I will see some aspects of the apple but not others. I will see its shape, because you can make shapes by arranging atoms in space, but I won't see its color. Then there are attributes like the fact that it grew on a tree, which I will be able to "see" if the atom-plot extends that far in space and time.

Before we go any further, I would like to know if this "counterargument by apple" is something you thought up by yourself, or if you got it from somewhere. I have an interest in knowing how these defensive memes spread.

ETA: I will try to write a little more in the way of rebuttal. But first, I will allow myself one complaint, that I have made before: arguments like this should not even be necessary. It should be obvious that, e.g., if you had a universe consisting of an arrangement of particles in space whose only properties are their relative positions, that nothing in that universe has a color. The property of being colored just does not exist there. And so, if you want to maintain that conscious mental states exist in such a universe, and that they include the experience of color, you are going to have to introduce color as an additional property somehow - a property that exists somewhere inside the assemblages of particles that are supposed to be the experiences.

So what of the attempt to rebut this with "appleness", as a reductio ad absurdum? Well, we can start by distinguishing between the apple that exists in the external world, the experience of the apple, and the concept of an apple. Before atomism, before neuroscience, human beings are supposedly naive realists who think that what they experience is the thing itself - though if they are grown up just a little, they will already be positing that reality is a little different to their experience, just by supposing that entities continue to exist even when they are out of sight.

But let's suppose that we have come to believe that the world of experience is somehow just "in our minds" or "in our brains", and that it is an imperfect image or representation of an external world. This distinction has been understood for centuries. It is presupposed by the further distinction between primary and secondary properties that has been methodologically important for the development of physics: we will develop theories of space, time, shape, and motion, but we won't worry about color, taste, or smell, because those qualities are in the perceiver only, not in the external world.

So here I sit, I see an apple, and it looks red. The physicist tells me that the apple in the external world is not red in that way. It is a colorless object made of colorless particles, but they have the property of reflecting light at a certain wavelength, and when that arrives in my eye it stimulates my brain to construct the experience of redness with which I am familiar. All right; it may be disorienting to the former naive realist to suppose that the external world doesn't contain color, that it's just an arrangement of atoms possessing the property of location but no property of coloredness. But the scientific realist just has to get used to the idea that everything they are seeing is in their head, including the colors.

But wait! Now it's the era of neuroscience and molecular biology and cognitive science. The inside of your head is now also supposed to be made of colorless atoms. So it now seems like there's no place left in the universe where you can find an object that is actually colored. Outside your head and inside your head, there is nothing but colorless particles arranged in space. And yet there are the colors, right in front of you. The apple looks as objectively red as it ever did.

Historically, property dualism and strong emergence has been a common response to this situation, among people who thought clearly enough to see the difficulty. For example, see Bertrand Russell writing about two types of space, physical space and subjective space. Physical space is where the atoms are located, subjective space is where the colors and the experienced objects are located.

So why don't functionalists and other contemporary materialists openly avow property dualism? I think a lot of them just habitually associate experiences and mental activity with "brain states" and "computation", and don't actually notice that they are lining up two different things. The attitudes of instinctive programmers towards computers probably also contribute somehow. People get used to attributing semantic states and numerous other properties to what goes on in a computer, and forget, or never even learn, that those attributed properties are not intrinsic properties of the physical computer, no more than the shapes of letters on a page are intrinsically connected to the sounds and the meanings that they represent. The meanings that are associated with those shapes are a product of culture and of the mental intentionality of the person actively interpreting those shapes as symbols. This also applies to just about everything that goes on in a computer. A computer is a universal state machine capable of temporarily instantiating specific state machines which can causally model just about anything. But the computer doesn't literally contain what it is causally modeling, just as emails don't literally contain the meanings that people extract from them.

Another confusion that occurs is treating basic sensory properties like categories. There is no reason to believe in a fundamental property of "appleness". If I identify an object I experience as an apple, it is because it possesses a conjunction of other properties, like shape, color, perhaps taste, perhaps physical context, which lead me to deduce that this thing in front of me is one of those edible objects, grown on a plant, that I have encountered before. But consider the properties on the basis of which that identification is made. Sometimes it is argued that, for example, "red" or "redness" is also just a category, and so if you can show that the brain is a computer which computationally classifies optical stimuli according to wavelength, you have accounted for the existence of colors. It may also be added that different cultures have different color words, whose scope is not the same, so there is no reason to believe in colors above and beyond cognitive and cultural constructs, and wavelengths of light.

But what color categories classify are specific instances of specific shades of color. We can group and regroup the spectrum of shades differently, but in the end the instances of color have an existence independent of, and prior to, the words and categories we use to designate them. And that is the level at which the existence of color refutes any claim to the ontological completeness of a physics of colorless particles. You can organize the motions of particles so that they form state machines undergoing conditional changes of state that can be termed "classification of stimuli". But you do not thereby magically bring into being the existence of color itself.

Ironically, in a sense, such magic is precisely what a functionalist theory of consciousness (and of the existence of conscious persons) claims: that just the existence of the appropriate state machine is enough to guarantee the existence of the associated experience or the associated person. Since the ontological ingredients of these experiences can be lacking in the computational substrate, the implication is that they come into being when the state machine does, in a type of lawful property dualism where the fundamental laws of psychophysical parallelism refer to computational properties on the physical side.

Now of course, people who believe in mind uploading would viscerally reject the idea that they are saying that nonmaterial qualia or even nonmaterial souls would materialize when their emulation started running on the computers of the post-singularity future. That's supposed to be a dumb idea reserved perhaps for Hollywood, and writers and an audience whose minds are still half-choked with spiritual delusions about the nature of personhood, and for whom computers and technology are just props for a new type of magic. CGI can show a misty soul congealing around the microprocessors, ghosts of the departed can show up in virtual reality, Neo can have his "matrix vision" even when he's unplugged and in the real world...

My thesis is that people who believe in standard materialist theories of mind, and who would pride themselves on knowing enough to reject that sort of hokum, are doing exactly the same thing on a higher level. These aren't childish delusions because they are based on a lot of genuine knowledge. It is actually the case that you can put a chip in someone's brain and it will restore certain simple neurological functions. It does appear that large tracts of the nervous system truly can be understood as a type of physical computer. But that's because we are describing unconscious activities, activities that take place "out of sight" - more precisely, out of awareness - so problems like "where is the color" don't even arise. "Consciousness" or "experience" is the problem, because it is the repository for all the types of Being that we experience, but which are not present in the ontology of the natural sciences.