Well, that's most things. We don't know its nature. We don't know whether it can be explained by the physics that we know now. We don't don't know if only the brain is involved or if there is some other entity involved as well. We don't know whether it can occur only in living organisms or it can occur in some computer-like machine. We don't know to what extent processes similar to those in a computer are involved. We don't know if something in the brain besides neural connections is involved. We don't know just what animals it occurs in and to what extent. We don't know if it is a special case of some more general phenomenon.
All I can do is to exclude some possibilities, summarize some of what we do know and do a little bit of speculating about what we don't know.
What we know about consciousness comes from three sources. The first is introspection, our ability to perceive part of the workings of our mind. The second is communication with other conscious beings. The third is the observation of other conscious beings.
Introspection is incomplete. How often have you had a feeling that you could not explain the reason for, even to yourself? How often do people lie to themselves? It is possible that some sensory information bypasses the conscious mind e.g. pheromones if such things do have an effect on humans. Nevertheless your own consciousness is the only one that you can directly perceive. There is information available from introspection that is not available from other sources. In fact we only that other people are conscious by inferring from our experience of our own consciousness. We perceive our own consciousness. We observe that other human beings are entities similar to ourselves. We observe that they behave in similar ways to ourselves. They communicate their conscious states. From this we know that they are conscious. Our perception of our own consciousness is an essential part of this inference. It is what we compare the communications and observations to.
The problem is others cannot directly perceive our consciousness, only our communications and actions. Introspection is a poor candidate for scientific experimentation. We cannot check what others are doing inside their heads and so it is difficult to demonstrate ones introspections to others and to verify them. There is the danger of seeing in oneself what one wishes to see. Thus scientific methodology tends to restrict itself to those introspections that we can be sure that everyone shares. These are the ones that we can clearly communicate to another person. This tendency leads to the temptation to reject introspection altogether as being unscientific. This can lead to communication and observation being regarded as by themselves providing all the information about consciousness that can be found. In the name of objectivity the subjective is ignored even when the subjective is what is being studied.
But we have to somehow include our self-perceptions in any complete study of consciousness. It has to be studied from the inside as well as from the outside. Either by itself will provide an incomplete picture.
Communication includes both languages and systems of signals. A language has a syntax and a set of symbols. Symbols are signs which have a meaning attached to them by the users' choice. This can be and usually is a collective and tacit choice. The same word can have different meanings in different languages. The syntax is the set of rules by which the symbols are combined to convey concepts that cannot be conveyed by any single symbol. Signals are unchosen signs e.g. a growl or a smell or so-called body language. (Body language does not have a syntax or symbols and hence technically it is not a language even though it is a structured communication system.)
Much of our communication of emotions is through body language and audible signals. We have enough body language and audible signals in common with some other terrestrial vertebrates to be able to read their emotions to some extent. We can do this reasonably well with other mammals and to some extent with birds and at least some reptiles. We can be sure that they have at least some emotions and hence are conscious. We know that there is something in there.
We can teach a syntactic language to the great apes. We know from communication with them and from observing their behavior that they are self-aware like us. I know of no evidence of self-awareness in any other animals and think they are the only self-aware creatures other than ourselves.
Some vertebrates are the only entities other than ourselves that we know are conscious to some extent. We know that because there is some communication with them. Consciousness could be found in a wider variety of animals but we can't be certain because we can't communicate with them.
Since the senses of fish and amphibians are similar to our own it is quite likely that the subjective perception of sensory data is similar. Since the senses and behavior of cephalopods are similar to those of vertebrates it is quite plausible that their subjective world is similar. But then again maybe not. The brain has been rewired a lot as vertebrates evolved. For instance more of the brain is involved in vision in a mammal than a fish's optic lobes.
For other animals we only have their behavior to go on. I don't know of any completely convincing evidence of consciousness in any other animals. I would not be surprised if there is a rudimentary form of consciousness in amphibians, some fish and some cephalopods. I would be surprised if it occurred in any animals other than the ones that I have mentioned. While many arthropods have complicated behavior it is very stereotyped and I believe that consciousness does not help explain it. The behavior of animals other than chordates, arthropods and molluscs is simpler and can be explained without consciousness.
