Darwinian Evolution Is Dead: Defending 'Intelligent Design' - By Joseph Gallagher

8/3/2019 Darwinian Evolution Is Dead: Defending 'Intelligent Design' - By Joseph Gallagher

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"Intelligent Design":DefendingI.D in MolecularBiology 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 particularweb-page that attempts to refute the theory ofIntelligent Design in molecular

biology. Their one-page manifesto onIntelligent Design totally fails, and I willexamine it in detail, and show howI.D can easily withstand all of their criticisms.

Here is theiranti-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 andcertain I.C Molecular Machines could only have ever arisenvia 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 firstLife onEarth. The question of the origin ofbiological 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 everycellupon Earth). DNA is digital

information, and it employs multiple codes for storing and transmitting that info- sowhere did that info. come from? In fact, we only have 3 choices: 1:by Chance: from

chance processes of chemicals 2:by Necessity: via someLaw of Nature, like aLaw

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.
http://extraordinarybus.wordpress.com/2010/09/21/intelligent-design/http://extraordinarybus.wordpress.com/2010/09/21/intelligent-design/http://www.signatureinthecell.com/http://www.signatureinthecell.com/http://www.signatureinthecell.com/http://www.signatureinthecell.com/http://www.signatureinthecell.com/http://www.signatureinthecell.com/http://extraordinarybus.wordpress.com/2010/09/21/intelligent-design/


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

"The Claims:

"Intelligent design (ID) is the proposition that some features of life on Earth werecreated 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 theycould not have evolved gradually: they must have been created as fully functional

wholes.

The Evidence:

Claimsof irreducible complexity have beenshownto befalse. 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 thedesigner 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 forits origins.
http://www.millerandlevine.com/km/evol/design2/article.htmlhttp://www.millerandlevine.com/km/evol/design2/article.htmlhttp://www.ncbi.nlm.nih.gov/pubmed/11520608http://www.ncbi.nlm.nih.gov/pubmed/11520608http://www.ncbi.nlm.nih.gov/pubmed/11520608http://jb.asm.org/cgi/content/full/181/23/7149http://jb.asm.org/cgi/content/full/181/23/7149http://jb.asm.org/cgi/content/full/181/23/7149http://jb.asm.org/cgi/content/full/181/23/7149http://www.ncbi.nlm.nih.gov/pubmed/11520608http://www.millerandlevine.com/km/evol/design2/article.html


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Conclusion:

Up until today (September 2010), the ID movement has not published a single peer-

reviewed article in a recognized scientific journal. ID is religious in nature, being a

modern form ofCreationism, 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 theYoung Earthhypothesis.

Links:Wikipedia Entry on Intelligent Design;Skeptics Dictionary Entry on

Intelligent Design;The Flagellum Unspun: The Collapse of Irreducible

ComplexityMiller, K. 2004;Bacterial Flagella and Type III Secretion Systems

Aizawa, S.-I., 2001;The Bacterial Flagellum: Reversible Rotary Propellor and Type

III Export ApparatusMcNab, 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, theirmost recent source was an article via biologistKen Miller (2004), who was prominent

in the 'Dover debacle' (2005)- and I will deal with him specifically up ahead and

show that his argument againstID 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 latestDNA developments, these 2

papers are key. It seems the CFI is oblivious to the fact that DNA isExtraordinary!

