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First off - my link was more extensive in quantity than yours, so hey, if you don't read it all, I understand (I barely have time for the one you gave me).

Understand, though, that creation science and intelligent design are two totally different arguments. I find the former to be totally abhorrent on solid scientific ground; your link only adresseses the latter though, so I'll address that.

I believe that ID is fine as a philosophical/religious concept. I believe that God is ultimately responsible for the "design" of the universe, so to speak, only I maintain that this is not a scientific conclusion, nor or we able to draw such a conclusion on solely scientific grounds. Section-by-section:

Life appears designed.

This by itself is a rather subjective observation, as explained. Basically, the comparison is made here between biological systems and manmade objects (e.g. clocks, factories, etc.). This is not really a valid comparison, as manmade objects are not able to reproduce on their own accord, and hence have no inherent means of self-modification, which is the entire premise of evolutionary theory. In any case, something having the "appearance" of design doesn't necessarily conclude it was "intelligently" designed.

Is the appearance of design just an illusion?

First of all, numerous comparisons are made to the SETI project in this article; it should be kept in mind that SETI is a project that is considered itself to be on the fringes of science - it is not universally considered to be on solid scientific ground as evolutionary biology is - so it really isn't a very good comparison, either.

The article goes on to say "If law and chance can adequately explain an apparently specified system, then a design inference is not warranted." The only problem is, one can never conclusively prove this - there are just too many boundary conditions on a biological system to draw a solid inference on a specific case - too many unknown factors to determine what the "probability" for evolution of a specific characteristic. If "design" is determined to be the best explanation, exactly what quantifiable consequences does that have?

No known natural law appears to account for the semantic character of biological information - the message bearing sequences in DNA.

I read this section a couple times, it appears to remain very vague about what they mean by "semantic character" and "information". If they mean that we don't exactly know the complete process of how DNA was originally formed, I believe they are correct. (This by itself, though, just shows a void in our knowledge - calling it intelligent design remains a premature conclusion.) If they are trying to say that new genetic information cannot naturally be added to DNA, this is quite untrue - the mechanisms through which this can happen (gene replication, etc.) are quite well understood, and our understanding is improving.

The extreme complexity of biological systems tends to rule out chance as a reasonable explanation for the origin of life.

The article is correct in stating that the chances of seeing the outcome that we observe for the specific protein sequencing that we see are astronomically small, but this does not mean the process wasn't natural or random. For one, it assumes the outcome that we see is somehow a preferred outcome - you cannot make inferences from probability retroactively. For example - draw any 5 cards from a deck and look at them. The odds for drawing those cards in that order in less than 1 in 300,000,000 - if you happen to observe a preferred pattern in that draw, it doesn't mean there was an "intelligent" plan for that to happen.

Conceptual Difficulties.

This section seems to exploit the "evolution hasn't explained everything, so there must be something else involved" argument. Well, I can't prove that wrong; the Theory of Evolution doesn't claim to have the instant answers to all biological quandaries. Its strength lies in the fact that it provides a consistent model, makes predictions which can be subsequently verified in many cases, and can be potentially falsified. ID provides explanations, but it doesn't give any predictions about what to look for to potentially verify or falsify it - that's where it falls short as science.

Evidentiary difficulties.

The article states" Darwinian evolution has not been adequately tested (a) because it is an historical hypothesis about singular events and processes occurring in the distant past that cannot be confirmed by experiment, and (b) because it has not been properly evaluated against all the relevant evidence" . Two points here (a) lab controlled experiments are not the only way evidence is collected in science, it is just one of many ways; the experiments that can be reproduced in a controlled setting do continue to lend credence to evolutionary theory. (b) is again vague - the theory has been evaluated against a great deal of relevant evidence; not all of it - this standard is impossible for any scientific theory to meet.

Darwinian Evolution has been protected from criticism.

This is not really true. The scientific community is active in protecting their theories from sectarian criticism, but scientific criticism is always welcome. In fact, the Theory of Evolution has been upgraded immensely since Darwin's time; it has benefited from scientific criticism; lateral gene transfer and genetic drift (among other mechanisms) are now known to contribute to evolution in addition to natural selection (this short link does a better job at (briefly) explaining some of the criticisms that have increased understanding of the theory.

Recent Polls and Congress Show a Demand For Objectivity in Origins Science

Not relevant - scientific theories aren't decided by a public vote; they are decided by research and subsequent review of the research by scientists.

In describing the AAAS statement, the author responds " Thus, rather than a true criticism of ID, the AAAS resolution is nothing less than an attempt to teach our children that methodological naturalism/scientific materialism is the only path to true knowledge about our past." This is a bit like complaining that "science is biased toward scientific explanations". Of course it is! Science rejects supernatural intervention as a cause of events because such intervention yields no predictable consequences and no basis on which to form a scientific theory. It's fine to discuss the supernatural, but this is a philosophical concept, and has no place in empirical scientific inquiry. Science is not about espousing a particular worldview, it is about providing falsifiable explanations of physical phenomena, that is all.