I believe that self-awareness is restricted to humans and great apes. I believe that emotion is restricted to mammals, birds and reptiles. I believe that subjective sensation, true awareness is restricted to vertebrates and cephalopods. To put it mildly these lists are tentative.
The main argument I can think of for rudimentary consciousness in animals other than vertebrates and cephalopods is an evolutionary one. Consciousness evolved with the elaboration of the nervous system. Could there be some precursor or rudimentary form in more primitive animals? The main argument against this is that there is no apparent benefit of consciousness in lower animals and nothing in their behavior that needs consciousness as an explanation.
Could a computer or some other non living system become conscious? We don't know. I believe that a computer as we know them cannot. All computers are Turing machines. They are all purpose symbol manipulators. They can carry out any algorithm with any symbol set and set of rules for manipulating them. But an algorithm is just the symbols, the rules and a set of actions using them. Any symbol can have any meaning that we give it. Thus the meaning of what is done is not part of an algorithm. The same algorithm can have different meanings. For example we could calculate the mean weight of ten fruit. The fruit could be apples or oranges. The algorithm involved is the same. The meaning of what a computer does is assigned to it by us - it is not a property of the algorithm or the computer.
This does not mean that computable processes are not part of what is going on. Turing machines could be components of the machinery of consciousness. However they might be taking a role that could also be take by something acting in a non computable manner - say something using some random quantum process.
The ability of the neurons of the brain to modify themselves might be involved. This is only a plausible speculation. If this is the case then the hardware and software of the brain might not be distinct concepts. We will have to look at things another way - even self-modifying programs are probably not similar enough to conscious processes to offer us much insight.
MRI and other new techniques can pinpoint what areas of the brain are active when particular mental processes are going on. This still does not tell us what is happening. Just what is the relationship between the observed neural activity and the mental processes?
The nerves of vertebrates are different from those of other animals. The axons (long nerve fibers) are encased in myelin sheaths formed by of a type of cell called a glial cell. These allow much faster transmission of nerve impulses than in the unmyelinated nerve fibers of most invertebrates. (The giant motor axons in cephalopods allow even faster transmission of nerve impulses.) Are the glial cells involved in consciousness in ways other than as impulse accelerators?
Contemplate the colour blue. This is the sensation that we get when light of a certain range of wavelengths hits the retina. If the pigments in the cones were different we would gain this sensation from a different range of wavelengths. What we perceive is some mental representation of light not light itself. Our perception of the colour blue is not something that exists in the world outside our skulls. So just what is it?
This suggests that perhaps our perception of space and time is a representation rather than the real thing. We can directly visualize only three spatial dimensions but can mathematically handle any number.
We perceive our subjective selves as some sort of entities. Perhaps this is an illusion - a subjective representation and there is no thing at the core of us that does the perceiving. Perhaps the real us is just a process in a structure. But we certainly feel like we are some sort of thing. This is the strongest argument that I know of for there being something other than just the brain involved in consciousness.
People are usually vague when they talk about a soul. Is it connected to life or to consciousness? Life is well enough understood for us to say there is no need for any non physical entity to be involved. One can make a case for the soul as the non physical core of consciousness. But it cannot be conscious by itself. What affects the brain affects the mind. If the brain is inactive you are not conscious.
If the soul exists and is the core of consciousness then how can it be in a fetus before the parts of the nervous system that are involved in consciousness are active. If it is not involved in life and it is not the core of consciousness then what difference does having one make?
Is consciousness an special example of something happening around us that we are not recognizing? Yet when it occurs all its instances are isolated. As far as we know we have no direct contact with any consciousness other than our own. We only known them by communicating with them and by their effects.
We are certainly looking at something the wrong way. I believe that we are at least two major scientific breakthroughs away from understanding consciousness. I believe that something is going on that current physics cannot explain. And even after the required physical insights have occurred we will need another breakthrough to allow them to explain subjective experience.
I think that consciousness is an indicator of a major gap in physics in the same way that evolution and uniformitarianism indicated a major gap in nineteenth century physics. I believe that it will take decades or even a century or two before we understand consciousness to the same extent that we understand life now . Scientific advances do take time.