Something you might be interested in looking into, as a candidate for your "Initial Alteration" , is the ARHGAP11B mutation.

You can find some relevant links in this discussion on another forum. (That discussion did go on for a long time, and is to a significant degree an atheist vs theist discussion between people with a long history that devolved into a flame war, but I think you can find the most informative links in the first page of the discussion.)

This article aims to show that if we assume two things as given, that of an interactionist view point and the theory of evolution by mutation and natural selection, it follows that there is a particular moment in time I label the initial alteration.

I might argue there is no particular moment so described, but rather a long more or less continuous development of human consciousness. More or less in that there are jumps here and there, but overall a kind of continuity with various aspects of mind appearing as a kind of dynamical system influenced by feedback from environment.

But the whole point I'm making is of the behavior of matter in the brain. If the atoms in the brain continue to exhibit the exact behavior you would predict via physics given their mass, velocity, charge ect.. then you could explain the behavior of said organism simply knowing these things. This does not appear to be true for humans, who talk and write about Qualia after they experience it. If there is no change in behavior of matter, they could have NEVER experienced Qualia in the first place and their behavior would be exactly the same. If there is a change in the behavior of matter, there had to be a FIRST change in the behavior of matter evolutionarily. A gradual process has to start somewhere.

If the atoms in the brain continue to exhibit the exact behavior you would predict via physics — Francis

But the same can be said for all organic life-forms. Organic molecules, specifically DNA, the most primitive and basic life-forms, have attributes and characteristics that can't be accounted for, or reduced to, simple physicality.

If the atoms in the brain continue to exhibit the exact behavior you would predict via physics given their mass, velocity, charge ect.. then you could explain the behavior of said organism simply knowing these things. This does not appear to be true for humans ... — Francis

It does not follow that a system being a purely physical process, that the behavior of the system can necessarily be explained. It may require a greater understanding than is currently possessed.
For instance, one could in principle simulate (down to the classic electro-chemical level) an entire human being and his environment, and the human would (per monism) behave and describe the same qualia as a human, and yet nobody (the simulated human, the computer, or those that programmed it) would have be able to explain this behavior.
Your comment also exhibits anthropocentrism, that concludes that only humans have this relationship since only they utter the word 'qualia', which is an incredibly poor assumption if you're going to examine this from an evolutionary approach. You seem not to maintain this through the paper, which is good. I mean, ants appear to experience pain, even if it obviously isn't human pain.

Anyway, not my point to debate your biases. I was wanting to read and comment on the paper since few do this sort of thing.

A simplistic definition of Monism is that it attributes a kind of oneness to the mind and brain.

I'd correct that to oneness to the mind and body, or rather, oneness to system and processes of that system. A brain is just part of it, and in isolation, doesn't have the attributes of which you speak.

You speak of epiphenomenalism, but there can be no evidence of this. The subject mind cannot report the qualia felt for instance, so any such report is not coming from it. I take it you're not supporting such a position.

You quote Robinson on interactionalism:
"mind having a causal influence over the brain implies that some matter in the brain of humans (and possibly some other organisms) is behaving differently than would be expected if that matter had been governed completely by the conventions established for their behavior by physics and chemistry."

This leaves the door open for other creatures, and it says in short that there must be a violation of physics/chemistry going on somewhere for this interaction to occur. I content that it doesn't necessarily need to occur in the brain, but it could be elsewhere. Heck, there are things that feel, experience, learn and teach, all sans brains altogether. Anyway, I agree about the physics violation, and it is that which should be sought out by the proponent of this position, instead of avoided as is the usual reaction.

Robinson says that 'physical closure' says 'every event has a physical cause' which quantum mechanics has shown not to be true, but one can note that biological process for information processing tend to evolve structures which exhibit classical behavior from quantum effects, just as do transistors say. Hence there does not appear to be structures designed to amplify quantum randomness. And trust me, if there was information to be had in reading such randomness, structures would have evolved to take advantage of it. We don't see that but it might be there. A search for such a thing is still a window for the interaction.

The Neural Correlates of Consciousness or “the minimum neuronal mechanisms jointly sufficient for any one specific conscious experience.” (Wu, 2018) The Neural Correlates of Consciousness reference the set of objects in the brain which give rise to consciousness but does not exactly mention the reaction of the brain to consciousness.

I don't think Wu is using 'consciousness' in the same way you are, which is 'something separate to which a connection must be made'. Not sure. Maybe he is.

it is safe to assume this creature also had a primitive mind and experienced Qualia (the name given to single instances of subjective experience). So how did we get from these organisms to humans today?

Unimportant. If they're already connected to a mind, the question is how they went from a physical creature obeying physical law to one that isn't. The answer is how the chimp got there, not how some common ancestor of the chimp evolved into us. All this is moot if you can actually locate where the violation occurs, in which case one can simply backtrack, looking to see which being have such a mechanism and which don't.

So you should be looking for some mutation which causes the physical creature to gain beneficial information from non-physical sources. Did the mutation cause access to this 'mind' thing already there waiting for something with which to interact, or did the mutation somehow create something non-physical in such a way as to maintain a connection to it? I don't know your model.

Meaning, there was a first time the behavior of matter in the brain of some organism in our evolutionary past was altered from its behavior that would be expected if it were behaving purely by the conventions of physics and chemistry.

Yes, exactly, but still with the questions above.

From an interactionist standpoint, the only alternative to this conclusion is that the initial alteration in the behavior of matter happened before organisms developed brains.

Please don't discount this. There are non-brained things that potentially qualify. There are undoubtedly aliens which don't have anything resembling Earth biology. This is irrelevant of course in a pursuit of how it came about in Earth biology.

Some questions that could be asked are: In what organism did this take place? How long ago in our evolutionary history did it take place? What objects in the brain were involved? How many objects in the brain were involved?

Did it take place more than once? (plenty of examples of parallel evolution)
Were brains involved at all at the time?
You ask if consciousness was involved, but you've not really given your definition of that. I mean, I have a pretty loose definition of a system being able to measure its environment and react to it, but you probably envision something more complex than that, something on the order of 'is like me'.

You ask how many 'objects' in our brain are involved in [human] consciousness, which is dependent on your definition, but probably 'a lot of the cortex', but this implies that creatures lacking one don't 'feel' things, which is very likely wrong. The cortex is the slow part of your brain that is mostly the thing getting trained in all those years in school.

I am unclear on your section on experimentation. I don't see a proposal. Do X and measure Y. None of that. If you're not looking for the specific point of physics violation, then all you're seeming to be doing is searching for a better 'explanation' of the monist view. Once the 'violation' is isolated, you look for that structure in other beings to get a good idea of its evolutionary history.