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).
http://extraordinarybus.wordpress.com/2010/09/21/creationism/http://extraordinarybus.wordpress.com/2010/09/21/creationism/http://extraordinarybus.wordpress.com/2010/09/21/creationism/http://extraordinarybus.wordpress.com/2010/09/21/young-earth/http://extraordinarybus.wordpress.com/2010/09/21/young-earth/http://extraordinarybus.wordpress.com/2010/09/21/young-earth/http://en.wikipedia.org/wiki/Intelligent_designhttp://en.wikipedia.org/wiki/Intelligent_designhttp://en.wikipedia.org/wiki/Intelligent_designhttp://www.skepdic.com/intelligentdesign.htmlhttp://www.skepdic.com/intelligentdesign.htmlhttp://www.skepdic.com/intelligentdesign.htmlhttp://www.skepdic.com/intelligentdesign.htmlhttp://www.millerandlevine.com/km/evol/design2/article.htmlhttp://www.millerandlevine.com/km/evol/design2/article.htmlhttp://www.millerandlevine.com/km/evol/design2/article.htmlhttp://www.millerandlevine.com/km/evol/design2/article.htmlhttp://www.ncbi.nlm.nih.gov/pubmed/11520608http://www.ncbi.nlm.nih.gov/pubmed/11520608http://www.ncbi.nlm.nih.gov/pubmed/11520608http://jb.asm.org/cgi/content/full/181/23/7149http://jb.asm.org/cgi/content/full/181/23/7149http://jb.asm.org/cgi/content/full/181/23/7149http://jb.asm.org/cgi/content/full/181/23/7149http://jb.asm.org/cgi/content/full/181/23/7149http://www.ncbi.nlm.nih.gov/pubmed/12540920http://www.ncbi.nlm.nih.gov/pubmed/12540920http://www.nature.com/news/2010/100505/full/465016a.htmlhttp://www.nature.com/news/2010/100505/full/465016a.htmlhttp://www.nature.com/news/2010/100505/full/465016a.htmlhttp://www.ncbi.nlm.nih.gov/pubmed/12540920http://jb.asm.org/cgi/content/full/181/23/7149http://jb.asm.org/cgi/content/full/181/23/7149http://www.ncbi.nlm.nih.gov/pubmed/11520608http://www.millerandlevine.com/km/evol/design2/article.htmlhttp://www.millerandlevine.com/km/evol/design2/article.htmlhttp://www.skepdic.com/intelligentdesign.htmlhttp://www.skepdic.com/intelligentdesign.htmlhttp://en.wikipedia.org/wiki/Intelligent_designhttp://extraordinarybus.wordpress.com/2010/09/21/young-earth/http://extraordinarybus.wordpress.com/2010/09/21/creationism/


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The theory ofIntelligent Design viabiology 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 theDesign-Inference easily holds, as

Science already uses it for many fields in the Historical Sciences!

Thebiological case for Design concerns the origin of theDigital Code(s) found in

DNA, and also, how certainIrreducibly 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 partsarranged together in a specific temporal sequence to even

work at all!).

But again, I must stress thatID can only say that "we have detected Design"- muchlike archaeologists, forensic scientists, cryptographers, or scientists working onSETIdoID 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 easilyevident from the reams of digital codes which constitute the very basis ofLife itself).

The CFI Article: Some features of biological organisms areconsidered 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 cannotfunction 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 regardingmolecular

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 inferringDesign based on

thedigital information found within theDNA molecule (Complex Specified

Information that could only have ever arisen via an 'Intelligent Cause' of somekind):http://www.signatureinthecell.com/.
http://www.signatureinthecell.com/http://www.signatureinthecell.com/http://www.signatureinthecell.com/http://www.signatureinthecell.com/


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Meyer's ideas first went public in 2004, when he wrote that no materialistic theory

can account for the origin of thebiological 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 ofdigital

code are needed). So where did thisbiological information come from? Using a formofAbductive Reasoning, like Darwinism and the rest of the Historical Sciences,

Meyer argues thatInformation can only ever come into existence via anIntelligent

sourceof 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-BasedTheories regarding the origin of DNA, and to disprove the

contention that DNA could only have come from anIntelligent Source, we need tosee proof thatInformation 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 ofcausal reality constantly confirms that Information (be it a

software code, languages, or sheet music etc.) can only ever come from aMind/Intelligence (not natural processes ofMatter and Energy).Information never

comes fromNature, but rather fromMinds. Information is an entity entirely

different from physical forces ofMatter andEnergy (i.e - Information is not the ink).

This is the insurmountable problem forNaturalism/Materialism: Matter and Energyby itself can never causeInformation (esp. highly-specified codes) to come into

existence, only anIntelligence/Mindcan. If one maintains otherwise, that

Information can arise from just Matter & Energy alone (without anIntelligence

being involved), then they're basing that solely onFaith, 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 ofMicro-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 anIntelligentsource of some kind, and not natural/physical processes ofMatter & Energy alone.
http://www.discovery.org/a/2177http://www.discovery.org/a/2177http://www.discovery.org/a/2177http://www.discovery.org/a/2177


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

Chance-Based or even Necessity-Based Processes ofMatter and Energy alone couldnever have produced Complex Specified Information. Necessity-Based Law-like

forces produce patterns and redundancy, not complex specificity & irregularity(whatDNA entails). It is sound to infer that anIntelligence has played a part in the

origin of DNA's digital code(s) as our repeated and uniform experience ofcausalreality 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 ofotherA/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 isdigital instructions for building every known celluar nano-

protein machine on Earth, andInstructions/blue-prints = Information.Matter &Energy alone can never cause Information to come into existence, only a

Mind/Intelligence can! How come the CFIrefuses to even mentionDigital DNA?!

