I've been debating ID online for the last couple of months. These are my conclusions so far.
The ID Claims
Some of the ID folks I have debated accept most of mainstream evolutionary science. Some even accept macroevolution, i.e., the idea that speciation is explained by natural selection and mutation. What they generally don't accept is that the pool of genes that is responsible for even the most primitive life could have evolved using undirected mechanistic processes. Instead, the sharper IDists focus on "front loading" - the idea that a designer programmed all the original genes, and mechanistic evolution took over from there. They're basically saying that a designer built all of the lego blocks, and natural processes built stuff out of those blocks.
Needless to say, they don't want to talk about the designer, who is presumed to be God. However, the term "supernatural explanation" is an oxymoron. The supernatural is a name we give to the unexplainable. Invoking the supernatural gives you a well-deserved one-way ticket out of the scientific enterprise. So ID proponents aim to find some scientific signature of design, but without reference to the nature of the designer.
To this end, IDists have tried to cook up some measures of whether or not a system is designed. The first measure is something called irreducible complexity (IC). A system is IC if it does not function if any one of its multiple parts is removed. For example, the blood-clotting mechanism in humans may fail if any one of certain proteins are not present. IDists argue that IC systems could not have evolved (at least not with high probability) because a system with multiple components could not have evolved incrementally, but would have to have evolved all at once.
As defined, IC systems do exist. However, the conclusion that they could not have evolved has been soundly refuted. For the ID claim to be valid, they have to show that none of the components of the IC system could have had any selective advantage outside the IC system itself. If a protein used in blood-clotting has no possible use outside the clotting mechanism, then ID has a more compelling case. However, if that protein has any other benefits to a life form, then evolution will have replicated the genes for making that protein anyway. It doesn't even matter whether life still has an alternative need for that protein. Though the protein may no longer be needed for anything except blood-clotting, as long as it was once useful for something, evolution has no trouble accounting for it.
The other idea that ID proponents refer to is something called complex specified information or CSI (yes, it's named after the TV show). CSI is very poorly defined. The concept has no credibility among mathematicians and scientists. ID advocate William Dembski has tried to cook up a formula for calculating CSI, but it has been solidly refuted. Dembski has claimed that information cannot be created through unguided mechanistic processes, but this is clearly false. Genetic computer algorithms do this every day by computing solutions to complicated problems.
Design as Science
Certainly, there are situations in which design is a scientific hypothesis. In archaeology and criminal investigations we regularly pursue design hypotheses. However, in these cases, we also know through direct experimental test that intelligent entities are present and available to do the designing.
What about cases where we have no other evidence of intelligence? The search for extraterrestrial intelligence (SETI) is a case in which we hope to detect intelligence in transmissions without otherwise observing the intelligent aliens. If we see a narrowband transmission containing a repeating sequence prime numbers, we're likely to think that it originated from an intelligent source. There are two things that would tip us off to the intelligence behind such a message. The first is artificiality - the signal is unlike anything predicted by alternative natural causes. The second is utility - narrowband transmissions containing mathematical data have utility to an intelligence.
Artificiality is sometimes easy to detect. If you find a intricate, mathematically precise structure made of a bulk material (like a titanium alloy), then this is a good signature of life, if not intelligence. Bulk materials like metals can easily be studied in the lab, and we can generally test the material to see that it doesn't spontaneously form such structures over a range of different formation conditions.
Yet, the artificiality of a structure is extremely difficult to detect when we don't have the knowledge or skillset to be able to synthesize a comparable structure in the lab. This is the case with the nanomachinery of living cells. Today, we have neither the knowledge nor the technology to fabricate an artificial amoeba. So, we don't understand the dynamics of cell structure formation or abiogenesis. For this reason, we cannot point to biological structures and say they are artificial because they are not expected under the laws of biochemistry. For all we know, such structures might have formed easily in Earth's primordial soup.
You can't claim the artificiality of a structure when you don't have detailed knowledge of the physics involved in its history.
Utility is a more compelling signal of design. Let's revisit our SETI example. Narrowband signals are harder to generate, but they use a lot less power, and power efficiency is useful. Also, a sequence of transmitted primes has utility as a universal greeting message for alien civilizations.
The same applies for the common examples of intelligent design by humans. For example, we can observe that a flint axe has utility to a creature that has limited intrinsic ability to cut flesh and bone.
Consider a simple steel girder. Such a girder has utility in construction. In fact, any collection of regularly shaped macroscopic objects will typically have a utility. We manufacture things in regular sizes so that we can apply rule-based procedures to them in their application or for commerce.
