shadowdude said:
Most of those arguments make illogical leaps to the conclusions that the writer wanted to get to.
Nevertheless, I will answer to the arguments:
"Everything has a beginning"
Everything within the universe appears to have a beginning, but the universe may be eternal. We will likely never know.
Anyway, even if we need an external first cause, having a deity do it doesn't really solve our problem. What is the deity's first cause? And why the heck does the deity of first cause care about us, anyway? Why should it matter if some external force started everything? Why does agreeing that some deity may have started the universe automatically mean that any religion is right?
Basically, I doubt a deity did it, and even if a deity did, it's unlikely that he cares about us, and even if he does, I would have no way of knowing which religion - if any - tells the right story about the deity and tells me what to do to win the deity's favor.
So, in conclusion, primary cause is a problem, but it's just as problematic if we dress up the solution in a good costume.
Physics + Astonomy:
As was already said, life developed in the universe, and it would not exist if it would not have adapted for this universe and this planet. Whoever thinks these arguments make sense apparently sees things backwards. The universe was here before life evolved, and when life evolved it evolved in this universe, to fit this universe's conditions.
Biochemistry
If it were so clear to biochemists that these thingies could never have been spontaneously created, I'm pretty sure these biochemists would have made sure that the theory of evolution is discredited and that everybody knows it. Science, unlike dogma, does not resist change, and so most scientists would have no problem refuting a theory. Thus, I doubt that this is true, it sounds like demagoguery.
It is also possible that some biochemists really do think there are things that are irreducibly complex, but just because with our current technology and understanding we don't know how they could have possibly been spontaneously created doesn't mean they really couldn't have. There are many things we may never know.
Biology
If you know what a computer is, you know what programming is, and you find a computer and find it's programming language, then you already know that an intelligent creature has created it because that's a part of what defines a computer.
So, essentially, this argument is only correct if a part of your definition of life is that it was created by an intelligent being.
Concoiusness
Again, just because we cannot yet understand how something can be, or how something can be created, doesn't mean it can't have been created like everything else, at random. The only reason to say this means you have a soul is that whoever claims this already believes you have a soul and just uses this argument as an excuse to claim that.