"The First Flaw
In my opinion, atheism already contradicts itself for not believing in faith. They believe that science does not rely on faith. Completely wrong...Science does rely on faith. A scientific inquiry or theory that has been developed must be accepted by others. They must have FAITH in that theory so they can BELIEVE it is true. Example, for hundreds of years scientists declared that damage to the spinal cord is irreversible...FALSE! The spinal cord does regenerate, but at a much slower pace than any other part in the body."
Scientists do not take the claims of others on faith, but on the evidence. Nor do they take other people's evidence on faith, but require disclosure of the methods and materials used so that they can themselves replicate the findings.
While scientists may individually believe some things, such as the irreversibility of spinal injuries, they do not make such beliefs unchallengeable. It is believed on the current evidence, and is subject to revision in the light of new evidence. This is why it was even possible to develop treatments to restore function to damaged spines; because any "received wisdom" is always a tentative conclusion, regardless of evidence, and open to further investigation and revision.
Contrast this with religious dogma.
"The Second Flaw
Atheists claim to be "free thinkers" when evidently they're not. They prescribe to scientific theories that have been developed by humans. This clearly does defeat the purpose of free thinking because in effect they only are listening to one source (science in this case). Me as a Christian I look at one source the bible, but I take it as a whole and find the deeper meaning to the words. Not just like "So the chicken came before the egg gotcha" (atheist perspective) vs. "So Why did the chicken come first" (Christian/religious perspective)."
There is no other proven source of thought except humans, so of course scientists are going to use human developed ideas. Any idea is permissible in science - including ghosts, demons, psychics, aliens and angels - as long as it is provable. Having an idea you can't prove is pointless as you can never then obtain the evidence needed to convince other scientists, who (as explained above) will not simply take your word for it.
That's not to say that science doesn't have it's fair share of speculative hypotheses, it does. It helpfully highlights this fact by referring to them as "speculation", "hypotheses" or "speculative hypotheses".
Oh, and the chicken did not come before the egg.
Contrast this with biblical literalism.
"The Third Flaw
How will you prove using the scientific method does produce truth? Because it's "scientific"? Because science said so? Again, the question "By what authority does science have by proclaiming to be the truth than religion"? The statement "The results of the scientific method should be followed" is unscientific because it is a value statement that does not get its authority from anywhere but itself.
"We should use the scientific method." Why should we? "It proves itself." How does it prove itself? "It uses the scientific method."
Atheist Statement: "The scientific method is true because it works and because it is axiomatic (self-evident)."
Christian answer: Sounds a lot like faith to me. Who decides what is axiomatic? Does the scientific method decide it? That makes it circular if it does. If not, then it is not scientific itself."
Short answer: Science works. Faith does not.
Science is a way of discarding ideas that do not conform with reality. For an idea to be accepted by science it must simultaneously explain all the known facts and be contradicted by none of them. This means that at the very least the results of the scientific method work for all known cases.
The idea of "truth" in science is "confirmation". New results confirm or refute current theories, and no amount of evidence ever demonstrates that something is "true" in the absolute sense. Knowing the absolute truth of anything in the real world is impossible, which is why the people who routinely claim to know the absolute truth are also the people who demand you take their "knowledge" on faith.
It is axiomatic to science that there exists an external reality that is amenable to study and which operates by a system of well defined and comprehensible principles. This is because the purpose of science is to study that reality and determine those principles; so if this were not so science would be unable to operate. But even this "axiom" can be contested, if you have the evidence.
Science not only works, but its methods of combating self-delusion, corruption, fraud, conscious and unconscious bias, and multiple - often confounding - effects can be successfully applied to other fields, so that what is real can be distinguished from what has been merely imagined.
Hence on the basis of all the available evidence; intercessionary prayer isn't, faith healing doesn't, creation science isn't, and biblical history wasn't.
Contrast this with apologetics.
"Atheism serves no goal in one's life except Surviving. This goal is one that not even I can comprehend for if your only goal would be for surviving the truly you should look deeper into what life truly means"
Atheism isn't synonymous with science, and most scientists are not atheists. Being an atheist probably contributes little to a person's survival unless it also leads them to reject some religious explanation and/or solution to a medical or psychological problem and seek professional, evidence-based help.
Atheists do not uniformly reject the supernatural, the existence of anything beyond the empirical, the transcendent, or an external meaning to life. Though what is probably true of most atheists is that they can determine for themselves what is important, what goal they want their life to have, what standards they wish to both reach and teach.
Contrast this with biblical standards of morality and freedom.