The ghost in the machine means the consciousness or mind carried in a physical entity. Gilbert Ryle coined the term in his 1949 work The Concept of Mind as a criticism of René Descartes. Descartes believed in dualism, the idea that the human mind is not physical, that it exists independently of the human brain. Ryle referred to this idea as the ghost in the machine. He believed that human consciousness and mind are very dependent on the human brain. The term ghost in the machine has come to also describe the supposed consciousness in a device that behaves as if it has a will that is independent of what the human operator wants the device to do. Computer programmers have appropriated the term ghost in the machine to explain when a programs runs contrary to their expectations. The idiom ghost in the machine is a metaphor, which is a comparison that is made figuratively.The term is derogatory It refers to natives trying to explain how a steam locomotive can move without houses. Referring to belief in the soul as "ghost in the machine" is like calling religious people primitive and superstitious.
Gilbert Ryle once ridiculed substance dualism, describing it as the view that we are a “ghost in the machine.” Since that time, substance dualism has found few defenders, and a presumption toward naturalism has dominated philosophical inquiry. Here, I offer an unapologetic defense this unfashionable view of the self.To think as a scientific modern one must hold that we are merely very complex clockwork mice. I could not accept that view even as an atheist. There is no reason to reduce us from the mental creature we know ourselves to be. I have always felt that the researchers really hold out for their own specialness.
Atheists who try to reduce God belief to primitive terms equating belief in a transcendent reality with ghost in the machine;God is the ghost in the machine of the universe. But I counter this with the concept of the transcendental signified; It's not pinned down to a specific understanding but is equated to function not substance. In terms of belief in God this can best be understood through the analogy of mind and use the paradigm of universal mind.
(1) universal mind, offers the best understanding of TS
The reason modern thought is missing the unity (the TS, the nature of the universe, and meaning) is because it leaves out mind as the basis of the ἀρχή; minds organize and communicate meaning, thus modern thought is missing the connecting link between the TS and the nature of things (such as hierarchical organizing). Thomas Nagel in his book Mind and Cosmos (the subtitle: of the book says it-- “...the Materialist Noe-Darwinian Conception of Nature is Almost Certainly False”) argued that mind is the missing dimension with which modern thought refuses to deal, and this is why they can't solve the so called “hard problem.” He did not argue that evolution is wrong but that the reductionist understanding will never unlock the hard problem because they can't admit there's an aspect of the world their methods can't grasp. He says it's not just about brain and mind but that “it invades our understanding of the entire cosmos and its history...a true appreciation of the difficulty of the problem must eventually change our conception of the place of the physical sciences in describing the natural order.” Now this doesn’t prove that turning to introduce mind into the equation proves the solution, but it gives us reason to think that if leaving mind out of the equation is a major part of the problem, then including it is probably part of the best hope we have of solving it.
Even so the single first principle by itself is missing the dimension of mind. It's the dimension of mind that really enables an explanation uniting all the major areas of human being: the physical nature of the universe, the moral, and the existential or the dimension of our being where higher meaning and sheer existence meet. This is the full elucidation of being por soir. Science is wiling to stick with en soir. And that's acceptable because it's purpose is not to explain purpose of our being. That's a job for theology. Science really does not require the God hypothesis because it's function is not to unify these noetoic aspects of being. Being in itself is fine for scientific explanation. But we need more. Mind is the missing dimension because mind gives purpose. Consciousness seeks understanding, If the top of the metaphysical hierarchy is mind it would explain how meaning and moral precept and/or virtue could be part of the fabric of what is.
The elephant in the room on this premise is the insistence by physicalism and materialist thinkers that mind is merely brain activity. The skeptic will argue how can there be mind without a brain? The brain/mind reductionism has become so all pervasive in atheist circles any discussion of God or mind on the internet will result in that argument. There are major researchers who don't go along with the reductionist view. Raymond Tallis former professior at University of Manchester, denounces what he calls “neurohype,” “the claims made on behalf of neuroscience in areas outside those in which it has any kind of explanatory power….”
The fundamental assumption is that we are our brains and this, I will argue presently, is not true. But this is not the only reason why neuroscience does not tell us what human beings “really” are: it does not even tell us how the brain works, how bits of the brain work, or (even if you accept the dubious assumption that human living could be parcelled up into a number of discrete functions) which bit of the brain is responsible for which function. The rationale for thinking of the kind – “This bit of the brain houses that bit of us...” – is mind-numbingly simplistic.
Aside from arguments based upon neuroscience there's an even better reason to discount the reductionists. The nature of the human mind is not the issue here. We are talking about the assumption of mind in understanding the TS. The nature of biological organisms is irrelevant. There is no justification for thinking of God as a big biological organism. God is not analogous to the most powerful being. He's not Zeus he's not superman. He's not really a “He.” “He's” not even analogous to the laws of physics. “He's” the basis upon which the laws of physics cohere. At that level we can consider God as pure mind or mind itself. It's not a mind, it is mind. The source and origin of mind.
