observable to us now. So to give some examples: Archaeologists, they can't see who left spear points and other artifacts in the ground thousands of years ago; Paleontologists, what happened to the dinosaurs; Geologists, observe the processes in the past that are responsible for geological features seen today; and Darwinian Evolutionists, can never observe the process of undirected chemical evolution that led to the first Life on Earth, nor its foundational mechanism of

27 Macro-Evolution. So, in short, the Historical Sciences never directly observe the 'Cause' of a Presently-Given-Effect', rather, they must infer it using Abductive Reasoning: one uses empirical data (a Presently-Given-Effect), and then makes an inference towards its most likely Past Causal Factor (and that Past Cause is UnObservable (it is all about looking backwards, hence why they're called 'Historical Sciences')). Clearly, Physics and Chemistry are not concerned with that, as they're all about Natural Laws and Inductive Reasoning; but many people assume that Science is solely pre-occupied with figuring out Natural Laws and predicting how things will happen, and that crucially neglects the Historical Sciences and the valid Abductive Reasoning that they all employ. Remember what the CFI claimed?: that we can't have a valid hypothesis based on an Un-Observable Cause because that Cause can't be verified through observation & experimentation?- well, many disciplines in Science are all about inferring an Un-Observable Past Cause to a Presently-GivenEffect! so, if Science followed what the CFI demanded, the Historical Sciences would vacuously collapse with a bang! The CFI and other critics along a similar vein fail to realize that the case for I.D in biology uses the same Abductive Reasoning and Methodology that Darwinism uses.

Here are some common accusations leveled at the theory of Intelligent Design that critics say disqualify if from being accepted as a valid and proper scientific theory. Actually, if these charges correctly dictate what constitutes an improper scientific theory- then Darwinian Evo. and others will also be disqualified from being Science!

1) "It invokes an Un-Observable Entity". 2) "It is not testable". 3) "It doesn't explain by reference to Natural Law". 4) ""It makes no predictions". 5) "It is not falsifiable". 1) "It Invokes An Un-Observable Entity": so, does reference to an UnObservable Cause provide good reason to say that a theory is "un-scientific"? In fact, that criteria would render many other scientific theories "un-scientific"! The Historical Sciences are all about inferring Un-Observable-Past-Causes from

28 Presently-Given-Effects, and if we held to the criteria that a theory is "un-scientific" if it posits Un-Observable Causes/Entities to account for Presently-Given-Effectsthen say good-bye to all of the Historical Sciences! (including Darwinism). But also, say farewell to Physical Forces, like Electro-Magnetism and Gravity Fields, as well as Physical Entities, such as Atoms, Quarks, and Bio-Molecular Structures (all those things listed are Un-Observable Causes inferred from Presently-GivenEffects). Other critics say, "you cannot infer an Intelligent Cause/a Mind, but rather only a Material/Natural Cause"- but that is also ludicrous! and would demolish fields such as Archaeology, Cryptography, Forensics, and SETI: whose sole aims are inferring Intelligence as the Un-Observable-Past-Cause to a Presently-Given-Effect.

#2) "It Is Not Testable": If empirical considerations can refute I.D, or support
it, then it is testable. If a scientist asserts that DNA or certain Irreducibly Complex Molecular Machines were "Designed", and DNA and those I.C protein-machines are physical (in other words, are empirical evidence)- then another scientist can test that hypothesis by studying them & ascertaining if they exhibit signs of Design or not.

#3) "It Doesn't Explain By Reference To Natural Law": This is

confusing the aims of particular scientific fields! Explanation by reference to Natural Law is the aim of Natural Sciences, like Physics or Chemistry, not the Historical Sciences though. Physics & Chemistry seek to explain or describe something by Natural Law (a very broad enterprise), whereas the Historical Sciences are focused on a much more specific question: namely, what was the Un-Observable Past Cause to some Presently-Given-Effect. For example, Newton 'described' "Gravitational Attraction" by reference to Natural Law, but he didn't explain what 'Caused' itThe strict sciences seek to only describe or predict Forces/Processes by way of Natural Law, but the Historical Sciences, in a much different vein, try to find out what Caused specific Effects to happen. The case for the theory of Intelligent Design, and the methodological reasoning it employs, clearly situates it as a

29 Historical Science: it uses Presently-Given-Effects (Observable Evidence), such as DNA & I.C Molecular Machines, and then assesses various Material-Based Hypotheses (using the principle of Multiple Competing Hypotheses) to see if they have the Causal Adequacy to account for their origins, and then after ruling out their formation to Chance or Necessity-Based Forces/Causes, the scientist can then justifiably infer that Intelligent Design "Best Explains" them. When it comes to explaining the origin of biological information, ID has the most Causal Adequacy, and not other Material-Based Theories. The idea that only Minds can create Information is not an abstract hypothesis, indeed, we have 3 pieces of evidence to confirm it: 1) our present experience of causal reality always shows Information arising through some Mind/Intelligence, and we have never seen otherwise (whether it be music symbols, codes, written languages, software programs), 2) experiments from 2010 showed that Intelligent Guidance/Design (via the experimenters) is needed to create new information, and 3) see 'the Law of Conservation of Information' (which states that Natural Laws can only transmist Info., not create it).

