We start by defining a non-coding sequence equal (but not identical) to zero. Such a sequence of bases have no genetic factors on the left and no genetic factors on the right. This is zero (<:>). Let us assume that these bases are AGCT. Now we create a surreal number by putting nothing on the right and zero o the left. “Nothing” may actually be nothing or it may be any non-coding sequence – one that is not a genetic factor. In our example we had <:> identical to AGCT. So we may empirically discover that one, (nothing on the right and zero on the left) is AGCTAGCT (<AGCT:> where identity receives a representation in terms of duplications). Given the definition of negative one, in our representative case we have <:AGCT> but this is also AGCTAGCT. Wow – that can not be correct! Our symbolism appears to have negative one and one as the same. Of course the problem here, biologically, is that non-coding sequences and not genetic factors may not actually be the same.
We will be able to show that we can use surreal numbers categorize heritable non-coding sequences into surreal identities and equalities and distribute them into classes that correlate or do not correlate with genetic factors which in some instances may be non-coding. This will enable us to say a bit more about junk DNA than the circumspection the moniker appellation may have in fact denoted unawares. In fact we will be able to see how repetitive non-coding DNA has an anti-symmetric connotation with respect to the functionality the base sequences effect. For now just assume that even though AGCTAGCT appear indistinguishable as one and minus one this is only because we attempted to say what “nothing” is terms of actual bases when what we really need is a function from a given base sequence to place locations that may be considered as non-factor positions without respect to a random set of positions RELEVANT to using a linear ordering – associated with chromosomes - to separate the gametogenetic factorizations. This will require finding a surreal representation into which the genetic representation is contained. That is the subject matter of surreal genetics.
Now assuming that we will get these things right at zero, let’s just explore what analogizing such gets us. For instance – the original infinite bisection appears to offer an infinite sequence of non-coding representations if the same duplication is used for each day of creation.
Given that all the sequences are composed of ACGT with A-T and C-G( purine-pyrimidine ) We can consider that a double stranded DNA composed of left and right are two different players of two games where one game is A-T and the other is C-G. Each player(R,L) plays one game at a time choosing either an A or T in Game 1 or C or G in Game 2. In the zero game if you do not move and do not play in Game It is illegal to make a move at any time for either player and if when it is your turn to move you don’t move you loose. This is what we were missing in our use of AGCT above. We did not express what it was to be “illegal to make a move”. In other words we can not simply just use any old sequence that is not a gene (factor) but only that that doing so would be illegal with respect to gene factors in all of the games that can be played. There are at least two games going on so the question is what happens when no one is moving, when there is no base being “played”. This is the state of the cell when it both is not being mutated and when it exists as the material of inheritance for a specific individual organism. It is the state of the cell which is attempting to keep the left and right as purine and pyrimidine pairs. Are there any circumstances in which the zero game is being played? What is the molecular biology of left and right strands that cannot make a change to a base but nonetheless change which side could possibly change but actually are not changing a base?
The zero game is being played by the conversation over whether the strand copied into mRNA should be considered the template strand or whether the opposite strand which “reflects” the sequence in the mRNA should be because the corresponding codons are copied into protein. Thus in some way then we can consider the triple of the mRNA, tRNA and rRNA as participating the zero game but to do so would require us to categorize the ribosomal RNA variations combined with proteins sequences they create as reciprocally correlating with the tRNA and the DNA from which combinations relate. Are viruses with RNA -dependent RNApolymerases that only read one side – game zero players – playing the RNA association double game layout? Are not RNA viruses which avoid use of DNA dependent RNA polymerases to effect replication game zero players? They do not have a “back up” DNA copy because the sequences they encode never have to play a more complicated “game” of mutation effected change dynamics. Can we look to these kinds of viruses to establish what the zero non-coding sequence is? Following with the analogy then – can we take a partition of RNA viral heritable sequences to produce a distribution of k-mers that can position where in non-coding sequences we can bound genetic factorizations?
Ok , let’s assume we can do this and that we then have what is legal and illegal. We determine that it is silly for virologists to think that it is a “problem” for RNA viruses that cells do not have RNA-dependent RNA polymerases. Rather we must ask ourselves how RNA polymerase production from RNA templates is equivalent biophysically to triple relations of tRNA, mRNA and rRNA. Reverse transcription of RNA genomes of game into DNA is an example surreal zero game playing.
What is Zero + T. Now we choose to not move in Zero since that is an illegal(RNAviral)Polio move. Now the next player does not move in Zero either. Next player one moves a reverse complement. Also since the two players are playing in AT or GC the play comes to an end. When this end is the for the welfare of the individual organism then we can say that model matches reality. This Zero + T is isomorphic to T. If the outcome of Zero is pen#2 then are not plus strand RNA viruses ( ones that when deproteinated infectiously produce viral RNA polymerase)?
Can we use the difference in the proteins of + and – RNA viruses to relate the amino acid sequences to the base sequences presented in actual tRNA, mRNA and rRNA??
Thus the RNAviral derived surreal distributions thus define what we were looking for in the beginning – “nothing” they define what is on the right in ONE is nothing. The + and – strand RNAs decide ( according to template inheritance views of heritability) the initial position( - strandRNA distribution )and final (+ strand RNA distribution)position game [`\-\,]=:<0:>=:One The only legal move is from the intial to final position – to derive a distribution and end based on going from a – strand RNA distribution to a + DNA distribution. We take the set of all – RNA distributions and develop the k-mer set of sequences that are possible and cabable of converting a – RNA strand sequence partition into a + RNA strand partition. There are nothing on the rights in all of these sequence games even though there is a sequence. Thus in this intial-final game we will be finally able to show how ACGTACGT was not simply a confusion but instead in infusion of two viral vectors into our DNA. With that information we will be able to say rather more about the junk in this trunk but it will matter whether this is the front or the back of the elephant in the room.