This is not an 'Argument from Ignorance', where we're authenticating I.D solelybecause Materialism cannot explain the origin ofbiological 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 ofbiological informationdoes 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 mostcausal adequacy ,

which best explains the origin of theEffect in question). So we compare theDesign

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 mostcausal adequacy is then chosen as theBestExplanation concerning the origin of the digital information within DNA and the

cell's information-processing system. So I.D'sDigital-DNA-Argument goes:

Premise 1:Despite a thorough search, no material causes have been discoveredthat demonstrate the ability to produce Complex Specified Information.

Premise 2:Intelligent Causes have demonstrated the power to produce largeamounts ofComplex Specified Information.

Conclusion:therefore, I.D constitutes the best, most causally adequate explanationregarding the origin of DNA's digital code.

That cannot be an 'Argument from Ignorance', it is anInference to the BestExplanation- a mode of argumentation used by all of the Historical Sciences.


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The CFI Article: Claims of irreducible complexity have beenshown 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 bacterialflagellum as an evolved type III secretory apparatus (McNab 1999,

Aizawa 2001).

Me:

First: they totally misrepresent the concept ofIrreducible Complexity (also what

Ken Miller does) as they claim that theBacterial flagellum (with its 30-part rotary

engine) "can still functionwithout some of its parts"- but sorry, that issimply not true: for if even one single part is removed from that30+-part rotary-

engine, over-all function in that system becomes impossible (just like if you were toremove a single piece from a mouse-trap; then the whole thing would cease to work).

Then the CFIgoes 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 thebacterial flagellum lost some of its parts (which would necessarily destroy over-allfunction 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 longerbe a bacterial flagellum in the slightest! and 2) that still does nothing to refute the

Inference to Design based onI. Cwithin the flagellum's 30+-part-rotary-engine.
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Bio-ChemistDr. Michael Behe first came up with the concept ofIrreducible

Complexity inmolecular 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 theseIrreducibly Complex Nano-Molecular

Machines found within the Cellis (to paraphrase): "throughNatural Selection, theseIrreducibly Complex Nano-Molecular Machines were built up from smaller sub-

systems" (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 theDesign Inference in biological systems based on

Irreducible Complexity within the flagellum's rotary-engine, and they only useKen

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 thefunctional parts of other simpler systems, and his purported smoking-

gun 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 thebacterial flagellum. For Miller, the key thing is that the T3SS is usually found inside

other bacterium, so he therefore assumes that the T3SS is anancestor or precursor-

system to thebacterial 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 MILLER-By Dr. William A. Dembski, 2.17.03, v.1" (2004):

http://www.designinference.com/documents/2003.02.Miller_Response.htm.
http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.designinference.com/documents/2003.02.Miller_Response.htmhttp://www.designinference.com/documents/2003.02.Miller_Response.htmhttp://www.designinference.com/documents/2003.02.Miller_Response.htmhttp://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496http://www.amazon.com/Debating-Design-Darwin-William-Dembski/dp/0521829496


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Ken Miller Is Missing 3 Key Things

1) he doesn't mention the mysterious composition of the bacterial flagellum: it hasover20 other unaccounted forprotein parts.

2) If usingNatural Selection, Miller fails to recognize how all of the rotary-engine's protein-parts would have needed to have been assembled in theright

temporal sequence (if to attain over-all function).

3)he 'Begs the Question' (specifically: he forgets that every time we observe theselittle nano-protein-machines getting assembled inside the Cell, like cars on a factory

floor- it is solely thanks toDNA'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 ofIrreducible 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 aneven 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+ otherproteins 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's30+-part rotary-engine originated!

