Reducible complexity

The contribution of intelligent design advocate, biochemist Michael Behe consists solely of the scientifically refuted notion that a multicomponent functional system cannot have arisen by "Darwinian" evolution. In essence, Behe argues that because removal of any component will render the system non-functional, such a system could not be produced by continuously improving the initial function (which continues to work by the same mechanism) by slight, successive modifications of a precursor system (p.39 of Darwin's Black Box: The Biochemical Challenge to Evolution). Behe targetted several complex systems as purportedly providing support for this flawed proposal: evolution of the eye, clotting cascades and complement system, and the bacterial flagellum.

There are major problems with Michael Behe's contrived challenge of 'irreducible complexity'.
First, the implicit assumption that the components of currently functional system have 'always and only' performed the function that they currently display. The most obvious illustration of this flaw lies in an examination of Behe's for-the-scientifically-ignorant analogy of a spring-based mouse trap. All the components of a spring-based mouse trap can be found, in modified forms, functioning in a variety of settings. It is only the assemblage of these modified forms within a mouse trap that renders each a necessary component of the trap's function. (Intelligent design devotees seem incapable of grasping the point that analogies are useful in explanatory descriptions, but that fallacious arguments from analogy are rapidly invalidated as arguments aimed at attacking scientific facts.) Second, research in medical genetics has uncovered mechanisms that explain 'reducible' complexity. Third, research has demonstrated that assembly of pre-existing modifications operate in subsequently evolved features.

1.
Inherited epigenetic variation--revisiting soft inheritance..
Phenotypic variation is traditionally parsed into components that are directed by genetic and environmental variation. The line between these two components is blurred by inherited epigenetic variation, which is potentially sensitive to environmental inputs. Chromatin and DNA methylation-based mechanisms mediate a semi-independent epigenetic inheritance system at the interface between genetic control and the environment. Should the existence of inherited epigenetic variation alter our thinking about evolutionary change?
Richards EJ. Inherited epigenetic variation--revisiting soft inheritance. Nat Rev Genet. 2006 May;7(5):395-401.


Insights into the spliceosome suggest new explanations for generating biological complexity. modified, hyperlinks inserted:
While politicians debate whether evolution occurs, scientists are busy debating how it occurs. . . .there are more ways than previously thought to achieve the impressive complexity characteristic of humans. Many organisms — including humans — evolve in part by using a complex mechanism by which strands of RNA are spliced together in a two-step process, and delicate balancing of the way this process is executed can generate an enormous number of new gene products, providing a vast reservoir of material for selection during evolution. . . between the “important” coding sections of RNA lie non-coding patches — introns — and as RNA is made it’s the job of a cellular machine called the spliceosome to chop the introns out and splice the rest of the coding sections back together. . . the two steps in this process require the spliceosome to change its shape, flipping back and forth between two distinct conformations. . . Changes in the balance between these two states — referred to as equilibrium — will cause the spliceosome to dwell longer in one conformation at the cost of the other, improving one of the two steps of splicing, to the detriment of the other step. Mutations either in spliceosomal components or in the intron RNA strands can change how the RNA and the spliceosome interact with one another and thus affect the equilibrium. . . there are an abundance of mutated intron splice sites in human DNA, also called alternative splice sites. . . when the equilibrium of the spliceosome is changed — either because the mutated splice sites interact with it differently or because other accessory molecules bind to the spliceosome — they can be recognized and spliced. The utilization of alternative splice sites allows for different combinations of coding RNA sequences to be put together, so that one RNA transcript can make a variety of different products, each with a potentially different function. This explains why, when the human genome was first sequenced, relatively few genes were found. . . This has allowed our genome to develop in complexity.”
Molecular Cell 21(4): 543-553 (February 17, 2006)

2.
Lenski et al have demonstrated that complex features can evolve by expanding earlier, simpler functions, and that an intermediate stage is not necessary for this evolution. Thus, they have demonstrated how to reconstruct a complete evolutionary history of a complex genetically encoded function. Their computations vindicate Darwin's idea that the target of natural selection constantly changes, and that the complex feature of today may share very little with the original function. Darwin wrote, "if we look to an organ common to all the members of a large class in order to discover the early transitional grades through which the organ has passed, we should have to look to very ancient ancestral forms, long since become extinct."

The work of Lenski et al and the experiments of Bridgham et al (below) demonstrate that Behe's contrived challenge to Darwinian evolution, namely "irreducible complexity", is not a valid criticism of the mechanisms of evolution. The two groups have demonstrated that complex systems can evolve and lend disproof to the claim that complex systems must have been designed.

The evolutionary origin of complex features.
A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms--computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.
Lenski RE, Ofria C, Pennock RT, Adami C. The evolutionary origin of complex features. Nature. 2003 May 8;423(6936):139-44.


