The following is an answer and/or comment by inhahe aka ColorStorm (inhahe.com - myriachromat.wordpress.com).
Q: What's the problem with viewing the universe as a giant machine from a scientific perspective?

A: How many problems there are with this view depends on how loosely you define “machine.”

For one, the universe is filled with chaos, many many extremely small parts interacting and buzzing around in different directions without any apparent/overall/macroscopic order. This isn’t characteristic of what we think of when we think “machine.” We tend to think of something that’s well-ordered, with disorder and entropy being possible features, but usually unwanted features, and in any case, the details of the tiny chaotic interactions aren’t considered when considering how the machine works.

Two, there are things like superposition and entanglement. And these aren’t just the rare exception; scientists say that all particles are entangled with all other particles, and what we commonly call entanglement is merely when experimentalists disentangle particles with the rest of the universe and leave them entangled only with each other. And all particles have a wave nature, where the wave is a probability wave, which often means the particle is in superposition. And famously, photons are known to be in all possible positions at once while in transit. And when we think of “machines,” I think we tend to think in terms of classical mechanics where every part has a definite position and all of causality can be attributed to local variables, as opposed to nonlocal ones.

Three, there are the effects of relativity, including time dilation and light cones, which limit what parts of the universe can interact with what other parts. And due to the expansion of space, there are some parts of the universe whose light cones will *never* meet the light cones of other parts. I think when we think of machines, we may not typically have to consider things like time dilation, and we probably tend to think of every part of the machine as being able to affect every other part, at least if we want it to, or via vibrations and such, and where we do consider a speed at which one part can affect another part, it tends to be for more classical reasons like the speeds at which various parts move or the speed of sound through the particular mediums.

Four, machines are normally thought of as things invented by humans to serve specific purposes. They make use of only some of the principles of physics, and they’re constructed in a modular rather than holistic way, while some parts of the universe itself may behave more holistically, such as biological beings, and of course every principle physics plays a crucial part.

Five, perhaps most importantly, to the best of our knowledge, the universe is not deterministic. Quantum mechanics. which describes everything in the universe, includes an element of inherent unpredictability, or what may be termed “absolute randomness.” It’s possible that the universe is still deterministic and we just lack the means to predict quantum-random events, but there’s no way to know that, and to assume it would presumptuous. And when we think of machines, we think of things that have well-defined, deterministic behavior on the level of abstraction we think of them on, except when they’re not functioning correctly.

And lastly, I would say there’s an entire spiritual/nonphysical reality, or set of objects, beings, principles, phenomena, substances, etc., which interact with physical reality but are non-mechanistic and therefore couldn’t be thought of as machinic, even if we were aware of them all. But this is perhaps not strictly relevant to your question, since it asks “from a scientific perspective,” and physics doesn’t recognize such things.

Eric Jones:
Very good…except for the religious part.

Richard A. Nichols III:
Thanks!
But spirituality is not religion. It’s unfortunate that a lot of people categorize spirituality in with religion, because one is true, good, and beautiful, and the other is mostly ridiculous and toxic. Religion is like spirituality filtered through the stupidity of the masses. It’s also unfortunate that most people who like science, physics, etc. are automatically dismissive of anything nonphysical/invisible/not recognized by science. It shows a profound narrowmindedness, lack of awareness, conformist scientism/rationalism/mechanicalism of our zeitgeist, and an irrational willingness to write off the inexplicable paranormal experiences that almost everyone has at some point(s) in their lives with facile, reaching, unlikely physicalist explanations.

Eric Jones:
Okay, except for the spiritually part…and the metaphysical part…etc.