Language symbols also have utility for storing information. Even if we could not translate the text in a message, we might be able to perceive some utility to its design.
Now, evolution also predicts we will find structures that have utility. The one utility evolution predicts is survival. Evolutionary processes will generate structures that have selective advantages, i.e., that make their biological hosts fitter in their respective environments. So, if you're looking for signs of ID in biological life, you need to look for structures that have utility, but which have no survival benefit (neither for the species in question, nor for its ancestors).
So, if you look at a biological structure, e.g., the human eye, you cannot argue that its utility is enough to infer ID unless you can show that the human eye has no selective advantage (which, clearly it does have).
One problem for ID proponents who favor early-stage design (as opposed to ongoing intelligent tampering) is that sexual reproduction, mutation and natural selection will probably have pruned from ancestral life any feature which had no selective advantage. If an alien seeded Earth's life with programmed DNA, any part of that program that wasn't related to the system's survival would likely have been eliminated by natural evolutionary processes.
When challenging ID proponents to make predictions, they commonly respond by saying that unguided evolution (UE) makes no predictions. IDists are making two mistakes when they do this. The first is in assuming that ID and UE are theories. They are not theories per se. They are classes of theories. A theory that aims to explain a facet of evolution using specific unguided mechanistic processes would be categorized as a UE theory. A theory that proposed that a biological system was designed for a particular utility by a particular designer using some specified technique would be a theory that falls into the ID category.
UE contains many predictive theories. UE theories predict inherited mutations, varying rates of speciation, patterns of adaptation, etc. UE theories are statistical. They cannot predict exactly what evolution will produce, only that it will produce something with statistical, selective advantage in its environment. UE is predictive because it contains theories that are predictive.
ID fails to be predictive because there are no scientific theories that fall into the ID category. In an effort to bypass the question of God, IDists ignore the question of utility. A discussion of utility would force them to speak about the utility of life beyond mere survival. Unless you know something about the designer, you cannot say what would be useful to him/her/it/them. This forces them to consider artificiality alone, and to hopelessly do so in a realm where the physics are poorly understood.
A Word About Probability
You'll hear ID proponents talk about the low probabilities that life formed by undirected mechanistic processes. Most of this handwaving is pure bantha poodu. I once saw a presentation in which the speaker spoke of the astronomical odds against a DNA molecule forming out of its constituent atoms in a vacuum! What does this have to do with evolution? Nothing. It just generates irrelevant numbers to throw at non-expert audiences. No one thinks that life formed by individual atoms flying together all at once. Atoms would have formed into precursors like amino acids, proteins, and membranes. More complex molecules would have formed from the precursors. Little research has been done in this area, so no one knows the odds of life forming in a planet-sized bath of such precursors. It could be unlikely, or it might be a virtual certainty. We don't know.
However, even if we did know that the formation of life is improbable under those conditions, one cannot use this as an argument for design. We are not independent observers of the creation of life on this planet. We are dependent observers. We are not free to observe life not forming on Earth 3.8 billion years ago. That is, the probability that life formed on Earth and led to our existence is unity.
This scenario is very different from us, say, observing that new life developed independently on another planet. In that case, our existence as observers does not depend on the formation of life on this other world. If we see life improbably popping up elsewhere, then we have a clue that we don't understand what's happening in abiogenesis.
This question of observer independence is closely related to the Doomsday Argument and the Adam and Eve Paradox. If you try to apply probability measures when you're not an independent observer, you run into all sorts of nasty paradoxes.
By the way, sound reasoning about probability reveals that there is no cosmological fine-tuning problem, either.
There are two scientific signatures for design: artificiality and utility.
Our ability to detect artificiality is limited by gaps in our knowledge of natural phenomena in biochemistry. Today, ID relies on these gaps in our knowledge of natural processes to suggest that artificiality lurks within biology.
The only utility we have observed in life so far is selective advantage. This is exactly what we would expect of life that was created through unguided evolutionary processes. As far as I can tell, there are no ID predictions about utility because God has no scientific utility for life.
No trace of ID has been found by either method. No experiment has been proposed to test an theory of ID because there are no actual theories of ID.
The frequent misbehavior of ID proponents cited by the Judge in the Dover case has raised the bar even higher for ID theories. ID theories (if we ever see any) will require extraordinary evidence in order to overcome the noise of all the false claims floating around in ID-land.