In the name of Allah, the most Gracious, the most Merciful!
Sorry, I didn’t know that this post was also addressed to me. It was so way up there and invisible among others but still…
Come on freethinker, don't you think I would know you've something called internet through which you can find almost zillions of rebuttals, some even by illiterate people, and then would try to make your point here? That's so sad then!
1. I am using the Muslim definition of god ie an omnipotent, omnipresent, omniscient, conscious being.
Yeah that is now better!

See, in this way if you'll reply to my questions, we would inshAllah (if God wills) have no problem!
2. The analogy he uses fails because he is assuming there has to be a creator, there doesn't. Objects and machines have creators, but those things are unnatural (they don't occur in nature, people have to make them.) The universe is natural. We can see natural things grow and there is no intelligence behind it. It is just a natural phenomenon. The universe is natural as well, so why assume there was a conscious being behind its creation?
And what is the definition of “natural”? Perhaps “something which is not created”? Is that what you mean? Is “universe” natural? But I read that it was created in a big bang?! What do you say about this?
Every living creature was “formed” from the primary raw materials present like carbon, hydrogen etc. (As you know carbohydrates consists of carbon and hydrogen; proteins have carbon, hydrogen, nitrogen, oxy etc!)
So that means none of us are natural??? I’m not natural?
You said:
they don't occur in nature,
So universe doesn’t occur in nature because it WAS created??? Ouchi! My head hurts by taking in such an ill-logical point!
The analogy he uses fails because he is assuming there has to be a creator, there doesn't.
So there is no point of discussion here and the whole purpose of discussion fails because “you are PRESUMING that there is no Creator?” You see, YOU ASSUME TOO, many, many things! Like you’ve assumed that there is no Creator! So we Muslims are not the only one here “assuming: things.
3. The scientific "miracles" in the Qur'an can be explained logically. There was an exmuslim on youtube who made a good video on the subject. His user name is "discussislam" but he took all his videos down.
Sad!

But don’t worry; I can give you the links of 5 or 6 anti-Islamic forums and sites where many ex-muslims and Atheists have tried to rebuttal this lecture or tried to “explain” the scientific miracles of Quran.
4. Read the book "God is not great" by Hitchens. Chapter 9 is titled "The Koran is borrowed from both Jewish and Christian myths" You can probably find it online for free, if you have the desire to.
Thanks for increasing my list of anti-Islamic books. I’ll include this book too. So what were you saying…? Yeah! “So do YOU believe that Koran is borrowed from both Jewish and Christian myths”? Hmmm?
5. Francis Bacon lived in the 1500s before we knew about DNA, evolution, radio activity, and a billion other things. I don't think his quote stands the test of time.
You are not making any sense here! Why a “quote” would needs to pass the test of time? Why are you trying to change the words? It is the “religions” and “concepts” which should pass the test of time.
Now about Francis Bacon, do you know he was a scientist also? And BECAUSE of his experience in science, he said that
“Little knowledge of science makes man an atheist, but an in-depth study of science makes him a believer in God.”
If a person has knowledge about some subject, then I think it allows him to pass statements regarding it. Right?
Don’t you realize that believers have covered or traveled one more level than the non-believers? Because every believer was once a non-believer till Allah gave him/her guidance.
But still, if you don’t agree with Francis Bacon’s quote because “he lived in 1500s before we knew about DNA, evolution, radio activity, and a billion other things” then okay. I live in your century and now we have discovered many, many things, and now I say that
“Little knowledge of science makes man an atheist, but an in-depth study of science makes him a believer in God”, so you agree? Just kidding!

(of course my quotes hold no importance)
And now, seriously, if you don’t agree with Francis Bacon’s quote then simply ignore it.