What I'd like to ask anyone who doesn't believe in Creation is-
How can something come from nothing?
Agreed - it's quite hard to wrap our heads around. But then where does God come from? If God just 'is' - he is eternal and his presence (from nothing) requires no other explanation - why are you demanding an explanation for the creation of the super dense molecule? Why couldn't that just 'be'? 'God' does not answer this question - it just creates more questions. And if you can believe in the massive complexity of an all knowing deity just existing, then you have a bit of a cheek suggesting that atheists are the unreasonable for ones for accepting that one tiny molecule got more and more dense until it exploded.
Where did that something come from?
Where did God come from? if he just 'is' then you cannot ask other people to explain where everything else came from - that's hypocritical. You can believe that something massively complex can just exist but we can't believe that complex things can develop on their own? Even though - unlike you - we have proof and are still trying to work out the answers to bits we don't understand?
How can complex physiology come by chance?
It didn't. You have failed to understand evolution. Random changes happen by chance. Some of those changes are beneficial - and the organisms with that characteristic survive and reproduce and pass it on. Some of these random changes are not beneficial - and those that have it die out. Over millions of years these random changes (genetic mutations - and you can't deny genetic mutations can just happen - we see them all over. Cancer is a form of genetic mutation) get passed on, more genetic changes happen and eventually you get organisms we recognise today. It's still ongoing - but it takes millions of years, so you don't ever see it in real time. There is ample evidence in the fossil record.
How does it make sense that your bodily systems work together so well?
That would be evolution. However our systems are not as perfect as all that. The eye (so beloved as 'proof' in creationism) is actually a pretty inefficient design. We have left over bits we don't need and - let's be honest - having a pelvis that allows us to walk upright has made birth difficult and dangerous for all human women. This all makes sense if we have evolved from random changes (the changes aren't sentient - they aren't actually trying to design anything good) and we have just settled into a best fit for now. It makes a lot less sense if an intelligent creator chose to design us all so badly.
Where are all the 'in-between' beings from evolution?
In the fossil record. They died out.
How can beauty come from mess?
What has this got to do with anything? Both 'Beauty' and 'mess' are relative, human terms. Beauty is in the eye of the beholder. We find things beautiful not because they are but because we think they are. We have an emotional reaction to it - and being social creatures we share ideas of what constitutes beauty and agree to it. But between individuals these ideas can differ - what is beauty and what is a mess can be different to different people - look at different interpretations of artwork . However in some species beauty is a part of their evolution e.g flowers being pretty to attract the insects to pollinate them. 'Beauty' can have an evolutionary purpose - it can evolve same as eyes and dorsal fins.
How is there order in the world?
In what sense? Evolution sees to biological systems. Some organisms have evolved to be symbiotic with others (back to flowers and insects) which creates a sort of order. But you only have to look at the state of the world: poverty, hunger, famines, droughts, wars - to see that there is no intrinsic order to the way we live - and that nature can act against us. If you mean things like gravity and the speed of light then your back to scientific explanations - for which there are proof. If you mean these things simply can't exist on their own - but require a more powerful intelligent creator to put them in place - with no explanation for how he can simply exist beyond 'he does' - then you are back to hypocrisy.
How even does everything work?
Read a science text book.
Doesn't everything need someone to make it?
By that argument, God also needs someone to make him. To claim that mountains require someone to put them there but that God can just exist is ... say it with me ... hypocrisy
The second law of thermodynamics shows that everything is in a worse state than it's first state, how does this apply to everything become better and more complex than it's initial state at the assumed beginning of time?
ah the second law of thermodynamics argument - proving you neither understand thermodynamics or evolution. Here are some links www.talkorigins.org/faqs/thermo.html for anyone who thinks this is a gotcha. It's not.
But - put briefly - entropy is not the same as disorder as we commonly use the word, so trying to conflate the two is unscientific.
life is not a closed system - therefore the law doesn't act upon it the way creationist think it should.
evolution does not disprove the second law of thermodynamics or vice versa. They can both exist side by side quite nicely because they're not linked - and were never supposed to be.