The issue here is not the production of mind but the content. The notion of meaning necessitates purpose. Meaning is the communicated purpose involved in an utterance. That requires consciousness, self awareness and rational purpose. These are all qualities of mind. We can't prove mind behind the universe but we can show that there is no coherence between the various organizing principles (Op's) if we assume naturalistic ends. Yet we can understand coherent unity between Ops, moral precepts, an existential meaning if we assume mind. If we assume a creating mind is responsible for hierarchical ordering we can see rationale for organizing, moral motions, and a purposive existence for humans all cohering in the unity of creative wisdom and purpose. That would seem to indicate that mind is the best explanation. Thomas Nagel points out that mind is the missing dimension that naturalism has left out. Nagel was scathingly criticized as a creationist (he's an atheist) the man himself avowed in the work that he sought to make the naturalistic explanation more complete. A theory of everything has to explain mind and reductionism merely explains it away. The point is that without linking purpose to meaning we have a sort of localized meaning, private truth good for each individual not related to the whole.
I came into this world, I understood nothing, I saw many things what they meant they only meant that to me. No one else knows that meaning, no one cares nor do I know what those things mean to others. Soon I will be gone. Those things that meant something to me will soon cease to mean anything to anyone. They and I will be forgotten. That is what we get with a purely naturalistic reading of life. That is truly meaningless in any final or lasting sense. That sort of existence is a brute fact only. Some revel in the brute nature of such facts. But we must ask the question, not out of mere personal feeling but in spite of it: are these brute facts or deep structures? If the latter the things we have seen, the lives we live the deaths we all die are not merely brute facts. They are deep structures because they have meaning. They have a sort of meaning that lives on after us and is more than us. Of course a lot skeptics will say that I merely can't take anonymity. They can't either. If they can why do we leave things for posterity? Why do we care about how we leave the earth for future generations? While it seems that so many reductionists want to be robots and don't care about meaning if it's true they revel in being meaningless why do they blog? Why social media? Why are we concerned with what violence is purported upon others or what bigoted things Presidential candidates utter? Because meaning is more to us than just a private, relative, and through away. If that weren’t true we would not have sought so long for a logos or a TS or a theory of everything.
(2) Concept of God unites TS with universal mind, therefore, offers best explanation for a view that is RCM
God is Derrida's Prime example of TS. Nancy Murphy and James McClendon, speaking in the context of Derriodian thought, state, "Without God, who has been the ultimate Transcendent Signified, there is no central perspective, no objective truth of things, no real thing beyond language."  Creating, ordering, and sustaining the cosmos and grounding meaning and all reality would require a metaphysical ἀρχή (first principal) with God-like attributes (from the glossary: The eternal and necessary foundational aspect of all being which creates all things and chooses to do so is compatible with the definition of "God" found in any many major world religions, including Christianity ).
God and Mind
I am arguing for warranted religious belief, and belief in God in a general sense, not for any particular tradition, I do have Christian belief and I am committed to the Christian tradition and to a relationship with Jesus, but I am bracketing that for now to deal with the ideas in a more general sense. I understand God to be universal mind which is not only part of the basis of Christian mysticism and the orthodox Church but also reflected in such modern thinkers as Paul Tillich, John Macquarrie, and Hans Urs Von Balthasar. Tillich and others filter it through Heidegger, saying God is being itself. In History of Christian Thought Tillich interprets Dionysius to say God is the ground of everything, the super essential God beyond everything, inclining Platonic ideas and essences, he says Dionysius thought God is God beyond God (Ibid). That ties the Dionysian concept decisively to Tillich's view.
If we want a rational view of the universe we need to plug mind back in to our understanding. There is a problem in that the imposition of a TS may be understood as a contradiction to the Heidegerrian/Tlillichian view that discussed above.
'Staff, "Ghost In the machine" Grammarist
Matthew Andrew Skene, Putting the Ghost Back in the Machine: A Defense of Common Sense Dualism, PDF.Dissertation, Syracuse University (2013)
David Chalmers “Facing up to the Problem of Consciousness,” On line resource University of Arizona, URL:
http://consc.net/papers/facing.html accessed 11/25/16
Chalmer's concept for for summing up the unresolved aspect of consciousness studies, a precise understanding of what conciousness actually is a nd how to understand itat the experioential level, and how it differed from brain function and what causes it,
Thomas Nagel, Mind and Cosmos:Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False,. Oxfor: Oxford, London: New York University Press, first edition, 2012,3. (see chapter 1). The reason why a rendition of bran functions is not answer to the hard problem is because the question demands an understanding from the inside out,
 Raymond Tallis, “Ideas for Godless People” New Haumanist.org.uk (blog—online researche) volume 124 Issue 6 (Nov/Dec 2009) URL: http://newhumanist.org.uk/2172/neurotrash acessed 5/9/12
Thomas Nagel, Mind and Cosmos:...op cit., 3.
 Nancy Murphy and James McClendon jr." Distinguishing Modern and Postmodern Theologies." Modern Theology, 5:3 April 1989, 211
Paul Tillich, Systematic Theology volume II, Chicago: University of Chicago Press, 1957, 10-11.
John MacQuarrie Principles of Christian Theology. New York: Charles Scribner’s Sons, 1966. 92,97
Hans Urs Von Balthasar “A Resume of my Thought,” in David L. Schindler,Hans Urs Von Balthasar: His Life and Work. San Francisco:Ignatious Press, 1991, 3.
Paul Tillich, A History of Christian thought, New York, NY:TouchStonme books. 1967, 92