What do you see as being the distinction? One is consciousness, the other what what you are conscious of. So, the consciousness is the program running on the computer, which is the brain. The contents of consciousness are the data that is being processed by that program.
Let me try.
To me and many other Hindus consciousness is not only the of manifest objects and feelings. We transit through three different states/forms of consciousness: waking, dreaming, and sleeping. In these three states, the form of consciousness is different: gross, subtle, and lack of awareness. But in waking and dreaming the sense of self persists. The sense of self apparently does not seem to persist through the deep sleep but if that were so, one may not return from sleep as the same person. The sense of sense is not contained in intellect. It is deeper than that and controlst all our mental tendencies.
This is approximately analogous to three forms of water: liquid water, ice and steam. These have different forms because they have different associations with other factors, heat in this case. But what underlies these three states of water is different from these three forms.
Similarly the underlying consciousness is not manifest but its first manifestation is "I" sense, which as per Vedanta is the beginning of mind. The mind, in Vedanta is not only the manifest waking state cognition of physical and mental objects but is four fold: Intellect (the debater, analyser), mind (repository of all memory, including the genetic), EGO (I am sense), and pure attribute less mind (called citta, which is nearest to consciousness). The main point to remember here is that the mind contains an information of the specific self "I am this" etc.
So, to me consciousness is the seer of the three states of consciousness and is ineffable in itself to the intellect because it is the very source of the intellect.
Science, it would seem. considers only the waking state manifestations as consciousness and probably equates that with with mind.
What do you see as the 'fundamental difference'? One is an external view dreaming, and of the other. If it is a reliable recording, all the aspects of the conscious state can be read from it.
There are several category differences, which IMO are unbridgeable.
1. What is the electrical signature of "I am this" or "I am Atanu", and how that will differ from signature of "I am Polymath"? This is most crucial. Person to person variations depend on this and the full of mental content that stores the genetic information.
2. The very forms of consciousness in three states of waking, dreaming, and sleeping are different. Do the electrical signatures capture these category differences?
3. Same applies to consciousness of fainting man, dying man, or a man experiencing non dual boundaryless-selfless consciousness. Spiritual teachers call this non dual consciousness as unborn. Experiencing and abidance in this non dual state is a paradigm shifting event for a fate bound human. One realises that one is not bound to any forms, which are creations of consciousness-mind. Many will term the above as delusion. But for me it is not so. Non dual experience is very real and is paradigm changing.
So, how does third party waking state recording of his stupendous event capture the reality?
4. Physical science can perhaps demonstrate correlations between physical conditions of one sort or another and conscious states of one sort or another; but this does not explain consciousness. Correlation is not explanation. The mere fact that something goes on in your brain when you think does not explain what thinking essentially is.
5. The consciousness on one hand and its manifestations, which are of unlimited variety, on the other hand, are not of the same category. We are recording only the manifestations and that too through a teller, who can only speak of speakable experiences and somethings from dreaming. He has no way to tell about the deep sleep state, although the deeper "Identity" consciousness persists through this state.
......
There are many more points but I will limit to this much.
Best.