Okay, I'm misreading you, then. Sorry about that. But I'm still not sure where I went wrong.
I appreciate the humility of this concession, thank you.
Allow me to explain, if I am able. Where you went wrong was with the statement about "dead particles coming alive." No, dead particles remain always dead. They don't come alive. Rather, these particles that aren't alive constitute things that are alive. How is it that I am alive when all the atoms and molecules which constitute me are not themselves alive?
It is a fascinating mystery—a fact, to be sure, but a mystery. As I said in an earlier response, right now I lean toward emergentism as an explanation, or the start of one anyhow.
My monistic materialism regards all matter as alive/sentient.
See, this is where you lose me to confusion. And it's not that you lack eloquence but rather that you so frequently contradict yourself. You also equivocate at least three separate terms—alive, sentient, and soul—differentiating them in one place but then equating them a few sentences later. Is there a distinction between them or are they interchangeable? I can't tell. All of this makes it very hard to track what you're saying.
For example, you say that all matter in the universe (apart from souls) is "negligibly alive." But then you immediately contradict that by saying, "For all practical purposes [such matter] is dead." Which is it? I'll say it again: Something that is "negligibly alive" is alive. Someone horribly wounded in a tragic accident and "negligibly alive" is heroically saved by ER doctors because she is precisely not dead.
Given the law of excluded middle, either something is alive or it is not. Have the courage to state your beliefs clearly and ditch the adverb "negligibly." It just confuses things needlessly. Own your belief confidently. Say, "All matter in the universe is alive." Sure, there are degrees of being alive; however, at the end of the day, it's all "alive" in one sense or another. So, be clear and just say "alive."
And if, on your view, alive and sentient are interchangeable terms (and you said they are), then use just one of them—the most helpful and meaningful one—and ditch the other. You pick. I don't care which, but pick one. Up to this point you have been using "alive" in one context and "sentient" in another, but if they are interchangeable terms then by using them in distinct contexts you are committing the fallacy of equivocation.
Following this advice, your view could be expressed thus: "All matter in the universe (apart from souls) is sentient to one degree or another, including the human body—but only the human soul is fully sentient." Clear, concise, consistent, and comprehensible. It is intelligible, it makes sense to me. I could interact with that. (If the terms alive and sentient are basically interchangeable, and if the term alive is essentially meaningless apart from sentience, I inferred the latter to be the most relevant term and ditched the former.)
Simple organisms, in my view, are barely sentient ...
By the way, the same principle applies here. Something that is "barely sentient" is sentient. So, ditch the adverb: "Simple organisms, in my view, are sentient—although, without a brain or sufficiently sophisticated nervous system, their bodies are not conducive to helping their soul flow its thought-currents" and so forth (whatever that means).
Anything classified by biologists as life or living, in my view, probably has a soul (assuming that biologists are competent).
I am still experiencing some confusion here. Earlier you said that innate life is a soul. Specifically, you said that all living things have innate life (sentience), and that "this innate life must be a God-given soul." If that is the case, then it's not just biological life that has a soul. It turns out that anything constituted by matter has a soul. Rocks have souls, plasmids have souls, even atoms have souls—because all matter in the universe is alive/sentient, and this innate life must be a soul, you said.
But then if everything and anything has a soul, the term is rendered fundamentally meaningless, for it can't be distinguished from anything else.
A simple organism, then, is almost as dead as a rock, ...
There's no such thing as "dead as a rock" when not even rocks are dead. Again, this continued pattern of inconsistency betrays the inherent weaknesses of your view.
It's a matter of perspective. Is my body alive or dead? Yes and No, right?
No. Your body is alive. It is not dead.
The soul is a living entity merged to every cell (albeit divinely hidden from human instruments of detection).
If the soul is divinely hidden from human instruments of detection, then in what sense is it tangibly material?
The protoplasm, left on its own, would be dead (negligibly sentient), ... [emphasis mind]
That is a self-contradicting term. If something is dead, it does not have life—not even negligibly. Something that is "negligibly alive" is alive, something that is "barely sentient" is sentient. These adverbs are demonstrating that your view lacks intelligibility.
Protoplasm "has the appearance of life" because it actually is alive. It must be, for all matter in the universe is alive.
Life exists where God has chosen to place a soul. He has opted to do this for select arrangements of matter that we call "species".
No. Life exists everywhere, remember? If life exists where God has placed a soul, and if all matter in the universe is alive, then he chosen to place souls absolutely everywhere, not just in biological species. Continued patterns of inconsistency here. When God sees a human zygote, he places a soul there. When he sees a pebble, he places a soul there. Again, the term soul is rendered fundamentally meaningless if it can't be distinguished from anything else.
In fact, the sperm and egg themselves might already have souls, for all I know.
They do, on your view. Even the molecules and atoms which comprise them have souls—because, on your view, all matter in the universe is alive and that innate life is a soul.
They are alive if they have a soul, otherwise they are dead (negligibly sentient).
Of course they are alive if they have a soul, because innate life IS a soul—remember? Or is this more patterns of inconsistency?
I don't believe that the term "alive" has any valuable meaning unless it refers to at least a primordial sentience.
And since everything is more or less sentient, there is never a time when the term alive doesn't refer to at least a primordial sentience.
Suppose I'm wrong that bacteria have souls.
Here is a good question: How would you know whether or not you were wrong about that? In other words, is your belief falsifiable? (Avoid further inconsistency by keeping in mind that you said souls are divinely hidden from human instruments of detection.)