#4) "It Makes No Predictions": Utterly wrong, as supposed JUNK-DNA

ended up showing otherwiseIn the 90s, Darwinists were clamoring that empirical Junk-DNA confirmed their predictions of gradual and random evolution (because if evolution was a diddly-piddly process of trial and error, then the gene sequences of organisms should be replete with old junk (meaning some of the amino acids in the DNA sequence should be "non-coding regions" and perform no function). However, new discoveries in the past 4 years have blown that assertion out of the water. It now turns out that almost all of that supposed junk, all of those non-coding regions, actually perform crucial higher-order functions within the cell. That was an initial 15year old prediction that I.D made, then the Darwinists countered with their own, and thought it was confirmed for a few years, but in the end, I.D's prediction has gotten solidly confirmed. The supposed Junk-DNA/Non-Coding regions of the nucleotide base-sequence have now been proven to have these functions: 1) directs the function of RNA molecules that regulate the use of the protein coding regions of DNA 2) regulates DNA replication 3) regulates transcription 4) marks sites for programmed rearrangements of genetic material 5) influences the proper folding and maintenance of chromosomes 6) controls the interactions of chromosomes with the nuclear membrane and matrix 7) controls RNA processing, editing, and splicing 8) modulates translation 9) regulates embryological development 10) repairs DNA 11) aids in immuno-defense and fighting disease.

What about future predictions? Here are 10 major ones, which will either be validated or falsified through research in the not-too-distant future (from Stephen

30 Meyer's 'Signature in the Cell' pg. 496): "1: No undirected process will demonstrate the capacity to generate 500 bits of new information starting from a nonbiological source 2: Informational accounting will reveal that sources of active information are responsible for putatively successful computer-based evolutionary simulations 3) Future experiments will continue to show that RNA catalysts lack the capacities to render the RNA-World scenario plausible 4) Informational accounting will reveal that any improvements in replicase function in ribozymes are the result of active info supplied by ribozyme engineers 5) Investigation of the logic of regulatory and info-processing systems in cells will reveal the use of design strategies and logic that mirrors (though possibly exceeds in complexity) those used in systems by engineers. Cell biologists will find regulatory systems that function in accord with a logic that can be expressed as an algorithm. 6) Sophisticated imaging techniques will reveal nano-machines (turbines) in centrioles that play a role in cell division. Other evidence will show that malfunctions in the regulation of these machines are responsible for chromosomal damage. 7) If I.D played a role in the origin of Life, but not subsequently, prokaryotic cells should carry amounts of genetic info that exceeds their own needs or retain vestiges of having done so, and molecular biology should provide evidence of information-rich structures that exceed the causal powers of chance, necessity, or the combination of the two 8) The Fossil record, in particular, should show evidence of discrete infusions of information into the bio-sphere at episodic intervals as well as a top-down, rather than a bottom-up, pattern of appearance of new fossil forms 9) If the Flagellar Motor was intelligently designed and the Type-3 Secretory System devolved from it, the genes that code for the bacterial flagellar motor should be older than those that code for the proteins in the T3SS, and not the reverse. Alternatively, if the T3SS and the Flagellar motor arose by design independently, T3SS should have unique (nonhomologous) genes that are not present in the genome for the flagellar motor 10) The functional sequences within amino acid-sequence space should be extremely rare rather than common".

#5) "It's Not Falsifiable": the Design Inference at the bio-molecular level is
definitely falsifiable. The Darwinists brashly contended in the early 1990s that they had indeed falsified the Inference to Design at the level of DNA thanks to all of the supposed-Junk-DNA evidence rolling in (which was physical and empirical by the way- thus making the inference to Design at the bio-molecular level falsifiable). Other critics, Ken Miller especially, thought that the T3SS had falsified the claim that the flagellar motor was Irreducibly Complex; however, when further genetic analysis was completed in 2004, it turned out that the genes of the flagellar motor were older than the genes of the T3SS- thus, the T3SS could not have been a pre-cursor to the flagellar. The inference to Design in the Cell based on Irreducible Complexity in certain protein machines could have been falsified, but further research validated it!

31

The CFI: "ID is religious in nature, being a modern form of

Creationism, which is itself derived from a literal and fundamentalist interpretation of the biblical book of Genesis".