#2) The Assemblage Problem:

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


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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 ifall 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 aSPECIFIC TEMPORAL SEQUENCE (similar to the way an automobile is assembled

in a factory, or setting up a mouse-trap)- and that simply cannot happen withNatural

Selection under Neo-Darwinism. And why not? Because Natural Selection is onlysupposed 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, butpertinently, 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. NaturalSelection underNeoDarwinism is supposed to be a blind and undirected process

having no 'end-goal-in-sight'; it can only develop new adaptations that function andbenefit the organism immediately. It cannot 'save' non-functional things for down theroad; surely, that bespeaks ofForesight & 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 ofDNA-RNA-Protein-Reciprocity isitselfIrreducibly Complex! On a side note, this is what is known as the massive


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'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 whichone came first? The 'RNA World Hypothesis' has attempted to solve this paradox

becauseRNA acts as a 'go-between', but this theory still does nothing to explain the

origin of the biological information in RNA (it onlyBegs the Question and assumes

the existence ofComplex Specified Information). For how did the RNA molecule'samino acids ofA, T, C, and U become arranged into complex-information-richsequences? In fact, at bottom, but under Miller's assumed gaze, 'Co-option' theories

only explain Irreducible Complexity by assuming Irreducible Complexity! What Imean is that Miller takes for granted the fundamental DNA-RNA-Protein-

Reciprocal-System that makes and directs all activities within the Cell; it is itselfIrreducibly 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 TheBacterialFlagellum Could Not Have Evolved From The T3SS:

To put to rest the notion that the bacterial flagellum evolved from the T3SSmolecular-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 Flagellummotor' and the 'Type-3 Secretory System'/Molecular

Syringe/Pump) has revealed that the flagellum arose first, and then the T3SS camelater. The pump evolved from the motor, not vice-versa! M. Behe now stands verified.
http://www.sciencedirect.com/science/article/pii/S0966842X04000174http://www.sciencedirect.com/science/article/pii/S0966842X04000174http://www.sciencedirect.com/science/article/pii/S0966842X04000174http://www.sciencedirect.com/science/article/pii/S0966842X04000174http://www.sciencedirect.com/science/article/pii/S0966842X04000174http://www.sciencedirect.com/science/article/pii/S0966842X04000174http://www.sciencedirect.com/science/article/pii/S0966842X04000174http://www.sciencedirect.com/science/article/pii/S0966842X04000174


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Miller's ObjectiontoIrreducible ComplexityTotally Fails

Ken Miller insists that the T3SS refutes Behe's claim that the flagellar motor isIrreducibly 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 outsideof that system, and have another function! Therefore, the Bacterial Flagellum isnot irreducibly complex!" Sorry Miller, all Behe is saying is that (and this is thestrict concept of I.C) (paraphrasing again): "if you remove one part from an

Irreducibly Complex system, you will lose function IN THAT SYSTEM, nothingmore". Miller's objection/refutation totally misrepresents the strict concept ofI.C.

In Conclusion Regarding Behe and 'Irreducible Complexity':

The critics' theory of'co-option' underNeo-Darwinism, which is an Undirected

Process, does not provide a better CAUSALLY ADEQUATE EXPLANATIONfor

the origin of the flagellum'srotary-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
http://www.evolutionnews.org/2011/03/michael_behe_hasnt_been_refute044801.htmlhttp://www.evolutionnews.org/2011/03/michael_behe_hasnt_been_refute044801.htmlhttp://www.discovery.org/a/14791http://www.discovery.org/a/14791http://www.discovery.org/a/14791http://www.evolutionnews.org/2011/03/michael_behe_hasnt_been_refute044801.html


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Some 'Facebook-Bacterial Flagellum-Criticism'

Critic:

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

Me:

"It is not anArgument from Ignorance. AnArgument from Ignorance is all about

validating one idea simply based off thecasual inefficacy of another idea, yet without

citing anyPositive Evidence to support your own idea. In fact, certain molecular

protein-machines being I.C is based on what we know, not what wedo 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-trapIrreduciblyComplex? Yes it is, and the same with the bacterial flagellum; and just like with a

mouse-trap, to attainover-all function, all of the parts to the flagellar motor must beassembled 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 thatencompass itsrotary-engine- it would cease to function. But if to attainover-all

function, all of its parts must be assembled in the right temporal sequence, then how

could it have attainedover-all function throughNeo-Darwinism? which is supposed

to be a process that only uses changes thatbenefit the organism immediately? having

noForesight? 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- theDesign 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 theFlagellum (of course DNA is as it embodies the Bacterial Flagellum'sInstructions)-


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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 togetherunder 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'tif an out-board-motor type-unit iscomposed 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 ofDNA does tell us how the level of cellular nano-machinery cametogether, 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 ofbiological 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 plantsand 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 withinDNA! So they're simplyBegging the Question by claiming that similarities between

various organisms' DNA-Sequence prove that Darwinian Evo. is true, and ID, false.


