On the same page as the A.G. Cairnes arc-building example:

“In evolution, too, the organ or structure you are looking at may have had scaffolding in an ancestor which has since been removed.”

And this is what we find with flagella; which Behe claims to be proof of irreducible complexity.

From Carl Zimmer: (National Geographic)

http://www7.nationalgeographic.com/ngm/0611/feature4/text3.html

He lists his source material here:

http://scienceblogs.com/loom/2006/10/18/national_geographic_gets_compl.php

but I didn’t want to link directly to it because it is a pdf.

Some of life’s most marvelous structures are its smallest: the minute clockwork of molecules that make cells tick. E. coli, a bacterium found in the gut, swims with a tiny spinning tail made up of several dozen different proteins, all working together. Doubters of evolution are fond of pointing out that the flagellum, as this tail is called, needs every one of its parts to function. They argue that it could not have evolved bit by bit; it must have been created in its present form.

But by comparing the flagellar proteins to those in other bacterial structures, Mark Pallen of the University of Birmingham in England and his colleagues have found clues to how this intricate mechanism was assembled from simpler parts. For example, E. coli builds its flagellum with a kind of pump that squirts out proteins. The pump is nearly identical, protein for protein, to another pump found on many disease-causing bacteria, which use it not for building a tail but for priming a molecular syringe that injects toxins into host cells. The similarity is, in Pallen’s words, “an echo of history, because they have a common ancestor.”

Scientists have discovered enough of these echoes to envision how E. coli’s flagellum could have evolved. Pallen proposes that its pieces—all of which have counterparts in today’s microbes—came together step-by-step over millions of years. It all started with a pump-and-syringe assembly like those found on pathogens. In time, the syringe acquired a long needle, then a flexible hook at its base. Eventually it was linked to a power source: another kind of pump found in the cell membranes of many bacteria. Once the structure had a motor that could make it spin, the needle turned into a propeller, and microbes had new mobility.

Where Behe says “Can’t have happened without miracles.,” molecular biologists have shown that yes indeed it can. Dawkins here is using analogy as opposed to a factual premise in answer to an analogy. The point being, of course, that irreducible complexity can indeed be reduced. As to the need for a designer, where Behe thinks he has trumped biology, Dawkins has shown it to not be trumped.

Are your plethora more of these?

God of the gaps means that all we need to do is to fill the unanswered questions with the Designer. And I get the pun with supports and arches.

As far as dealing with Behe’s points, it is possible that he finds them so laughable as not to bother with them. I pointed you to one example where at least the flagellum is dealt with. But again the analogy of the arch is related to design because, yet, people build arches with stones. An arch is not irreducibly complex, any more than a mousetrap, the human eye, blood clotting, etc. And people build and design cars. But until you can show me a car that meets up with another car and makes other cars without people (such as or parents did to make us) the metaphor of car as designed object is not a perfect one when compared to life, either.

We know how babies are made, and even though technology is often called into make up for where nature as failed, animals and plants reproduced all on their own (often unsuccessfully) before humans came along to develop husbandry, agriculture and in vitro fertilization. Bacteria, yeast and algae were all able to reproduce to. And it seems to me that to carry the need for a designer to its logical conclusion, you would need to posit the creator’s hand in every step of reproduction (even of our own cells in our bodies.)

The first cause argument is an old philosophical question, and Dawkins responds to those who use it as evidence of a creator, when it is not such thing. Even the Big Bang, at which time was created along with matter doesn’t depend on cause and effect and matter-anti-matter pairs have been found to be spontaneously springing out of nothing.

I am going to copy-and-paste from a comment I made at Pharyngula to show how frustrated I get sometimes with ID/Creationists:

“My take is that Creationists do this because they keep on hoping that whatever they throw against the wall to defeat “darwinism” (which includes cosmology, btw,) someday something will actually stick. It won’t slide down. Something has to work to defeat secular interpretations of evolution because they “know” that it is wrong. And why is it wrong? Because it contradicts with their particular view of the universe (whatever it is.)

“And as soon as they finally destroy Darwinism, well, then they can address the heresies of the other creationists. So, they do what they do not as an end, but as a means.”

http://scienceblogs.com/pharyngula/2007/09/transitions.php#comment-560602

To try to use ID to deconstruct Dawkins is weak. If his critics attack him for glossing over the whole of philosophy and religious history in order to form his own conclusion, what does it say about the people in ID that they gloss over contradicting evidence, produce no work of their own and then claim victory over Darwinism?

Someday people of faith will need to admit that faith is what it is and it is not based on demonstrable fact as per the means of science. This is what riles us most; the insistence that God is demonstrable scientifically when God clearly is not. God is either natural or supernatural.

“The analogy is obviously ridiculous”

No, actually, it is a good analogy. Biological “things” are built up step by step and then the “keystone” can be inserted.

“I will agree that the origin and nature of God are still questions to be considered; however, that is a separate question, and must be kept distinct from the question of the creation of the universe.”

Why is the “nature of god” separate from his “creation”? Does not the supposed fact that he created the universe imply something (anything at all?) about him? Outside of space and time? Supernatural?

“ID, by the way, is a collection of hypotheses based upon existing scientific findings, as well as new.”

ID is “Goddidit” just like all its predecessors. There’s no real “cause and effect”, no science, no how or when or where or why. Just “poof” – something miraculously happened without leaving any trace.

“The point is merely that the facts are mounting against Darwinism and imply design”

Dream on, religious one. Scientists will continue to ignore all of your supernatural creations. Read the 1970s editorial in The American Spectator – Darwinisn is Almost Finished Now Any Day and We Really Mean It This Time. Well, it’s been 30 years and the worship of Darwin as a God – Darwinism – is still practiced in non-taxable churches all over the world – NOT. But evolution is stonger than ever, especially after ID’s last gasp at Dover. Took their creationist book and changed all references to “design proponents” – hilarious.