"I agree that information is an issue. What carries the information isn't. Since we are all made of energy on an atomic level, we are all made of "information". - Where do we get it? We have identified a plethora of carriers, but have never given a reasonable explanation for the how or where information originates. - 
 However, it begs the question from science... Why are we trying so hard to prove the non-existence of something that isn't there anyway? If an intelligent designer isn't there, we couldn't prove its non-existence. 
 
 It is the right of science in my opinion, to explain away the observable...to take all the mystery and "magic" out of life. If an Intelligent Designer does exist, it would certainly not reveal itself outright. We would just rationalize and explain it away. 
 Science has set a course for its own destruction when and if the empirical evidence finally suggests intelligent design. It's going to be much harder for the smartest people in the world to have to come to grips than the other way around. When and if the evidence suggests intelligent design, would science bend the knee while continuing its efforts to better humanity?" - Matt has provided a very cogent and incisive discussion of the mass of information that is obviously available and at work in nature, and the perverse role science plays in studying it. My own opinion is that the evidence is very strong and getting stronger for intelligent design.

I've decided to have a go at replying to Matt line by line:
(But the software will only allow me to do so in two parts, since the post is too long). PART 1: - Matt: "We know that information exists in atomic particles." 
GPJ: This of course depends on what you mean by "information" here. 
I may be somewhat old fashioned on this but I would say that there 
is mass and energy in atoms, but it only produces "information" if 
an observer observes it and records the results. - Matt: "But how an atom can "know" it's being observed by an outside 
source is amazing by itself." 
GPJ: It would be but it isn't because it doesn't. - Matt: "The problems to consider, in my humble opinion, are how these 
pieces "know" to fit together."
GPJ: This is more anthropomorphism. They are not conscious beings and don't know anything. - Matt: "How does the information in DNA "know" to attach itself to the DNA strand?" 
GPJ: The information in DNA is coded by the sequence of bases (ACGT). It is physically part of the DNA. How the information is copied from one molecule to another is indeed remarkable. The series of actions to carry this out has all been "programmed" by evolution into the cell's complex chemical system. It is not solely in the DNA itself. - Matt: "Why, when I look at a mountain in the distance; the information which is carried at the speed of light to register in my brain, does it not conflict with the other information coming from the mountain behind me?"
GPJ: I don't quite understand this. It seems to suppose that light can pass through Matt's head and impinge on his retina! - Matt: "How does my eyeball "know" to pick up only the information I'm looking at?"
GPJ: Why should it pick up any other information? You turn your head and the light entering your eyes is light that has come from the direction you are looking. The eye is a directional receiver, like a radar dish. - Matt: "Quantum theories have proven that science isn't really objective observance of natural phenomena after all."
GPJ: Not so. - Matt: "Observation can and does change the outcome of an otherwise "normal", repeatable occurrence." 
GPJ: This is to be expected on sub-atomic scales, because it is impossible to observe without disrupting the system. - Matt: "Therefore, science subjects, and is in itself subjective. This subjectivity IS the reality we live in...there is no such thing as the objective observer." 
GPJ: This is not a justifiable conclusion. Most observations of macroscopic events are perfectly objective. - Matt: "I agree that information is an issue. What carries the information isn't. Since we are all made of energy on an atomic level, we are all made of "information"."
GPJ: This seems to be saying that energy and information are the same thing. This is nonsense. - Matt: "The physical, observable part of that structure is what science studies; whether it be DNA, or atoms, or whatever. Science cannot study unobservable phenomena."
GPJ: Agreed. - Matt: "However... everyone knows it's there." 
GPJ: You speak for yourself! I of course take the view that unobservable phenomena are not phenomena. I'm assuming here of course that you mean "unobservable" in principle, rather than because of our lack of knowledge of how to make the observations or because our current technology is inadequate.

Part 2: - Matt: "As technology develops and allows scientists to look further into what used to be considered unobservable, we are becoming even more baffled by what we're finding." 
GPJ: I agree that quantum world is puzzling, but I don't think we are baffled. I think we have been making good progress in understanding it. - Matt: "It's as if the simplest of organisms and particles are capable of not only responding to stimuli, but are free thinking agents of which the observable world is the byproduct." 
GPJ: That is a rather sweeping supposition! The next two paragraphs, which I've left out, are an elaboration of this fantasy scenario. - Matt: "Dawkins' arguments of "who designed the designer?" are moot. The smartest people in the world can't even figure out how to put an energy efficient, cost effective vehicle on the road. However, they're smart enough to "know" that there is no God. The most basic, necessary, and applicable of inventions cannot be solved even with the materials and technology available...But the origin of the universe, life, and the endearing, quintessential question of "WHY"... Hey no problem." 
GPJ: Actually Dawkins doesn't say there is no God. He says there almost certainly is no God of the interfering type described in the Bible and believed in by most followers of the Abrahamic religions. It may be that there was a designer! As I've suggested in another post the parameters of our universe might have been set by advanced beings (Elohim?) in some previous universe. But the question would still remain, where did they come from in the first place? The most likely explanation is that they evolved. But the really most likely explanation is that they didn't exist and that we evolved. - Matt: "It shows me the lack of respect people like Dawkins have, even for their own predecessors. It smacks more of building a religious following than science. I do find it all very interesting." 
GPJ: I don't see any disrespect for earlier researchers. Quite the opposite. I see no religion building. Again, quite the opposite. - Matt: "However, it begs the question from science... Why are we trying so hard to prove the non-existence of something that isn't there anyway? If an intelligent designer isn't there, we couldn't prove its non-existence." 
GPJ: I disagree, though of course if you are demanding "absolute proof" that is impossible for anything. - Matt: "It is the right of science in my opinion, to explain away the observable...to take all the mystery and "magic" out of life." 
GPJ: I would say "it is the right of science to explain the observable", but why do you put in the word "away"? I don't agree that science takes away any of the magic and mystery from life. In fact I would say the universe uncovered by science over the past century is far more mysterious and magical and full of wonders than the mechanical universe of the late Victorians. - Matt: "If an Intelligent Designer does exist, it would certainly not reveal itself outright. We would just rationalize and explain it away."
GPJ: Why ever not? I'm sure it could make itself known unquestionably, but we might have a lot of questions for it. - Matt: "The fact that the "big questions" continue to elude us is a testimony in and of itself. Science keeps digging deeper, because every layer we uncover, we find more and more evidence of intelligent design." 
GPJ: Nonsense! Most of the old arguments for design have been made redundant. - Matt: "Therefore we must press on, in order to maintain the right to explain away the observable. Without that right, religious fanaticism would exercise its dogma upon the world..." 
GPJ: Away with that "away"! - Matt: "However science has taken it one step to far in that its position is to be the objective observer, not take up philosophical arguments based on perceived data." 
GPJ: I don't agree with this demarkation dispute between scientists and philosophers! We all have the right to philosophise. - Matt: "Science has set a course for its own destruction when and if the empirical evidence finally suggests intelligent design. It's going to be much harder for the smartest people in the world to have to come to grips than the other way around."
GPJ: More nonsense. Should such a discovery be made it would be Nobel Prize material of the first order! - Matt: "When and if the evidence suggests intelligent design, would science bend the knee while continuing its efforts to better humanity?" 
GPJ: That depends who or what this supposed intelligent designer is, and whether he she or it or them can be contacted, and what its future plans for us are. Matt's assumption appears to be that if found the GIT (Grand Intelligent Technologist) will be a benign figure and not a malicious demon or a crazed super-scientist.