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The case of DNA, or rather of the processes into which it enters: replication, transcription, translation, and perhaps less well known ones (quasi-lattice propagation?), is an especially interesting and complex one, but I am not well-qualified to analyze it, except in terms of broad suggestions ... herewith a few speculations:
The multi-scale, 3-level paradigm suggests that the sheer size and scale of DNA molecules matters importantly to their functions. A single, physically unified (i.e. relatively strongly self-interacting, chemically bound, quasi-crystalline, lattice-like extended quantum structure) DNA molecule nevertheless functions on a number of scales and so serves to link processes across such scales. There is an interesting parallel in the case of human artifacts, where it is linkage across time-scales, of long-term historical processes to short-term social-interactional or behavioral ones that is achieved by the material scale and durability of artifacts (see Across the Scales of Time). Multiple time-scales presumably matter as well in the functioning of DNA.
Consider the most macro-scale of DNA activity. In replication, there is the classic problem of linear replication mechanisms for a highly folded chain, with most solutions proposing segmental replications and requiring larger-scale mechanisms to insure proper re-assembly of the sliced segments. There is also the evidence for lattice-like propagation of electro-chemical effects up and down the DNA ladder, and the possibility therefore of global communication of information along the lattice. Might this play a role in replication?
What are the appropriate supersystem contexts for DNA information? we usually focus on the codon-level information, but that is a much smaller scale. In what respect to properties like the total mass of DNA molecules matter? or their overall electrochemical effects on ambient smaller molecular species in their vicinity in the nucleus? how does the overall chemical environment of the nucleus depend on the presence of giant DNA molecules? While DNA is held to be mainly chemically inert, this is a scale-dependent issue: what is inert on some scales may not be on others ... unfortunately I know too little about the physical and chemical properties of nucleoplasm, or how reactions may differ in that environment from otherwise similar reactions in extra-nuclear cytoplasm, or in vitro, to speculate further.
When DNA information at the level of n-codon sequences is read by m-RNA (m-RNA itself defines a relevant scale for DNA through these interactions), typological variety in one code is simply re-mapped as typological variety in another code. Such re-coding may be considered semiotic, but there is no new emergent level here (unless we consider m-RNA itself to be such a level, in its historical evolution), and no re-organization from typological to topological. However, when this information arrives at the ribosome, presumably it is not simply the codon typological information which functions to insure that a template is created for protein synthesis. There must be a larger scale system of interpretance at work in the ribsome such that the same codon sequence on an m-RNA molecule will be differently incorporated into the overall template machinery on different occasions depending on the dynamical state of this larger system. As this happens, it seem very likely that the topological conformations and charge-distribution patterns of the m-RNA, and not simply its codon sequence, will play a role; there may presumably even be more than one conformation assumed by the same m-RNA codon sequence under different ribosomal SI conditions.
This view is really not all that different from the well-accepted phenomena of 'guided folding' alluded to in discussing the other examples of alternation. There, the polypeptide residue sequence is not all that matters to the biological activity of the mature, folded protein molecule, nor indeed does canonical folding occur solely on the basis of intra-molecular forces, but rather the critical information for the protein's further functions (topological information, its folded shape and reactances) arises NOT simply from the scale below, but as an emergent property, realized at the protein molecular scale, of the interactional dynamics of a much larger system, the relevant cytoplasmic environment that guides the folding. Codon sequences, and amino acid residue sequences do not determine biological activity of proteins; they only provide the consituent-level [N-1] potential for the active protein, the functional protein itself also represents information created at its own scale level by interactions with other molecules, which overall process is constrained by (and so in effect represents informational input from) a still larger-scale system level. This is a canonical example of 'downward causation', in which behavior at a lower scale (protein folding) is determined NOT solely from below (by amino acid sequences and intra-molecular forces) but also from above. Indeed in an evolutionary perspective, the only reason that it matters how the protein folds is in order to potentiate it for interaction with other molecules, and as a ligand at membrane sites, with which it has never interacted and which play no role in the folding process. Both the mechanism of folding, and the match of ligand and site, are produced out of the emergent behavior of a system on a much larger spatial scale, and a much longer time scale (at least that of development, recapitulating the much longer scale of evolution, whose corresponding spatial scale is that of ecological systems and co-evolution).
Digression on Downward Causation, aka Supersystem Constraint, aka Context Dependence
We might note here that in the 3-level paradigm there is always already a supersystem context within which focal level interactions take place. To the extent that the supersystem is itself an emergent level of organization out of the focal level interactions, we could consider it to represent the possible self-consistent patterns of interaction at the focal level, rather than as acting as a constraint from above on them. But this assumes that it is coming into existence, and being maintained in existence, on the same time-scale as the focal level interactions themselves, whereas in fact it typically has much longer characteristic times, and always already exists with its own material inertia on a scale larger compared to any particular focal interactions of the micro-moment, so that in this sense it is a very real and functional constraint on them and not merely an epiphenomenon of them. Otherwise a lot of proteins just would not fold correctly. Here it is time-scale which is crucial, and likewise the material inertia of the supersystem. It is perhaps too easy to forget that because the supersystem in a complex system exists on a much larger and longer scale than focal interactions, it is maintained by many such interactions, including ones taking place too far away in space to be part of the self-consistent dynamics of any focal interactions now, and including ones both long prior and far subsequent in time. Moreover, the maintaining interactions for any larger scale supersystem are heterogeneous, they consist not only of this particular cluster of interactions among focal scale elements, but of many other quite different elements in quite different patterns of interaction. This too gives to the supersystem a high degree of autonomy from any particular set of focal interactions, and so gives it the power to autonomously constrain, control, guide the very focal level interactions from which it is collectively emergent, even though this appears paradoxical if we forget the relative autonomy conferred by spatial scale, temporal scale, heterogeneity of constituency, and material inertia.
Matters also appear paradoxical if we assume that every maintenance is just like the original first emergence, or if we forget that no new level emerges free of the downward constraint of some prior, higher supersystem level. Not since the Big Bang has there ever been a context-free emergence of organization ... if then.
See also "Material Sign Processes and Ecosocial Organization"