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Truly, when it comes to explaining the formation ofDNA and how its astronomically-

long chain of amino acids could have come together (the smallest bacterium on Earth

have chains of500,000 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 hasattained Function (aka. the ability toReplicate/Copy itself). Natural Selection could

only have ever emerged onto the scene after DNA firstbecameFunctional; only then

would the DNA molecule have been able to record and pass on any changes, thusallowing Darwinian Evo. by the mechanism ofNatural 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, theorigin

of Life (in other words)- Neo-Darwinists/Naturalists/Materialists can only appeal to

either 'Necessity-Based Theories' or 'Chance-Based Theories'. The most classicNecessity-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-sequencehad come together into a sequential arrangementdue 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, G-

never 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 inDNA. 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 onlyproduce patterns (as they ensure that the sameEffect is repeated if given the same


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conditions) - so one should see mostly redundancy and repetition characterizing

DNA's amino-acid sequence ifNecessity-Based ForcesCausedit to form.However, Chance-BasedForces produce Effects that are random, which means that

theEffects 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 ofChance). 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 ofDNA without firstaddressing 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'reassuming it means: namely, that if an Intelligent Designer designed the whole

program ofLife/DNA, apparent similarities at the physical and genetic levels betweenspecies 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 citedin 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 employdifferent 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 didall of that Info./Logic that dictates those VariantCoding Conventions derive from?!


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In 2011, world-class DNA-researcher Craig Venter mentioned the fact of theseVariant Coding Conventions at a majorEvolution 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 allLife evolved from a single ancestor gradually over vast epochs of time). The

Universality of the Genetic Code in all life-forms wouldcertainly 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 codeis 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 'startreading 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 ifDawkins 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 thesupposed "Universality" of the Genetic Code to prove Universal Common Descent!

"Venter vs. Dawkins on the Tree of Life - and Another DawkinsWhopper":

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-common-descent-dawkins-incredulous/.
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#564http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#564http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.htmlhttp://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.htmlhttp://www.uncommondescent.com/evolution/craig-venter-denies-common-descent-dawkins-incredulous/http://www.uncommondescent.com/evolution/craig-venter-denies-common-descent-dawkins-incredulous/http://www.uncommondescent.com/evolution/craig-venter-denies-common-descent-dawkins-incredulous/http://www.uncommondescent.com/evolution/craig-venter-denies-common-descent-dawkins-incredulous/http://www.uncommondescent.com/evolution/craig-venter-denies-common-descent-dawkins-incredulous/http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.htmlhttp://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#564


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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/the-

great-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 UniversalCommon 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 onelife 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 adifferent 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, areyou?"

Venter: "Well, I think the tree of life is an artifact of some early scientific studiesthat aren't really holding up...So, the tree, ya' know... there may be a bush oflife(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 CodingConventions)- then Dawkins:

Dawkins:"I'm intrigued, at Craig saying that the tree of life is a fiction. I mean...theDNA code of all creatures that have ever been looked at is all but identical". "Surelythat 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 CodingConventions found

within various organisms' DNA, and then Dawkins, a few minutes later, hilariouslyacting as if he wasn't listening to one of the greatest authorities on DNA/ Genetics.
http://thesciencenetwork.org/programs/the-great-debate-what-is-life/what-is-life-panel-http://thesciencenetwork.org/programs/the-great-debate-what-is-life/what-is-life-panel-http://thesciencenetwork.org/programs/the-great-debate-what-is-life/what-is-life-panel-http://thesciencenetwork.org/programs/the-great-debate-what-is-life/what-is-life-panel-http://thesciencenetwork.org/programs/the-great-debate-what-is-life/what-is-life-panel-http://thesciencenetwork.org/programs/the-great-debate-what-is-life/what-is-life-panel-


