To me, both sides accept what is written in their holy texts, to atheists it is books on physics and biology
Science and religion don't have to be at odds with each other. Religious people can and do also believe in physics and biology. In fact, some religious scientists believe more strongly in physics and biology than many atheists. Another example of religion/science not being at odds is the Roman Catholic church accepting evolution as a scientific fact.
On the flipside of the coin, many prominent scientists have also been very spiritual/religious. Newton, Einstein, Planck, and others either followed a particular religious dogma or described themselves as spiritual/religious or as believing in a supernatural force.
The way I see it, if science can explain something, then it's not in religion's realm anymore. Science explains the known, while religion explains the unknown.
Think about the old debates about the sun revolving around the earth, those beliefs were in large part based on the bible. Once science discovered how and why planets revolve around the sun, this was no longer a topic in the religious realm, it was no longer an "unknown". Or think about many ancient beliefs of the different roles that "Gods" played in creating rain, harvest, fire, thunder, etc. We no longer use religion to explain these phenomena because science has explained how much of the natural world works.
The difference that I see between the "holy books" that you reference is that religious holy books must be taken on "faith" for the most part (several different ones claim to be the word of God). In contrast, physics/biology/etc, the "holy" books of atheists, can be taken on reason and the scientific method.
natural science wants to be ordered, but I don't feel it is
It seems like you're a little harsh on science (although I'm probably biased coming from a scientific background). Natural science isn't perfect and never will be, as its goal is constant improvement/advancement of knowledge and understanding of the world around us. So, there are things that we believe are true now, which might change as we learn new information in the future. That's just the nature of science. However, that doesn't mean that the scientific method isn't valid.
If you're critical of the scientific method, the "religion" of many atheists (if you think physics/chemistry books are atheist "holy books"), then give some thought to the following:
Do you think the sun revolves around the earth? Why or why not?
How old do you think the earth is and why?
Do you think the bridge you drive over will support the weight of your car?
Do you trust the medicine that your doctor prescribes for you and why?
Do you think that smoking increases one's risk of cancer?
Do you think your microwave will heat up food when you turn it on?
Do you think people need to get a new flu shot each season and why?
In my experience, many people are critical of science and the scientific method if/when it challenges one of their deeply held religous beliefs, such as belief in the bible. However, these same people subconsciously build their lives and everyday non-religious beliefs around the scientific method.
I personally try to embrace the "uncertainty" of science, the fact that science can only tell us so much about our world at the current time. In the future, we may learn new scientific facts, which may change the way we view both science and religion (i.e. sun revolving around earth).
But just because one believes 100% in the scientific method doesn't mean they can't also believe 100% in a particular religion, as religion/spirituality describes the world where science leaves off. Or as Galileo put it, "The Bible shows how to go to heaven, not how the heavens go."