1. The AAAS claim is a "robust theory" is inconsistent with the AAAS proposal to protect it from criticism....

The paragraph goes on to state "a robust theory needs no protection". In that case, I'd like to know why ID proponents aren't submitting their articles to refereed journals for citation? There is a proper forum for scientific debate, like I said; a theory doesn't gain credibility through political means, but by data collection and subsequent testing. A robust theory has nothing to fear - if the Theory of Evolution was overturned based on scientific grounds I'd be the first to want to see it go out the window, but this has to be done legitimately. It's the scientific process itself that needs protection against political end-runs.

The AAAS fails to disclose the motivation for censoring ID...

I agree that science seeks to censor - it seeks to censor faulty science. If the paradigm of "Methodoligical Naturalism" (which is NOT the same thing as "Scientific Materialism", which is a worldview as oppose to a research method) is to be overturned, then a new method that retains predictive ability needs to be introduced, lest science lose its usefulness. This hasn't been done.

The AAAS resolution would ban ID from all discussion of biological origins...

The resolution doesn't "ban" anything, it only makes a collective statement that the concept currently known as ID is a political/philosophical movement as oppose to an empirical theory; this is because it hasn't presented the criteria by which it can be verified or falsified.

...evolutionary theory is scientifically controversial...

This is just blatantly untrue. Evolutionary theory is mainly the province of biologists, who are practically unanimous in their support of the theory. A perusal of peer-reviewed literature such as Nature or New Scientist reflects this. It is very, very few biologists indeed that believe the foundations of evolution are in jeopardy. (The Discovery Institute's famous list of "scientists who find evolutionary theory inadequate" shows no more than 70 biologists worldwide, the last time I checked a few months ago.) The NCSE's Project Steve makes a parodical point of this sort of statement. Once again, I know "might doesn't make right" for a theory, but I wanted to point out that this is a false statement.

The AAAS claim that the "ID movement has failed to offer credible evidence to support their claim is false..."

For reasons explained earlier, this isn't false - there's a lot of hand waving here - science requires more solid scrutiny of a theory.

The AAAS claim that a design inference is not testable is simply disingenuous...

A "design inference", as they call it, would only be potentially testable if you could really isolate all the variables known to influence the evolution of a specific trait, AND you could show that an unlikely outcome is actually a preferred outcome. ID proponents seem confident they can do this, but they have failed to convince anyone else (and generally don't seem to have made much effort to do so, based on the almost nonexistent number of journal submissions made on the subject). If this is really possible, they need to make their data available for scrutiny by other scientists. Considering how difficult it is to model even simple kinetic systems mathematically, this really isn't possible with today's technology. (If it someday is, I'm open to this field of inquiry, but till then....)

Implementation of the AAAS resolution will promote a naturalistic belief system that is antagonistic to theistic religions...

Most Christian and Jewish denominations seem to have no problem with the Theory of Evolution (including Roman Catholicism, the largest individual denomination in the U.S.). Science really has nothing to say about the religious implications of any theory, as I stated earlier. Science and religion address different spheres of the world - neither does the other a service by meddling in the other's affairs.

The AAAS resolution fails to address the constitutionality of state censorship of legitimate scientific views...

Like I said, scientific inquiry is not a democracy - some ideas work in its framework, others don't. Currently, the Supreme Court holds that religious views are not allowed to be taught in the science classroom. Like I said, I have no problem with ID in a philosophy setting (or perhaps as part of a discussion about the philosophy of science), but presenting it as scientific theory is inappropriate at this time.

...the ID movement...is advocating an objective un unbiased approch to the teaching of origins

The ID movement is advocating teaching a scientific controversy where none really exists. To use a rather extreme counterexample, if a few scientists out there believed the sun orbits the earth, should we advocate an "unbiased approach" to the teaching of astronomy to incorporate geocentrism? Science is necessarily biased toward scientifically derived conclusions.

I'm all for the objective and continual improvement of scientific theories. I also believe that God plays a crucial role in the universe as the Creator of everything, but it is important to recognize that this is not a scientific conclusion. I also fail to understand what some of the implications for ID are supposed to mean. Supposedly God designed the universe to make it look as if many of its features were naturally derived, but messed up on disguising some of them? We somehow have the means to discern this? Until the day comes that ID can clarify what it is can come up with specific falsifiable predictions, it will not gain a position in the scientific hierarchy of theories.

(Guess I went on for a while, but I wanted to thoroughly read and address the points in your link)