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The CFI: "The facts clearly demonstrate that all forms of life onEarth 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 ofLife on Earth form a Tree-of-Life". What a whopper! the tree of Life does notexist (see Venter's remark to Dawkins). Our very complete planetary fossil record

does not show agradual 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, holdinginstead that species have no historical connection to each other (known

as the parallel grass blades models"- instead, ID knows that all Lifefundamentally 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 (whoformulated the theory of "Punctuated Equilibrium"). P.E is all about Rapid-change,
http://www.youtube.com/watch?v=qe6XjGD684Ehttp://www.youtube.com/watch?v=qe6XjGD684Ehttp://www.youtube.com/watch?v=qe6XjGD684Ehttp://www.youtube.com/watch?v=qe6XjGD684Ehttp://www.youtube.com/watch?v=qe6XjGD684Ehttp://www.youtube.com/watch?v=qe6XjGD684Ehttp://www.youtube.com/watch?v=qe6XjGD684Ehttp://www.youtube.com/watch?v=qe6XjGD684Ehttp://www.youtube.com/watch?v=qe6XjGD684Ehttp://www.youtube.com/watch?v=qe6XjGD684Ehttp://www.youtube.com/watch?v=qe6XjGD684Ehttp://www.youtube.com/watch?v=qe6XjGD684E


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going against Darwin's nucleic theory ofGradual-Change, but Gould was spurred

into thinking this by the 'Very Complete Planetary Fossil Record', and he wastrying 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, thepattern of fossil appearance in the Cambrian contradicts the predictions ofNeo-

Darwinian and Punctuationalist evolutionary theory, and it soundly refutes themythical Tree of Life: for in it, we find complex new phyla (body plans) emergingwithout any proper pre-cursor ancestors, and those new phyla/body plans require

massive infusions of new biologicalinformation 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 2003pg: 323-402):http://www.discovery.org/scripts/viewDB/filesDB-

download.php?command=download&id=639).

The CFI:ID postulates the existence of an intelligent designer, notconsidered 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 followthe 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 ofEffects: 1)DNA's Digital Info., and 2) certain Irreducibly Complex

Protein-Nano-Machinery. DNA is observable as well as all of the molecularmachines, 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.
http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=639http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=639http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=639http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=639http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=639http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=639


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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 anIntelligenceeven 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 intoexistence (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 ourinference 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 onlyneeds 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 anIntelligence, 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 mindwhen they hear "Designer")- then that question cannot be fully answered by Science;

only by Philosophy (and easily enough): "God" is a necessarily-existing Un-

Caused/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 Spatio-

Temporal 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).


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The CFI:Since the designer is said to be beyond the realm of theobservable, 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 DigitalCode embedded along every cell's nucleus, as well as certain completely-mapped-outmolecular-machines found within the cell- and ID contends that anIntelligence of

some sort can Best Causally Explain the origin of thoseEffects in question (and notMaterialistic/Naturalistic Theories, either Necessity or Chance-Based).

If theDesign Inference"fails as a scientific hypothesis" then why does it useobjectively verifiable data? (Digital DNA & Irreducibly Complex Nano-Molecular

Machines) and a form ofAbductive Reasoning like the rest of the HistoricalSciences? IfID is not scientific, than neither is Darwinism, as Darwinism uses the

same form ofAbductive Reasoning: it uses empirical data (Presently-Given-

Effects) to make inferences toward Past Un-Observable Causes. Also, ifID 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 shouldhave '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 randomevolution). 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 thatwere then testable (hence, falsifiable)- and all thanks to rigorous experimentation.

The CFI:If, however, the Intelligent Designer is considered part ofthe natural world, it is a form of life. In this case, ID has created a
http://www.evolutionnews.org/2010/07/junk_rna_found_to_encode_pepti036961.htmlhttp://www.evolutionnews.org/2010/07/junk_rna_found_to_encode_pepti036961.htmlhttp://www.evolutionnews.org/2010/07/junk_rna_found_to_encode_pepti036961.htmlhttp://www.evolutionnews.org/2010/07/junk_rna_found_to_encode_pepti036961.htmlhttp://www.evolutionnews.org/2010/07/junk_rna_found_to_encode_pepti036961.html


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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 ofthe God Delusion(2006). Once again, a scientist making an Inference to Designwith physical data to go off from does not need a further explanation for his

explanation (another explanation that explains the Design Inference). If scientistsworking on the SETI projectreceived radio-signals from deep space, and we asked

them what 'Caused' them to arise, they could answer it 3 ways: by Chance, byNecessity, 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 deep-

space signals is Intelligent Design". But then Dawkins and his CFI disciples enterand 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 ofBeing/Intelligence that

could do such a thing other than us humans. But that kind of logic would shut down

SETI. The case for IDin biology concerns physical phenomenon (DNA & MolecularMachines) which were perhaps created by some kind of anIntelligence greater thanhuman 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 canstill justifiably infer that DNA was brought into existence by some kind ofIntelligent

Cause superior to humans- much how like SETI scientists would be warranted ininferring the existence of someIntelligence as being the Cause of somepresently-

given Effect (i.e radio-signals containing embedded information) even if they had no

knowledge up until then of any other kind ofIntelligence 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".


