As a general rule, a philosophical stance is shaky if one of its most well-respected rationales is an argument from ignorance. In the case of an immaterial soul, the argument from ignorance refers to the mystery of the brain code for information. Defenders of an immaterial soul may try to reckon that this ongoing mystery implies the impossibility of a soulless brain that operates according to boring theories of physics/chemistry/biology. As they may say, if everyone is currently ignorant of precisely how a brain composed of matter encodes the entire range of conscious experience, then isn't it more reasonable to revert to the ancient proposal that a soul is the mechanism instead?
I don't think so, but I willingly acknowledge that a soul could feel more satisfying. I've previously admitted that every objective explanation of conscious experience suffers from a "gap in immediacy". It's like the objective explanation that normal heat is infrared light, regardless of whether humans experience the two categories through differing senses or conscious experiences. In the same way, no matter how much human knowledge discovers about the brain code, the knowledge won't be an "intuitive" match. Broad reality isn't obligated to fit narrow human preconceptions. It's plainly ridiculous to demand that accurate discoveries about the brain code must be as easily teachable as all faith-based explanations.
On the other hand, I also acknowledge that this argument from ignorance is built upon a straightforward hypothetical question: is it possible for an ignorant but open-minded investigator to verify that information is coded somehow in an arrangement of matter like a soulless brain, despite their partial or total ignorance of the code it uses? Of course! Moreover, the number of illustrative metaphors from across human civilization is virtually limitless, especially now in the much-hyped Information Age. In an effort to select a common one that's neither too old nor too new, consider the compact disc. A clever and spectacularly uninformed investigator will attempt to determine whether information is coded on a compact disc. I'll call the investigator by the surname "Japp" (no relation to any other inspectors).
The most obvious solution is for Japp to place the disc in a corresponding machine that's manufactured to 1) read such discs and then 2) produce the encoded information and all its associated effects. Perhaps Japp has access to a laptop computer. As soon as Japp has a conscious experience of the information, such as a high-fidelity audio recording, Japp may report that the disc encodes the information. To be more certain that the information is encoded on the disc rather than in the disc reader, Japp could try repeating the experiment with other discs and other disc readers. This first attempt is like talking to a subject in order to confirm that they can describe the desired information whenever they're asked the right questions; if they can, then the questioner accepts that the information in the subject is coded by the subject's brain.
At this point, Japp might announce success in the small-scale investigation. But in a surprise twist, an objector suggests to Japp that perhaps the information isn't coded in the material of the disc itself. After all, it's evident that the disc is "only an object" and not a conscious experience of information. What if the information mostly consists of a ghost in another "plane" of existence altogether, but it happens to "coincide" with the disc? And the information ghost of the disc manifests because it temporarily possesses the disc reader? (Feel free to substitute "long-lasting quantum effect" for "ghost".)
Ever careful and patient, Japp responds by analyzing the internal structure of the disc and its reader in closer detail. Clearly the reader has a laser component. Japp tries temporarily obstructing and then exposing the laser component, perhaps with some opaque tape. These sneaky manipulations affect the information output of the reader via an extremely close correlation. Next Japp announces that if there is an information ghost, then it's affected by temporarily tampering with the materials of the disc and the reader. Whatever ghostly form that the information has, it's nevertheless dependent on the smooth operation of the material of the disc that's hit by the laser. This second attempt is like feeding a subject a chemical dose that affects the nervous system, such as alcohol; if the subject's ability to produce information is affected, then the outcome indicates that the information in the subject is dependent on the smooth operation of something material, i.e. the nervous system.
However, this demonstration isn't drastic enough. A second objector suggests a more nuanced interaction between the information ghost and the disc. What if it's dependent on the disc because it "flows through" the disc, and therefore the disc acts solely as a channel or conduit? In effect, the matter of the disc still doesn't predetermine the ghost, but the ghost requires the disc anyway.
Japp shrugs and remembers one of the details from the recent analysis of the disc's structure: it contains a definitive sequential order. Some sections of the disc come first, others are in the relative middle, and others are at the end. Japp grabs a tool, mentally divides the disc into seven sequential sections, and wrecks just the fifth of the seven sections. Then the information is reproduced from the disc once again. Unsurprisingly, the conscious experience of the sequence of reproduced information is mostly intact...except for when the information sequence has progressed to about five-sevenths of the whole. Japp notes that not only does the information as a whole correspond closely to the disc as a whole, but a part of the information corresponds closely to a part of the disc. This third attempt is like examining the recently traumatized brain of a subject who has a highly specific problem in their mental capabilities or memories; if the subject's brain shows problems in the corresponding area of that capability or memory, such as an abnormal growth, then the outcome indicates that the information (or behavior) in the subject is encoded bit by bit in the subject's brain.
Finally, after reviewing the previous discussions, a third objector suggests that Japp hasn't convincingly shown anything important about the original question. What if the contribution of the information ghost is yet more puzzling? Perhaps most of the information, or even almost all of it, is coded by the matter of the disc, but the ghost's role is to furnish an essential core or "organizing principle"? In effect, the ghost is responsible for making the information coherent and interesting. Unless it's proven directly that the material of the disc accounts for every last jot of information, the ghost could be a factor.
Japp groans and proceeds to learn about the engineering of the disc and the reader as well as the computations to transform the bits on the disc into the final information output. Japp delivers a series of lectures. The third objector complains that Japp is obscuring a topic that should be simple: a mundane sequence of information and a mundane circle of cheap material.