1. Why we need a proper theory of consciousness?
I agree full-heartedly with Lubos that our arguments (we, the physicists;-)) should be independent of our personal idiosyncracies, the details of our particular species, our culture, etc... It seems however that to achieve this freedom, "we" should have some kind of abstract overview about all possible species and all possible cultures. The only hope to achieve this kind of rough overview is by extending physics to a theory of consciousness allowing to say something very universal about life and intelligence. I am a little bit surprised how few theoreticians are taking this challenge seriously although the quantum consciousness movement began already at eighties (Esalem, Finkelstein). Perhaps super string models caught the attention of the most imaginative brains at that time.
2. Geometric time and experienced time
A proper theory of consciousness could remove a lot of mist floating around the concept of time. Experienced time and geometric time are very different things but for some odd reason most physicists stubbornly continue to identify them. The paradoxes are unavoidable. For instance, Lubos mentions the paradox implied by "Now as the maximum of entropy" assumption made by some cosmologists.
I think that the lack of understanding about the relation between experienced time (or "de-coherence arrow of time") and geometric time is the main source of confusion and a treasure trove of misleading arguments. If one accepts that these two times are different notions, one must among other things ask whether both of these times have an arrow. I would guess "Yes": by quantum classical correspondence space-time geometry should provide a representation for the sequence of quantum jumps and therefore for the contents of consciousness (in my own theory world). Note that this requires the failure of strict classical determinism for the dynamics of space-time surfaces and can serve as a valuable guideline. The directions of these arrows of time could in principle be independent. Indeed, for phase conjugate laser beams the arrow of geometric time and de-coherence time seem to be opposite. Self-assembly in living systems would be a decay in a reverse direction of geometric time and consistent with the second law a deeper level.
3. The issue of initial conditions
Lubos talked also about the issue of initial conditions and the new view about time allows a fresh approach to the problem. First of all, I would talk about boundary conditions in the geometric past since geometric time is in the same role as spatial dimensions in any relativistic theory. Secondly, the idea about the initial/boundary conditions as something fixed by God at the moment of creation carries a flavor of medieval theology. If theorist must fix initial conditions by some educated guess of what medieval God willed, most of the predictive power of theory is lost, and in principle the theory becomes intestable since one cannot compare the time evolutions of different classical worlds. It is somewhat surprising that theoreticians still use this medieval conceptualization. Perhaps an introductory course to philosophical problems of physics without professional jargon and in science fictive spirit would help.
The notion of boundary conditions at big bang has different interpretation if one accepts some amount of consciousness theory. Suppose that you believe that conscious existence is a sequence of quantum jumps replacing the quantum superposition of classical four-worlds (analogous to Bohr orbits) with a new one (what these quantum jumps are, is of course a non-trivial question). The key observation is that the average boundary/initial conditions defined by the quantum superposition change in every quantum jump. Quantum jump re-creates also the geometric past. Quantum jump sequences are expected to lead to asymptotic self organization patterns and they could correspond to rather specific boundary conditions in the geometric past (somewhat misleadingly, "moment of big bang"). The basin of attractor leading asymptotically to a particular effective cosmological history becomes a more natural notion.
In this framework the victories of anthropic principle could be interpreted differently. Asymptotic self organization patterns resulting in quantum jump sequences correspond to very specific values of coupling constant parameters of the theory. If one also accepts that quantum jump sequence gives rise to as genuine evolution then these values would favor intelligent life in some form. Genuine evolution would however require a new kind of variational principle. There is room for this kind of principle since there must be some law telling what it is possible to tell about dynamics of quantum jumps defining the dynamics of conscious existence. The first guess for the principle would be that the amount of conscious information in quantum jump is maximized (Negentropy Maximization Principle). The task would be to show that this principle is not conflict with the second law.
4. Universe or Universes?
Lubos talks about Universe as the only one of its kind and having age of about 13.7 billion years. I would talk in plural. This particular universe of ours would be a self-organization pattern extending 13.7 billion years to the geometric past. My motivation is that if one accepts space-time as a 4-D surface, one cannot avoid a profound generalization of space-time concept to what I call many-sheeted space-time. As the first step you end up with what you might call Russian doll cosmology. This idea can be probably expressed also in branish although I personally would prefer plain english.
5. What is space-time correlate for mind stuff?
Many-sheeted space-time is not all that is needed. Number theoretical vision about physics as something which is number theoretically universal leads to the introduction of infinite number p-adic variants of real number based physics requiring the fusion of real and p-adic variants of imbedding space together along algebraic points. This allows the identification of space-time correlates of cognition and intentions, the mind stuff of Descartes. But even this is not enough.
6. Dark matter and quantized Planck constant
Lubos did not mention dark matter at all. Perhaps he believes that dark matter is just some exotic particle. I do not believe this. Here I must introduce some more TGD related stuff. The basic dogma of quantum physics is still that Planck constant is a universal constant, just a conversion factor which can be taken to be hbar=1 in suitable units and nothing else. History has not respected the constancy of fundamental constants so that one has right to ask whether Planck constant is really a universal constant, could it be quantized, and if so, how.
Associating Planck constant with dark matter (there are also empirical motivations to do so) one could ask where there could exist a hierarchy of dark matters with levels labelled by different values of Planck constant. I believe that this is possible. At more technical level I propose that the hierarchy of dark matters corresponds to the hierarchy of Jones inclusions for hyper-finite factors of type II1 labelled by ADE groups appearing in McKay correspondence. The motivation comes from the observation that the infinite-dimensional Clifford algebra of the world of classical worlds is hyper-finite factor of type II1, and from the vision that entire TGD emerges in some sense from this kind of structure.
Topologically/geometrically the hierarchy of Planck constants requires a considerable generalization of the notion of 8-D imbedding space (counterpart of 10-D target space in super string models) since one cannot allow quantized Planck constant in quantum theory based on the standard view about space-time. Very loosely, different Planck constants correspond to different branches of imbedding space replaced with a tree like structure obtained by gluing various copies of imbedding space together along common M4 or CP2 factor. In this framework dark matter at a given level of hierarchy can quantum control the lower levels. This control hierarchy would make the matter living. Even phase transition changing Planck constants and identified as leakage between different branches becomes a well defined notion.
7. Angels and Gods and physicist
The predicted infinite hierarchy of conscious entities identified as levels of dark matter would be the physicists counterpart for the angels and spirits of religious world views. The core of religious world view is that there exists something better than this cruel everyday world and that we can directly experience this something now and then. Dark matter hierarchy could give a justification for this belief. The Universe itself would take the role of a dynamical God re-creating itself again and again ("moment of mercy" instead "updating" is perhaps a more proper word here;-)). Our recent physics would be only a humble beginning. A new period of voyages of discovery to the higher, more spriritual, levels of hierarchy using the methods of empirical science would be waiting for us whereas anthropic principle would define a foolproof recipe for the end of physics.