Lock before Key: Entrez PubMed: "According to Darwinian theory, complexity evolves by a stepwise process of elaboration and optimization under natural selection. Biological systems composed of tightly integrated parts seem to challenge this view, because it is not obvious how any element's function can be selected for unless the partners with which it interacts are already present. Here we demonstrate how an integrated molecular system-the specific functional interaction between the steroid hormone aldosterone and its partner the mineralocorticoid receptor-evolved by a stepwise Darwinian process. Using ancestral gene resurrection, we show that, long before the hormone evolved, the receptor's affinity for aldosterone was present as a structural by-product of its partnership with chemically similar, more ancient ligands. Introducing two amino acid changes into the ancestral sequence recapitulates the evolution of present-day receptor specificity. Our results indicate that tight interactions can evolve by molecular exploitation-recruitment of an older molecule, previously constrained for a different role, into a new functional complex."

Bridgham JT, Carroll SM, Thornton JW. Evolution of hormone-receptor complexity by molecular exploitation. Science. 2006 Apr 7;312(5770):97-101.
Comment in: Science. 2006 Apr 7;312(5770):61-3.

association fallacies

Association fallacies rely upon the negative implications of "guilt by association" or the positive implications of "honor by association."

These fallacies are based upon the implication that a claim is false or true based upon beliefs held by, or attributed to, the people or organizations that hold the belief.

Creationists, in line with the emotional basis for their claims, all too often resort to association fallacies. One example of the "honor by association" fallacy is to point out that scientists and Nobel Prize winners have signed a document against Darwinian theories, as though this lends credence to 'id' pseudoscience. Godwin's Law and Desperate Attacks on Darwinism provides an example of unfounded accusations that Darwin's ideas inevitable led to Nazi atrocities, as though this would demote evolution from fact (argumentum ad nazium, reductio ad Hitlerum).

Godwin's Law

"As a Usenet discussion grows longer, the probability of a comparison involving Nazis or Hitler approaches one. There is a tradition in many groups that, once this occurs, that thread is over, and whoever mentioned the Nazis has automatically lost whatever argument was in progress. Godwin's Law thus practically guarantees the existence of an upper bound on thread length in those groups."[def] Technically, Godwin's Law relates not to the fallacious employment of argumentum ad nazium or reductio ad Hitlerum (association fallacies), but to the contention that such arguments immediately render a debate concluded (and lost).

Of course, debaters frequently fail to acknowledge that they have technically lost an argument by resorting to irrelevant attacks or that they have resorted to irrelevant attacks because they have already lost the argument by failing to logically support their claims.

In the simplest analysis, inappropriate comparisons of whatever is under debate to Nazism or Hitler fall into the categories of irrelevant and biased guilty-by-implied-association attacks. Obviously if the debate is actually about the Third Reich, eugenics, the holocaust, or the phenomenon of scapegoating, then mention of the National Socialist Party or bad old Adolf would be relevant.

Godwin's Law and Desperate Attacks on Darwinism provides an example of biased, unfounded, emotional resort to unfounded analogies that are aimed at defaming scientific theories of evolution with the implicit counterclaim that God is the Creator. Needless to say, Godwin's Law will not be applied and Creationists will continue to make illogical, ad nauseam arguments, implicit or explicit, for Special Creation.

Godwin's Law and Desperate Attacks on Darwinism

"Author and Christian broadcaster Dr. D. James Kennedy connects the dots between Charles Darwin and Adolf Hitler in Darwin’s Deadly Legacy, a groundbreaking inquiry into Darwin’s chilling social impact.

The program features 14 scholars, scientists, and authors who outline the grim consequences of Darwin’s theory of evolution and show how his theory fueled Hitler’s ovens. " Reported on ChristianNewsWire, Aug. 18, 2006.

"Chilling social impact" and "fueled Hitler’s ovens"?!

Charles Darwin was a natural historian who carefully examined the fossil evidence and formulated a mechanism to explain the observed temporal alteration in life forms. Darwin also correctly predicted that his formulations would excite the ire of fellow scientists of religious persuasion. Within a decade, almost all European scientists had accepted Darwin's ideas.

Not so in segments of American society, where attacks on any evidence counter to dogmatic belief in Biblical literacy not only flourish, but are given undeserved media attention. Such illogical and emotion-driven attempts to discredit Darwin reflect back upon the accusers, drawing attention to the weakness of their arguments and their lack of genuine grounds for criticism of the modern synthesis of evolutionary theories.

"“The legacy of Charles Darwin,” said Dr. Kennedy, is “millions of deaths, the destruction of those deemed ‘inferior,’ the devaluing of human life, and increasing hopelessness. Darwin’s legacy has been deadly indeed.”"

Power-mongering based on emotional thinking – Aryans are superior, die Juden are to blame – was responsible for eugenics-as-conducted-in-das-Reich and the holocaust. Distorting history in order to defame the first reasonable scientific explanation for the fact of biological evolution is yet another example of emotional thinking because it is clearly biased and irrelevant. Such association fallacies as these run counter to educated understanding of sociopolitical and psychological mechanisms.

