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Irreducible complexity on the molecular level was, for me, the finishing blow for a general theory of evolution, when I read Michael Behe’s book.

I never had a religious problem with the General Theory, because it seemed to me that God could perfectly well have worked through evolution if He so chose. And the Catholic Church has gone out of its way to accommodate Evolution. But I have always had scientific problems with it.

Sure, there is intra species evolution. Darwin was quite right about that. Birds can develop longer beaks if they need them to pick insects out of the bark of trees or suck their food out of deeper flowers. Dogs can be bred to be faster, or larger, or whatever their owners find desirable, within reasonable limits. Deer can grow longer and faster legs at the same time that wolves do the same thing.

But how do you explain, using evolutionary theory, the development of the first eyeball, or the first wings. Because these excrescences would be counterproductive,a drag on the individual animals who developed them, UNTIL they finally became usable over a period of presumably thousands of years. How would an animal with half-developed wings slowing it down and holding it back and getting tangled in the grass beat out an animal who had the advantage of no burdensome half-wings? What advantage would there be in a half-developed eye that couldn’t yet see anything? Yes, lower order plants are phototropic, and respond to light, but there’s an unbridgeable gap between that and growing an eyeball.

That occurred to me as a teenager when I first studied biology. Of course, Behe’s cellular level complexity takes it to a whole new level of astronomical improbability.

Moreover, inter-species evolution has never been observed, only theorized about. And the general theory is no closer to being proved than it was when Darwin first proposed it.

Molecular “Machines” build themselves, when they have no point in even existing? How likely is that? This latest response to Behe sounds like a work of desperation.

It seems that Mr. Thomas seems to have “overlooked” vital parts of the article in his is attempt to refute its findings

Intelligent design mavens once cited flagella as evidence of their theory. Scientific fact dispelled that illusion. The mitochondria study does the same for protein transport.

“This analysis of protein transport provides a blueprint for the evolution of cellular machinery in general,” write the researchers, led by molecular biologist Trevor Lithgow at Australia’s Monash University. “The complexity of these machines is not irreducible.”

When they analyzed the genomes of proteobacteria, the family that spawned the ancestors of mitochondria, Lithgow’s team found two of the protein parts used in mitochondria to make TIM23.

The parts are located on bacterial cell membranes, making them ideally positioned for TIM23’s eventual protein-delivering role. Only one other part, a molecule called LivH, would make a rudimentary protein-transporting machine — and LivH is commonly found in proteobacteria.

The process by which parts accumulate until they’re ready to snap together is called preadaptation. It’s a form of “neutral evolution,” in which the buildup of the parts provides no immediate advantage or disadvantage. Neutral evolution falls outside the descriptions of Charles Darwin. But once the pieces gather, mutation and natural selection can take care of the rest, ultimately resulting in the now-complex form of TIM23.

“It hasn’t been possible up until this point to trace any of those proteins back to a bacterial ancestor,” said Dalhousie University cell biologist Michael Gray, one of the researchers who originally described the origins of mitochondria, but was not involved in the new study. “These three proteins don’t perform precisely the same function in proteobacteria, but with a simple mutation could be transformed into a simple protein transport machine that could start the whole thing off.”

“You look at cellular machines and say, why on earth would biology do anything like this? It’s too bizarre,” he said. “But when you think about it in a neutral evolutionary fashion, in which these machineries emerge before there’s a need for them, then it makes sense.”

I think the quote mining was a nice touch, subtle and not too obvious

Wikipedia has provided this indisputeable example of preadaptation, expation, or maybe preaddlepation:

“Another example is the hypothesis proposed by zoologist Jonathan Kingdon that before early humans became bipedal, they began engaging in squat feeding, i.e. turning over rocks and leaves to find insects, worms, snails and other food. Consequently, they adapted flatter feet than were necessary in their previous tree-dwelling ancestors, since that makes squatting much easier. Flatter feet are also extremely useful for bipedal animals, so they can be described as a preadaptation to bipedalism, even though (or rather because) the adaptation had nothing to do with bipedalism originally.”

I wonder how they walked around to find all this stuff to squat down to and why they would have such long legs to need to squat down?

Ooooo....Lyin' Brian Thomas MS* tripe.

Irreducible complexityis nothing more than a manufactured term and notion, made-up by ID/YECers, to be used as an argument in a debate they think can be won and is being won by them by simply saying "we established an artificial lower limit, scientifically proving that God did it"....nothing more.

The very structure of these systems--with their interdependent parts working all together or not at all--demands design, not chance.

False conclusion, Brian.

The fact that non-functioning "machine parts" are invisible to Darwinian selection is exactly what design theorists have observed.

You, Brian, don't even understand what you're talking about. The researchers posited that the non-functioning parts actually had a function in bacteria, but you need it to be different so you could set up a false conclusion.

Plans and purposes, however, are only known to arise from intelligent planners, never from mindless and chaotic laws of matter.

False statement, Brian. Given 4 billion years, proteins have plenty of time to be chaotically and randomly generated to have a function.....or mutated to have a slightly different function, or mutated a bajillion times over millions of generations to have a completely different function. Mutations change the protein's primary, secondary, and/or tertiary structure....changes the protein function for good/bad.

Instead of relying on unknown "self-organizing" principles and magical impossibilities to have constructed the living world, scientists can instead rely on Acts 4:24: "Lord, thou art God, which hast made heaven, and earth, and the sea, and all that in them is." Thus, a real, effectual, adequate Cause is responsible for irreducible molecular machines such as mitochondrial transport complexes.

BWAAAAhahahahaha.....translated: "Instead of paying attention to what I, with my uber-scientific edumacation, will deem to be 'magic'....pay attention to MY brand of 'magic'"

....but speaking of mtDNA, Brian, what's the YEC reason for mitochondrial DNA being entirely different than the rest of the DNA in ALL animals? LOVE to hear it...