Is atheism a scientific perspective?

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The first part of your argument seems really shallow. I think you know that we are not saying that "it looks designed therefore it was". It is "despite thorough search for another cause, only intelligence is a known cause that can produce what we see in designed systems". It is not that we are just appealing to our initial intuitions. These conclusions come after careful studying of the systems and proposed explanations. Your argument seems to be "because in the past we have seen apparent design turn out to be illusory, all apparent designs are illusory". 

I have cut out all of the post except the portion I am responding to in the interest of brevity and getting to the point.  I only skimmed rest, this part just caught my eye.

I believe I saw in this post that you were an undergraduate in biology.  Congratulations on getting higher learning.  But I think you need to pay a little better attention in class.  Particularly, what makes up a valid theory.  You cannot invoke a supernatural cause.  "Design" is a supernatural cause.  After taking college science courses it strikes me that you would have a little better understanding of science and would know that because a "thorough search for another cause" didn't turn up anything, whatever shit is leftover must be the answer.  That's how things work in the Sherlock Holmes universe, not in the real universe.  You don't find what's right by showing what's not.

Secondly, I'm sure you know a few ID believers.  What religion are each of those people you know?  Now be honest.  Do you really believe that their religious beliefs have no bearing whatsoever on their acceptance of ID?  Really?

Look at the facts.  A 2009 poll by the Pew Research Center found that evolution had reached 97% consensus while just 2% say evolution doesn't happen.  Of the 97% consensus, 8% say that evolution was guided by a supreme being.  There are 4x more scientists who accept evolution and believe it is guided by God than scientists who reject evolution altogether.  So if 97% of scientists agree evolution is a reality and 99.999% of those who reject evolution hold similar religious views, what does that tell you?  That is a clear indication of a bias.  Do you think these people came to their creationist beliefs after learning about evolution or before?

ID is creationism.  It was designed by creationists to replace overt creationism in schools immediately after the courts struck it down.  The original book created to support ID, Of Pandas and People was originally intended to be a creationism textbook.  It uses the exact same definition for ID that it used for creationism in an earlier draft.  That was the founding of intelligent design.  It is a religious belief made by people with religious beliefs to support their religious beliefs.  They started with their religious beliefs, came up with a few ideas why the science they didn't like was wrong and created a faux science based entirely on their religious beliefs.  There is no way in hell good science can possibly come of this, much less completely unchanged from the original biased, completely unscientific, religiously tainted origins.  Irreducible complexity is not part of a scientific theory.  It's and early idea they had which they then shoehorned into a faux scientific theory.  It's a produce of a religious think-tank group with the purpose of sneaking creationism back into schools after the court ruled it unconstitutional.

Which brings us full circle to my claim that I have to watch everything Christians say.  Here you are treating intelligent design like it's no different from any other science.  You must know its origins.  There is no way you don't know that intelligent design, which invokes a supernatural cause, is the brain-child of creationists trying to disguise creationism as some new science to sneak it back into schools.  The very founding of ID, itself, was a deception.  The claim they made that it was science, not creationism was a deception.  The book which introduced it was going to be a creationist book originally and was rewritten, saying exactly the same thing, to remove overt mentions of creationism and replace it with intelligent design.  ID is a lie.  That is its origin story.  It was a lie told to sneak creationism back into schools.  This is absolutely irrefutable.  You can look up the Dover court case and see the previous versions of the book which use creationism instead of intelligent design. You treat it like it's a real science, but it's not.  I know you really want to believe that it is, and I realize you aren't feeding me false information on purpose, but to treat ID like any real science is a deception, and someone with education in biology should know better.  A lie doesn't turn into science because it's a really good lie.  The chances that a bunch of people trying to deceive us all accidentally created good science from the lie they wove are laughable.  I know you think it sounds good, but that's because it's exactly what you want to hear.  The best lies always sound good.  But they're still lies.

It's not that I think you are inherently untrustworthy, or even stupid.  Honestly, I do think you're ignorant by choice.  That's not an insult, just an honest evaluation.  You probably think something similar of me, and I understand that.  It's the nature of our difference of beliefs.  It's not you I distrust, it's the things you choose to believe and the things you must ignore to maintain your belief system.  I don't think you intentionally try to deceive me.  I do think you make the choice to deceive yourself.  ID is shit.  I'm sorry, but that is absolutely true.  A turd of a lie does not become a gem just because it's a really good lie.  A lie is a lie and ID is very much a lie.  That's all it will ever be.  And by advocating ID you are spreading that lie.  Unintentionally, I'm sure, but when you say "ID has merit" you are saying, "It's not a lie".  I can show you its origins.  I can show you that it's creationism in disguise.  I can show you early drafts of the book which introduced ID which use "creationism" in place of "intelligent design".  I can show you the court transcripts which have the people behind ID claiming that it had nothing to do with creationism, even though early drafts used the word "creationism".  I can show you that ID started as a big fat lie.  Yet you seem to believe this lie was somehow miraculously scientific, pretty much unchanged from the original work of deception it was intended to be.  It wasn't intended as a science, it was intended as a lie.  But somehow it was scientific.  Through some magical miracle the lie they intended to tell was accidentally the science they claimed it to be, even though "science" was never their intent.  I'm sorry, but good science simply doesn't spring out of deceptions intended to present religion as science.  The very fact that it invokes a supernatural cause alone disqualifies it as scientific.

ID does not make a supernatural claim. Intelligence needs not be supernatural. I would agree with you that trying to identify the designer is not a scientific endeavor. Moreover, science can be defined as appealing to only undirected processes for answers, but that would render anthropology, archaeology, forensic science, and the search for extraterrestrial inteliigence (SETI) unscientific as well (the ideas for this sentence were largely from Meyer's book so as not to plagiarize). Similarly, you must ask if you want science to truly seek truth. If you do, then why should you start off with the notion that certain ideas cannot be considered, even if they are soundly based in the method of comparing competing hypothesis (which is not merely a Sherlock Holmes approach).

And I've already addressed the fact that religious scientists have a bias, but so do nonreligious scientists. But that doesn't present us from understanding biological systems or doing good science. In fact, because we have such an obvious bias, we must be more careful. Appealing to those statistics is a good way to avoid the actual arguments though.

And I don't think that you can just dismiss the arguments that ID proponents make by asserting that it is a conspiracy theory set up by the religious to corrupt science. That would be like me claiming that Darwin devised his theory because he was mad at God and wanted to instill a natural worldview into society. When you actually read the ID literature (instead of reading about ID from a biased website, which I presume you did), you will see a clear outline of the theory. They address why it fits within the parameters of science, they use scientific methods to arrive at their conclusions, and they defend against common attacks like those that you have thrown out. The difference between ID and creationism is that creationism uses the Bible as a starting point and works to fit all data into that. ID merely supports the statement that some aspects of life and the universe are best explained as the product of intelligence.

 And I'm glad that you are so far above the delusion that I clearly suffer from. And you're right, It goes both ways. I could sit back and say that you deny the scientific viability of the arguments because you don't want to acknowledge the implications. I could even go as far as to say that you are mad at God, that you fear His judgement, and that you would rather live in a world without being held morally accountable. How do you know it isn't you who has deceived yourself? You might have even deceived yourself to the point that you are willing to believe that everyone else has deceived themselves so that you can feel a personal sense of cognitive superiority. You said that you were not trying to be offensive, but I think that you have displayed a remarkable level of arrogance by implying that I am willingly ignorant of science.