The Wedge Document

The New Yorker: PRINTABLES:
"In 1999, a document from the Discovery Institute was posted, anonymously, on the Internet. This Wedge Document, as it came to be called, described not only the institute’s long-term goals but its strategies for accomplishing them. The document begins by labelling the idea that human beings are created in the image of God “one of the bedrock principles on which Western civilization was built.” It goes on to decry the catastrophic legacy of Darwin, Marx, and Freud—the alleged fathers of a “materialistic conception of reality” that eventually “infected virtually every area of our culture.” The mission of the Discovery Institute’s scientific wing is then spelled out: “nothing less than the overthrow of materialism and its cultural legacies.” It seems fair to conclude that the Discovery Institute has set its sights a bit higher than, say, reconstructing the origins of the bacterial flagellum."
See the original at: The Wedge Strategy

Contradictions within idism

The New Yorker: PRINTABLES:
"Dembski's views on the history of life contradict Behe's. Dembski believes that Darwinism is incapable of building anything interesting; Behe seems to believe that, given a cell, Darwinism might well have built you and me. Although proponents of I.D. routinely inflate the significance of minor squabbles among evolutionary biologists (did the peppered moth evolve dark color as a defense against birds or for other reasons?), they seldom acknowledge their own, often major differences of opinion. In the end, it's hard to view intelligent design as a coherent movement in any but a political sense.

It's also hard to view it as a real research program. Though people often picture science as a collection of clever theories, scientists are generally staunch pragmatists: to scientists, a good theory is one that inspires new experiments and provides unexpected insights into familiar phenomena. By this standard, Darwinism is one of the best theories in the history of science: it has produced countless important experiments (let's re-create a natural species in the lab - yes, that's been done) and sudden insight into once puzzling patterns (that's why there are no native land mammals on oceanic islands). In the nearly ten years since the publication of Behe's book, by contrast, I.D. has inspired no nontrivial experiments and has provided no surprising insights into biology. As the years pass, intelligent design looks less and less like the science it claimed to be and more and more like an extended exercise in polemics."

index

Index to Posts:

– God by Any Name
¿ God by Any Other Name is still God
¿ Refusal vs Refutation
¿ Illogical Deceit Theory
¿ Logic & Science
¿ Biological evolution
¿ Creationism vs Evolution
¿ Recapitulating recapitulation
¿ Reducible complexity
¿ Radio Daze

– Fallacies of Logic
¿ Fallacies of Logic
¿ over-extrapolating
¿ ad hominem
¿ ad nauseam
¿ association fallacies
¿ authority
¿ composing problems
¿ denial
¿ deliberate ambiguities
¿ fallatio
¿ Godwin's Law
¿ incredulity
¿ irrelevance
¿ proof-disproof muddles
¿ red herrings
¿ shifting the burden of proof
¿ huff & puff

key elements of fallacy:
A : accident : ad nauseam : appeal to authority : association : attack : authority
C : co-incidence : composition
D : denial : disbelief : distraction : doublespeak
E : equivocation
F : fallacy of four terms : false dichotomy : generalization : guilt by association :
G : Godwin's Law and association fallacies
H : honor by association : huff & puff
I : incredulity : ignorance - ignorantium : individuals to group : inappropriate authority : irrelevant authority
M : members to whole : misuse of authority : parts to whole : personal attack : proof-disproof : prove it!
Q : questionable authority
R : red herring
S : smoke screen : straw man
T : to the man
O : over-extrapolating, over-generalization
W : wild goose chase
Y: you also, you're another, you too :

common names of fallacy:
A : ad nauseam : "against" the man : appeal to authority : argument from ignorance : argument from incredulity : association fallacy :
C : composition
D : denial : disbelief : doublespeak
E : equivocation
F : fallacy of four terms : fallacious appeal to authority : fallacy of accident
G : Godwin's Law and association fallacies
I : inappropriate authority : incredulity : irrelevant authority
M : misuse of authority
Q : questionable authority
R : red herring
S : smoke screen : straw man : sweeping generalization
T : to the man
W : wild goose chase
Y : you also, you're another, you too

Latin names for fallacy:
Ad: ad hominem : ad nauseam : ad verecundiam : ad verecundiam fallacy
Argumentum : argumentum ad ignorantiam : argumentum ad verecundiam : argumentum ad nazium
Dicto : dicto simplicter
R : reductio ad Hitlerum
Tu : tu quoque
V : verecundiam :

– Court, Articles, News
¿ Godwin's Law and Desperate Attacks on Darwinism
¿ The Wedge Document
¿ Keeping up with the Jones decision
¿ On the teaching of Pseudoscience
¿ Contradictions within idism
¿ Scripture vs Scholarship
¿ Answers to Creationist Nonsense
¿ Creationist and ID confusion about Entropy
¿ Ignorance in Kansas
¿ Ignorance in the White House
¿ Scientists comments on "ID"