Me:
In fact, I.D and Creationism are fundamentally opposed to each other, and there is nothing in Genesis that has contributed to our scientific case for Design in molecular biology. Genesis is Literature, not ScienceHere's why I.D and Creationism are miles apart from each other: I.D follows the methodology of "Uniformitarianism", first propounded by Darwin's mentor, the geologist Charles Lyell (1797-1875). Lyell famously said that "the present is the key to the past"- meaning, that when looking for the Past Cause to a Presently-Given-Effect, utilize Causes that are still in operation Today (that have the demonstrated causal ability to produce the Effect in question)- otherwise, we'd be really second guessing. So what is the Cause that I.D cites? Intelligence. And is Intelligence still in operation today? Yes; and in our present experience of reality, we only ever observe it (Intelligence) creating specified information. Creationists, however, would rather cite Past Causes that are no longer operating in the Present, and that we have no experience of. Creationism says, "God did it", ID, "it was an Intelligence"- one theory is definitely more scientific than the other.

"Intelligent Design and Creationism Just Aren't the Same" (2002) by Dr. Jonathan Wells: http://www.discovery.org/a/1329

The CFI: Conclusion: Up until today (November 2010), the ID

movement has not published a single peer-reviewed article in a recognized scientific journal.

Me:
Wow! If that isn't a lie, than I cannot read. Here's a link to over 50 PhD peer-reviewed papers about ID in biology, as well as some university-press peer-reviewed ID books!

32

Why is the CFI shielding the public from I.D with such an outrageous statement like that? Are they just outdated and uninformed? The CFI's anti-ID-manifesto has made some major errors, and that quote about there being "no peer-reviewed articles in a recognized scientific journal" about ID in biology is wholly inaccurate. It only ends up confirming how strong the case for Intelligent Design in Molecular Biology is today. Check out this huge list of articles & books: http://www.discovery.org/a/2640.

Here Are Some Major Experimental Papers That Are Backing Up The Design Inference In Molecular Biology: On 'Biological Information'
'The Code Within the Code' - 'Nature 2010': http://www.nature.com/news/2010/100505/full/465016a.html.
The 2nd genetic code was announced in May 2010 by the U. of Toronto, not a new Variant Coding Convention, which are up to 17 right now- but specifically, a newfound code within the old code (suggesting a kind of hierarchical logic at work!). The researchers were able to crack the code within the code using specially tailoredmade code-breaking software. Arguably the greatest scientific discovery of the past fifty years, the finding was made public on May 6th in the journal 'Nature'. The code within the code is staggeringly complex, & it directs many key processes in the Cell.

'Deciphering the Second Genetic Code'- 'Science Interviews 2010':

http://www.thenakedscientists.com/HTML/content/interviews/interview/1327/ This is an interview with Dr Yoseph Barash of the University of Toronto, who found the code within the code (the code allows & directs alternate splicing within genes).

'Scientists Create Artificial Life' - 2010:

http://www.associatedcontent.com/article/5409946/scientists_create_artificial_life_a. html This major story from 2010 is about how Craig Venter`s team in the UK got a cell's processing system to accept newly-created genetic information when it was introduced into its nucleus; and without a doubt (but lost on many Darwinists,

33 Naturalists, Atheists, and general Science lovers) this experiment showed that Intelligent Agents are needed to create new biological information for the cell.

On 'Junk-DNA Not Being Junk'

'The Myth of Junk DNA' (2011):
http://www.mythofjunkdna.com/. This new book collects together every paper done about Junk-DNA in the past decade, and shatters the myth that it is junk. 2011 was indeed the year when Junk-DNA was finally put to rest, and when an even more complex picture of the cell and DNA emerged: the purported 'junk' (the non-codingregions in DNA) have been shown to perform many crucial higher-order functions. Watch 'The Myth of Junk DNA' trailer on You-Tube.

''Junk' DNA Has Important Role, Researchers Find' (2009):

http://www.sciencedaily.com/releases/2009/05/090520140408.htm. Here researchers say that Junk-DNA in a pond organism is not junk after all, and appears to be doing paramount duties, like directing how the organism grows! This is a key finding because it perhaps hints at how the Body Plan Enigma of molecular biology might be solved one day. The Body Plan Enigma refers to the mystery regarding how the organism develops; and the information that must direct that is not found within the coding-regions of the DNA sequence (as they are solely for protein construction). Enter supposed-Junk-DNA, it may provide the key to the Enigma. The information directing the development of an organism (which is utterly important) may be contained within those non-coding-regions (inside the 'Junk') - and the fact that the 'Junk' in this pond organism's DNA regulated its development, seems to suggest that.

'Redundant Genetic Instructions in Junk DNA Support Healthy Development' (2010):

http://www.sciencedaily.com/releases/2010/07/100716125835.htm. Another paper showing crucial functionality within the Junk-DNA of a fruit fly: the Junk-DNA has a hand in its development, and is responsible for turning certain genes on and off!

