Quote from: Copernicus

This is an argument from ignorance, any way you look at it. The prediction is a negative condition--that no natural explanation will or can be found for certain biological changes.

1. WAY DESIGNERS ACT WHEN DESIGNING (OBSERVATIONS) ...

Matt, I think that you need more than this.  It is not just about what intelligent designers do, but about how intelligent designs differ from those that arise through natural selection.  Remember that we are looking at Intelligent Design as an alternative to natural selection.  We already know that natural selection works.  We need to know why ID is a better explanation for what we observe in nature, not just that it is a possible explanation.  If both ID and evolution are possible explanations for a phenomenon, then evolution wins by default.  It does not rely on belief in miracles.

One point missing from your entire post is acknowledgment of a very significant difference between ID and "unguided" evolution.  Evolution theory cannot explain the removal of nonfunctional but innocuous aspects of a design.  By 'innocuous', I mean that they have no impact on the proliferation of the species.  So, one expects designs by natural selection to be "messy".  Conversely, one expects intelligent designs to be "clean".  The junk DNA issue, for example, is a problem for Intelligent Design, but not for evolution.  Even if most junk DNA turns out to have a function, that does not contradict the idea that the function arose through natural selection.  It would be a puzzle for natural selection if DNA turned out to be very parsimonious--lacking any detritus.

Another difference between evolution and ID is that the former is well understood.  We know exactly how it works, and we can even model it mathematically.  ID cannot be modeled, and IDists never provide an explanation of exactly how the design gets implemented.  That obscurity is partly intentional, because IDists like to maintain the facade that they are not appealing to supernatural causes.  

2. PREDICTIONS OF DESIGN (HYPOTHESIS)

(1) Natural structures will be found that contain many parts arranged in intricate patterns that
perform a specific function (e.g. complex and specified information).
(2) Forms containing large amounts of novel information will appear in the fossil record suddenly
and without similar precursors.
(3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in
different and unrelated organisms.
(4) Much so-called "junk DNA" will turn out to perform valuable functions.

(1)  The definition of "complex" and "specified" are problematic in that natural selection is known to give rise to very complex function over aeons of incremental change.  Having read Dembski's attempts to explain it, I can see no reason why the kind of structure that he's talking about could not arise over eons of time through natural selection.

(2)  Define "suddenly".  As for "without precursors", that is expected from the very nature of the fossil record itself.  Fossilization is rare, and the record is expected to be full of gaps.  So it is not at all unexpected that a given fossil might appear to have "similar precursors".  We can never expect to have a fossil record that lacks significant gaps, although evolution does predict that we will find transitional fossils inside the gaps, and there have been thousands of instances of that kind of discovery.  Such discoveries represent a continual stream of fulfilled expectations, which is one of the reasons that scientists are so firm in their conviction that evolution theory is right.

(3)  Evolution theory makes the same prediction.

(4)  I would put it somewhat differently.  Evolutionists expect there to be some messiness.  IDists would expect there to be little or no messiness.  None at all, if one thinks of the intelligent agent as a perfect being.

3. EXAMINING THE EVIDENCE (EXPERIMENTS AND CONCLUSION)

(1) Natural structures have been found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information), such as certain irreducibly complex machines within the cell. The bacterial flagellum is a prime example. The specified complexity of the simplest, self-reproducing cell is another.

Plausible paths of development for these structures exist under evolution theory. There is no reasonable need to posit supernatural explanations for their development.

(2) Biological complexity (i.e. new phyla) appear in the fossil record suddenly and without similar precursors. The Cambrian explosion is the prime example.

The Cambrian explosion represents a period of roughly 40-50 million years.  Do you have any conception of how long a period of time that is?  It was relatively short compared to the other periods, but it was not short from the perspective of biological evolution.  It is quite expected that such "explosions" or "leaps" in the fossil record will occur, especially when there are a lot of unfilled biological niches.  These phenomena are perfectly explainable under conventional Darwinian analysis.  Again, no need to appeal to powerful spiritual forces.

(3) Similar parts have been found in organisms that Darwinists themselves see as separated by more closely related forms that do not contain the similar parts in question. Clear examples include genes controlling eye or limb growth in different organisms whose alleged common ancestors are not thought to have had such forms of eyes or limbs.

Can you explain to me again why this is unbelievable from a Darwinian perspective?  Genes are opportunistic with respect to function.  They take advantage of whatever enhances survivability.

(4) Increased knowledge of genetics continues to uncover functions for various strands of "junk-DNA." Examples include functionality in some pseudogenes, microRNAs, introns, LINE and ALU elements. Examples of DNA of unknown function persist, but design theory encourages researchers to uncover as yet unknown function whereas In contrast, Darwinian theory has caused some scientists to wrongly assume that non-coding DNA is useless "junk."

I think that I've addressed this point several times now.  See above.

Hey guys
CP I didn't have time read everything so this is just a thought
If natraul selection is supposed to come out messy how does everything look so perfect? later

The world ecology isn't as bad off as some environmentalists would have you believe. I saw an interesting discussion about this recently. I don't remember the exact numbers, but someone offered the opinion that if the human population and drain on resources continued at its current rate, the planet would be perfectly inhabitable for several hundred million more years.

True, it's not a long time when you consider the planet is 4.5 billion years old, but it's not a disaster either. Plus, since many people are working to correct the damage from the past century, we're actually even better off than that.

However, I do agree with Cop's point - which I believe is if you imagine what the universe would be like without a god, you would expect it to be exactly as it is.