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The CFI: "ID has created a problem bigger than the one it attemptsto 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 eversay, "we have detected Design". For example, if archaeologists found arrow-heads

and pottery-shards in the ground, they could justifiably infer that they were theproducts 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 greaterCausal Adequacy and canBest Explain thePresently-Given-Effects (the arrow-heads 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 allthe 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?"mantrareveals 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 theIt/Thing that createdDNA's Digital Code, how could we

answer that? We only have physical evidence ofDNA's Digital Code exhibiting

Design, and though we wish it could, it cannot point us towards itsDesigner. 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: lifeon Earth is explained byassuming 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 ofGodmaking all of complexMaterial Reality

does not make sense because then Godwould need to be as complex & variegated as

theMaterial Reality that He Created; so therefore, saying that"God Caused it" ismeaningless and answers nothing". Now, let's stress that this Dawkin-ish retort is


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aimed at those that invoke anIntelligence as being the Cause of apparent

cosmological Design (the Cause of the Universe and its Fine-Tuning, which wouldhave to be God as aliens couldnt do that)- but when it comes to invoking an

Intelligence as being the Cause ofDNA and Irreducibly Complex MolecularMachines, 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 ifDNA 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 ofGod being the Cosmic Designer. But that displays an

un-appreciation of the Big Bang Model, and of the consensus now reached in currentcosmology 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 becomesreasonably manifest what properties God would have to necessarily possess ifHe was

the Cause of that (ifHe was the ultimate source of all Space/Time/Matter/Energy).

But now we're out ofID's territory, and into the realm ofTheology and Meta-Physics (using philosophy conjoined with the latest advances in Big Bang

Cosmology)- but this is a question that needs to be answered thoughApplyinga 1st

Cause to the Big Bang Singularity, or even a 1st

Cause to the Multi-Verse (if onewants 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 ofEntity. Critics like Dawkinsthink that God must be ultra-complex, when strangely and loudly enough, the early

church fathers and theologians always conceived ofHim as being a very SimpleBeing. Why? Here's how to answer: God is an Immaterial Entity; He is the 1

st

Cause of all Space and Time, so therefore, He is Non-Spatial/Non-Physical andTimeless. That would make HimChangeless, as well as not made out ofMatter andEnergy (which always undergo physical change). God has Freedom of the Will, forHe freely createdEverything out of Nothing (and not out ofHimself, for He is not

Physical). This all makes God more like an Un-Embodied Mind of sorts, and aMind 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 Craigwill 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 isstill simple. Thus, the Ultimate 1

stCause of the Cosmos is plausibly a Simple Entity.


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The CFI: "Since the designer is said to bebeyond the realm of theobservable, claims about its existencecan be neither supported nor

undermined by observation or experiment. Therefore ID does not followthe scientific method of systematic observation and experiment, andfails

as a scientific hypothesis".

Me:

The CFI said (to paraphrase them): "Because the Cause of this Presently-Given-

Effect (DNA) is "beyond the realm of the observable", this means that anyclaims 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 neverbe 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 theprocesses in the past that are responsible for geological features seen today; and

Darwinian Evolutionists, can never observe the process of undirected chemicalevolution that led to the first Life on Earth, nor its foundational mechanism of


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Macro-Evolution. So, in short, the Historical Sciences never directly observe the

'Cause' of a Presently-Given-Effect', rather, they must infer it using AbductiveReasoning: 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 Un-Observable (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 allabout Natural Laws and Inductive Reasoning; but many people assume that Scienceis 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 Causecan't be verified through observation & experimentation?- well,many disciplines in

Science are all about inferring an Un-Observable Past Cause to a Presently-Given-Effect! so, ifScience 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 ofIntelligent 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 notfalsifiable".