'Junk DNA' Defines Differences Between Humans and Chimps' (2011):

http://www.sciencedaily.com/releases/2011/10/111025122615.htm. A seminal paper that sheds light on the Body Plan Enigma, and perhaps lays to rest the common claim that we evolved from apes because our genetic sequence is so similar to theirs. That overblown similarity is found within the coding-regions of DNA used for protein construction, but proteins are not everything. Arguably something even more important would be the information needed to determine how the organism looks and develops, & Junk-DNA may be responsible for why we look so different from apes, despite the protein coding-regions of our DNA being similar.

34

'Francis Collins Changes His Tune On Junk DNA (2010)':

http://www.uncommondescent.com/intelligent-design/francis-collins-changes-histune-on-junk-dna/.

On 'Evolution and the Origin of Life'

'Michael Behe's Critiques Richard Lenski's E. Coli Evolution Experiments' (2010):
http://www.evolutionnews.org/2010/12/michael_behes_quarterly_review041221.html This is about Michel Behe's 2010 paper focusing on Richard Lenski's famous evolution-experiment with E-Coli bacteria (going on for decades, since 1998). Lenski's study is the longest-ever running experiment in the history of evolutionary biology, and after growing 50, 000 generations of bacteria, what has happened? any new digital information being added to the genomes of these bacteria? (thus demonstrating that natural processes can produce under Natural Selection the digital information needed to build major adaptations and new and novel animal forms?). What Behe found was that no new digital information was ever created, rather there was only a "re-arrangement" or "deletion" of already existing functional genetic information, thus all observed adaptive mutations constituted either a loss or modification--but not a gain--of Functional Coding Elements (FCTs). In Dawkins news again: Lenski's work was cited by Dawkins in his most recent book 'The Greatest Show on Earth' (2009) as the ultimate refutation of Irreducible Complexity. Strange, because Dawkins seems totally unaware of Behe's critiques of Lenski's research in his 'The Edge of Evolution' (2008), and now Dawkins' book is even more out-dated as Behe has published a peer-reviewed article in the "Quarterly Review of Biology" (2010) that goes even deeper into Lenski's research. Behe's conclusion is damming to the Neo-Darwinian Hypothesis, and surely as well, to Dawkins' ego.

'Is the Origin of Life in Hot Water?' (2010):

An article about a paper on the problem of the Origin of Life that appeared in the Proceedings of the National Academy of Sciences: http://www.evolutionnews.org/2010/12/is_the_origin_of_life_in_hot_w041311.html

'New BIO-Complexity Paper Shows Many Multi-Mutation Features Unlikely to Evolve in History of the Earth' (2011):
http://www.evolutionnews.org/2011/01/biocomplexity_paper_shows_man042611.html.

On the 'Bacterial Flagellum'

"Genetic Analysis of Coordinate Flagellar and Type III Regulatory Circuits" (2004):
http://www.discovery.org/scripts/viewDB/filesDB-download.php?id=389.

35 This 2004 conference paper about the flagellum underwent peer-review in order to be in the proceedings. In it, Minnich & Meyer do 3 things: 1) they refute a popular objection to Behe's argument for I.C in the flagellum. 2) they suggest that the T3SS is not an intermediate to the flagellum, but represents rather a degenerate form, and 3) they argue that Intelligent Design is better than the Neo-Darwinian mechanism when it comes to explaining the origin of the bacterial flagellum's 30+-part rotary-engine.

Videos and Debates to Check Out:

'Intelligent Design?' (a 2006 debate between Stephen Meyer & Peter Ward): http://www.youtube.com/watch?v=naGMex003SY. 'Darwin vs. Design DNA' (2 min): http://www.youtube.com/watch?v=zHXMbFo0zro. A Video Introduction to Signature in the Cell by Dr. Stephen Meyer (3 min): http://www.youtube.com/watch?v=TVkdQhNdzHU. "Journey Inside the Cell" (3 min): http://www.youtube.com/watch?v=1fiJupfbSpg&feature=related. "R.C Sproul Interviews Dr. Stephen Meyer" (2010): http://www.youtube.com/watch?v=kVHZrSuXZkY&feature=related. "Stephen Meyer & Richard Sternberg Impressively defeat Michael Shermer & Don Prothero on Evolution" (2010): http://www.youtube.com/watch?v=z0fR5IvsjJY. Watch a great 'Creation vs. Evolution' debate on the 'Michael Corren Show' here: http://www.youtube.com/watch?v=wr6uvUNJLww. "Is Intelligent Design Viable?" - a debate between Dr. William Lane Craig and Dr. Francisco Ayala (2009): http://www.youtube.com/watch?v=-jLNMBTlwYI.