Is atheism a scientific perspective?

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I appreciate the fact that you are actually evaluating the argument as opposed to name calling. 

Yes, I am aware that there are problems with the definition of specified. It is incredibly difficult to quantify information in the way that ID opponents demand. What I think Dembski is right about is that the quantity of information of a given sequence is directly proportional to the functionality that arises from said sequence. This is coupled with the fact that gene sequence exhibit an extremely high degree of functionality. While we don't know how to quantify it, this does not mean that we can't draw conclusions based on the qualitative features. I think he was premature in his attempt to draw probabilistic conclusions about these sequences when we don't know how much information we are talking about. However, I think the central argument that DNA contains information and that that information leads to specific functions is true.

So what?
DNA is a part of evolution like everything else.
I fail to see the import you are placing on this.
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The argument that I have been making over and over again is that we don't know if the major mechanism of evolution is adequate to produce the information bearing DNA. You asserting that it does is not helpful.

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It always amazes me how creatards are so wedded to that argument, especially when Darwin took the time to show why it's a bad one before elaborating his Theory of Evolution in On the Origin of Species. You'd think they'd be clever enough to not use an argument that's 150 years discredited, wouldn't you?

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Here's the last paper: http://m.nar.oxfordjournals.org/content/27/5/1223.full, which is discussing the evolution of genetic repair mechanisms in strains of E Coli and a species of yeast.

Interesting how Junk Status, a self-described post-grad biology student, tries to use evidence of evolution happening to disprove evolution happening. If one were a cynical bastard, one would have to conclude that he lied about his educational achievements.

NO. Go on.

I'm not a post-grad biology student, I'm an undergraduate. I never said I wasn't.

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I appreciate the fact that you are actually evaluating the argument as opposed to name calling. 

Yes, I am aware that there are problems with the definition of specified. It is incredibly difficult to quantify information in the way that ID opponents demand. What I think Dembski is right about is that the quantity of information of a given sequence is directly proportional to the functionality that arises from said sequence. This is coupled with the fact that gene sequence exhibit an extremely high degree of functionality. While we don't know how to quantify it, this does not mean that we can't draw conclusions based on the qualitative features. I think he was premature in his attempt to draw probabilistic conclusions about these sequences when we don't know how much information we are talking about. However, I think the central argument that DNA contains information and that that information leads to specific functions is true.

Your objections are a part of a larger argument that I have developed.  I would instead of dealing with them ex parte, include the whole.

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Contra Design -- Against the argument for design from biology

For many, the question of design is as simple as Justice Stewart's observations on obscenity, to wit, "I'll know it when I see it."  They start from the presumption that certain things look designed and go directly to "was designed" (Do not pass Go, do not collect $200).  But it takes a little more than that to make an actual argument.  There has to be something connecting the premise that "It looks designed," to the conclusion, "Therefore it is designed."

Schematically, it goes something like this:

P1) It looks designed;
P2) . . . .
P3)
P4)
C1) Therefore it was designed.

Now a first gander at P2, etc. is to suggest the following:

P1) It looks designed;
P2) If it looks designed, then it was designed;
C1) Therefore it was designed.

Unfortunately we know that P2 is not true.  There are things which look designed that weren't designed and vice versa.

So we try a different tack:

P1) It looks designed;
P2) Things that look like an intelligence designed them, are designed;
P3) It looks like a thing an intelligence designed;
C1) Therefore it was designed.

But the key question here is what does it mean to say that it looks like a thing an intelligence designed?  This is entirely too vague to be of use when debating whether something like the DNA in a cell was designed, wherein the target is clearly removed from any direct traces of a designer.  And we still have the problem of false positives; we can't infer design if our argument is only 'sometimes' right.

So we attempt to narrow in on what it means for something to look like it was designed by an intelligence.  Perhaps:

P1) It looks designed;
P2) Things that look like an intelligence designed them, are designed;
P3) It looks like a thing an intelligence designed if it is similar to the way humans design things;
P4)  It is similar to that;
C1) Therefore it was designed.

This brings a little focus to the question, but again it's rather vague.  We have two problems.  One, it's not specified in what ways the item must be similar to count for a design inference; obviously the color of an object is irrelevant.  The other problem is that for compositions as complex as a cell, we don't have similar things from human designers -- we're not that intelligent, so it leaves open the question of what we mean by similar if there are no similarly complex works of human design.  As Hume remarks on the relevant rule of analogy, "wherever you depart in the least, from the similarity of the cases, you diminish proportionably the evidence; and may at last bring it to a very weak analogy, which is confessedly liable to error and uncertainty" (Hume, Dialogues, Part II).  What aspects of human design are we comparing to a cell?

