[Popper] essentially makes an argument from faith that science will objectively discover the means by which the brain interprets sensory input and thus objectify the sensory input. This is problematic.Besides using Randianism as an exemplar (unless one is rebutting Rand directly and exclusively, employing Randianism can always be presumed to be a straw man argument), Bruce's objections assumes premises specifically denied by scientific reasoning.
In order for science to explain how the brain is subjectively interpreting an alleged objective, ontological reality, it has to identify a case of “distortion” by subjective interpretation (i.e. it needs an actual case to explain otherwise its explanatory power is the same as that as the ontological argument of Aquinas). A precondition of identifying an instance of subjective interpretation is to have both subjective and objective knowledge of some ontological fact.
It’s a chicken and egg scenario. Before we know how the brain subjectively treats X through observation, we need to compare subjective X to ontological X in its uninterpreted (i.e. unobserved) state. This precondition is impossible.
Bruce is correct: It is impossible under scientific reasoning to have positivistic, direct knowledge of "objective perception". Such observations assumed a priori to have veridical content are denied — implicitly or explicitly — in the scientific method. But having this sort of observation is not, as Bruce declares, the only way to justify belief that some aspect of perception is indeed subjectively established.
One does not need to go on at length about one's perceptual beliefs about one's toes. A more compelling and obvious example can be found in the grey square optical illusion. In this illusion, square B appears substantially lighter than square A. However, under different circumstances (such as covering up the rest of the picture except the two squares) the squares appear to be the same shade of grey. Furthermore, we can also examine the output of abstract measuring devices such as a light meter or the digital RGB values of the underlying image, leading to their own subjective impressions of seeing the same number.
Under the scientific method, as Bruce notes, the veracity of none of these observations can be assumed a priori: none can be assumed to be the "true" objective observation. Rather what we have are a collection of observations in apparent conflict. Note that all of these different modalities of observation do not yield the same sort of conflict when applied to square A and the square immediately adjacent to it in the top left (A'): all observational modalities yield "different shade". Likewise the square diagonal to A (A'') appears the same in all modalities.
To resolve this apparent conflict, we construct the simplest theoretical structure we can imagine to account for all the observations. I will leave the details to the scientists, but it seems clear even to the lay observer that the theory that our minds are supplying the difference in color because of adjacent visual context is simpler than the notion that the squares are changing their "objective" color when the context is manipulated, or when we use abstract measuring devices. Indeed we define the "objective" properties epistemically as those properties that do not change under alternative modalities; we define "subjective interpretation" as those properties which differ from alternative modalities, appearing only on direct human observation. (Furthermore, this definition entails the falsifiable hypothesis that there is some definitely identifiable computational structure in the brain, which we can identify by looking just at the neurons, that accounts for the subjective interpretation.)
The above evaluation highlights some of the objections and metaphysical "bullets" we have to bite to commit to confidence in the scientific method.
First of all, the notion of theory-laden observations (a light meter is a fairly complicated piece of equipment, and an examination of the digital pixel values of the binary version of the image rests on how computer monitors work) is not itself problematic. Even if such devices were the only way to get a different observational modality, what requires explanation is that A and B appear the same shade under these alternative modalities, whereas A and A' appear different under these modalities (and A and A'' appear the same on both direct observation and alternative modalities). Since the modalities are the same in all cases, they can be subtracted out without knowing their precise details.
More importantly, we cannot know whether some new fact will change our theory, and we cannot know if some new radically different theory will be simpler than our original theory. Not only that, we cannot measure or predict even the likelihood or probability that some new fact or theory will completely change our minds. (The only uncertainty we can actually measure is the probability that some correlation occurs by chance.) The best we can say is that any radically new theory will still have to account for the same facts, and will have to account for why our present theory appears to be the simplest.
This uncertainty is a metaphysical bullet the scientifically minded person must simply bite. The scientific method itself cannot be justified deductively or foundationally. The scientific method is justified only pragmatically: it does the job here and now we require of it, and on that basis we employ it until we have something better.
The alternative to biting the scientific bullet, though, is breaking one's teeth on a much harder bullet: Under the deductivist view, which demands either certainty or measurable uncertainty, we have not yet figured out a way of having any knowledge at all! For this reason, I find the deductivist critique of the scientific method uninteresting: No, the scientific method does not provide certainty or (Popper notwithstanding) even certain kinds of measurable uncertainty; this behavior is by design. Pointing out this lack of certainty is akin to criticizing democracy because it doesn't privilege an absolute leader, or criticizing meta-ethical subjective relativism because it doesn't provide an objectively determinable ethical system.
What is necessary to give any sort of power to the deductivist critique is an alternative account of knowledge. The best the deductivism has shown is mathematics, which simply defines itself to be correct in its axioms. And even if we admit mathematics as some sort of "knowledge", it fails to give us any knowledge about the details of (depending on how you want to phrase it) our actual world or our actual experiential life.
Update: Bruce responds to my essay