1)"It Invokes An Un-Observable Entity": so, does reference to an Un-Observable Cause provide good reason to say that a theory is "un-scientific"? In

fact, that criteria would render many other scientific theories "un-scientific"! TheHistorical Sciences are all about inferring Un-Observable-Past-Causes from


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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-Effects-then 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-Given-Effects). Other critics say, "you cannot infer anIntelligent Cause/a Mind, but ratheronly aMaterial/Natural Cause"- but that is also ludicrous! and would demolish fields

such as Archaeology, Cryptography, Forensics, and SETI: whose sole aims areinferring 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 supportit, then it is testable. If a scientist asserts that DNA or certain Irreducibly ComplexMolecular 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 isconfusing the aims of particular scientific fields! Explanation by reference to Natural

Law is the aim ofNatural Sciences, like Physics or Chemistry, not the Historical

Sciences though. Physics & Chemistry seek to explain or describe something byNatural Law (a very broad enterprise), whereas the Historical Sciences are focusedon 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 ofNatural Law, but the Historical Sciences, in a much different vein, try to find out

what Caused specificEffects to happen. The case for the theory ofIntelligentDesign, and the methodological reasoning it employs, clearly situates it as a


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Historical Science: it uses Presently-Given-Effects (Observable Evidence), such as

DNA & I.C Molecular Machines, and then assesses various Material-BasedHypotheses (using the principle ofMultiple 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 thatIntelligent Design "Best Explains" them. When it comes toexplaining the origin of biological information, ID has the most Causal Adequacy,and not other Material-Based Theories. The idea that only Minds can createInformation is not an abstract hypothesis, indeed, we have 3 pieces of evidence to

confirm it: 1) our present experience of causal reality always shows Informationarising through some Mind/Intelligence, and we have never seen otherwise (whether

it be music symbols, codes, written languages, software programs), 2) experimentsfrom 2010 showed that Intelligent Guidance/Design (via the experimenters) is

needed to create new information, and 3) see 'the Law of Conservation ofInformation' (which states that Natural Laws can only transmist Info., not create it).

#4) "It Makes No Predictions": Utterly wrong, as supposed JUNK-DNAended 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 theDNA 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 15-

year 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 gottensolidly confirmed. The supposed Junk-DNA/Non-Coding regions of the nucleotide

base-sequence have now been proven to have these functions: 1) directs the functionof 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 maintenanceof chromosomes 6) controls the interactions of chromosomes with the nuclearmembrane 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 bevalidated or falsified through research in the not-too-distant future (from Stephen


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Meyer's'Signature in the Cell' pg. 496): "1:No undirected process willdemonstrate the capacity to generate 500 bits of new information starting from a non-

biological source 2: Informational accounting will reveal that sources of activeinformation are responsible for putatively successful computer-based evolutionary

simulations 3) Future experiments will continue to show that RNA catalysts lack thecapacities to render the RNA-World scenario plausible 4) Informational accountingwill 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 regulatoryand 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 willreveal 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 designedand 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 isdefinitely falsifiable. The Darwinists brashly contended in the early 1990s that they

had indeed falsified the Inference to Design at the level ofDNA thanks to all of the

supposed-Junk-DNA evidence rolling in (which was physical and empirical by theway- 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 thatthe 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 Designin the Cell based on Irreducible Complexityincertainprotein machines could have been falsified, but further research validated it!
http://www.signatureinthecell.com/http://www.signatureinthecell.com/http://www.signatureinthecell.com/http://www.signatureinthecell.com/


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The CFI:"ID is religious in nature, beinga modern form ofCreationism, which is itselfderived 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 isnothing 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 aremiles 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 whenlooking 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 Effectin 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 ourpresent 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, "Goddid 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 IDmovementhas 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 alinkto over 50 PhD peer-reviewedpapers about ID in biology, as well as some university-press peer-reviewed ID books!
http://www.discovery.org/a/1329http://www.discovery.org/a/1329http://www.discovery.org/a/1329http://www.discovery.org/a/2640http://www.discovery.org/a/2640http://www.discovery.org/a/2640http://www.discovery.org/a/2640http://www.discovery.org/a/1329


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Why is the CFI shielding the public from I.D with such an outrageous statement likethat? 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 arecognized scientific journal" about ID in biology is wholly inaccurate. It only ends

up confirming how strong the case for Intelligent Design in Molecular Biology istoday. Check out this huge list of articles & books:http://www.discovery.org/a/2640.

Here Are Some Major Experimental Papers That AreBacking Up TheDesign 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 newVariant Coding Convention, which are up to 17 right now- but specifically, a new-found code within the old code (suggesting a kind ofhierarchical logic at work!).The researchers were able to crack the code within the code using specially tailored-

made 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 t

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Darwinian Evolution Is Dead: Defending 'Intelligent Design' - By Joseph Gallagher

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