This is where complex specified information, ala Dembski comes in:

P1) It looks designed;
P2) It looks designed because it has CSI;
P3) Things that have CSI, are designed;
C1) Therefore it was designed.

Unfortunately, as you seem to be admitting, and I'm claiming, Dembski jumped the gun in terms of a rigorous, usable definition for CSI.  So what happens if we adopt your language that "The specified part is indicating that the information is used to accomplish a desired function."  So being specified alludes to the item having specific functional significance.  Here's the problem with that.  Consider a bird's wing. Its function is to allow the bird to fly.  It's not information, supposedly that's in the DNA for the creation of the wing, but ceterus paribus, the cases are parallel.  Whether you agree with evolution or not, it is the case that we have mapped out how it is possible for this function to have arisen naturally.  Function isn't specific only to designed systems.  As I said before, function is in the eye of the beholder.  If there is a possibility that the function of the wing arose naturally, then obviously function cannot be used to split the baby.  For if it is even possible that specified information can arise naturally, it's no longer a flag for design.  Now you may think the situation is different with abiogenesis, but it's not.  All that has to be shown is that a possible sequence from a simpler organism without that function could lead to that more developed organism, all the way back to the first cell and beyond.  (Not directly relevant, but think of the bacterial flagellum and the Type III secretory system.) We don't have to show probability or even have a complete map of the process to conclude from the evidence of the past 100 years that abiogenesis is a significant possibility.

So, in a nutshell, talk of "used to accomplish a desired function" doesn't work as function can be attributed to intelligent and natural causes.  It's not a divider.

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". 

And the functionality of the wing is the result of elaborate informational output by the cell.  Obviously the wing itself is not information, but I think it is impossible to argue that its functionality is not the result of information. And you say "For if it is even possible that specified information can arise natrually, it's no longer a flag for design." You seem to be suggesting that if it's possible that something arose without design, then it was not designed. This is illogical for several reasons. Also, we have no good reason to assume that it can arise without the help of a designing intelligence. If you have a reason that you think it was can you provide it? You say that abiogenesis is a significant possibility, but I think that's just wishful thinking. We don't have to assign probability to design either, because we know based on repeated experience that intelligence is adequate.

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Look up scientific materialism:

Materialism is a form of philosophical monism which holds that matter is the fundamental substance in nature, and that all phenomena, including mental phenomena and consciousness, are results of material interactions. Materialism is closely related to physicalism, the view that all that exists is ultimately physical. 

That's how I was using the word, and it was used correctly. That takes care of about 99/100 ths of your reply.

You may have found that definition by typing 'scientific materialism' into Google, but it's the definition of metaphysical or philosophical materialism. The closest you can come to 'scientific materialism' is methodological naturalism, the position that science can only discover natural explanations for phenomena, not supernatural explanations...it's not the position that the supernatural doesn't exist, but that if it does, it's not something science can study.

Ok, that's fine with me. I just put that there because some person said that materialism meant collecting possessions and then went on to mock me for half a page about how I used the word wrong when in fact, this is how it was used.

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I can appeal to peer-reviewed articles if you want.

That wasn't the point I was making.  Are you saying that these peer-reviewed articles are questioning the validity of the theory of evolution?  Have they found something that undermines some or all of the theory and is forcing the scientific community to scrap those ideas and seek answers elsewhere?

I know that's not the point you were making. Demanding that I peer-review my ideas before you take them seriously is a joke. If that is what you are waiting for, then we aren't going to get anywhere. 

And no, the authors almost certainly attribute the source of the amazing features and systems they describe to evolutionary forces. I just put those out to show that there are conclusions with what I believe to be theistic implications commonly presented in the peer-reviewed literature. 

And they don't find something that undermines the whole theory. This again is a ridiculous demand. However, one of the articles is attempting to explain the evolutionary origin of DNA repair enzymes, and one of the first things they note is that there are considerable differences in terms of the gene sequences that are present or absent in closely related species. Notice that we aren't talking about a few nucleotides being different. We are talking about entire gene sequences being different.