Quantum Life Science

ANALOGUE WORKING

THE NUCLEOLUS AS ION/PROTON SOURCE?

The functional parallel here is not difficult to identify in so far as coaggregation of the five short condensed arms encoding rRNA underpins formation of the nucleolus, a sub-nuclear organelle, whose emergence then presents an invariant geometry for the internal organisation of the nucleus, the chromosomal array and, thereby, the cell - see below (left). 

Given the arrangements as we find them we can propose that the nucleolus has the effective functionality of a sort of vacuole collecting both water and free ions, an intuition shared by Mario Nenno at least and illustrated below (right).  Might it not also then, effectively therein, present to cellular working a novel, sub-nuclear, bounded quantum environment which by its own expansion in emergence, generates a sort of quantum vacuum?

(Drosophila spp.) Chromosomes extend from the nucleolus and thread through the nuclear lumen

Illustration from the work of Mario Nenno

Schematic illustration of the nucleolar arrangements for the human genome is given above whereby the five rRNA encoding short DNA arms co-gather in formation of the nucleolus.  Analogue modelling rquires that the nucleolus can act as a proton or ion attractor and, in some sort of intake vacuole function, we might expect that the emergence of this novel and deeply system-embedded reaction controlled space acts first to control the flow of water - a guaranteed proton source - but then that those flow dynamics arise out of an entrained flow of free ions which, by their capture in the nucleolus, serve to provide an atomic 'environmental snapshot' of 'external' conditions to inform the continued working of the genome. 

Our previous exploration of the centrosome and centriole dynamics in quantum terms has thrown up the possibility of the pericentriolar material being a matrix for the capture of free ions and this of course overlies the nucleolus and might then be expected to act as a direct feed.  Indeed, it may well be that the nucelolus is induced to arise in this position because of the gathered ionic array.  Also, as previously suggested, each of the five highly condensed arms made up of multiple repeats of DNA coding for ribosomal RNA, in condensed state, may then act as an organic photonic crystal, i.e., providing a nano-scale array of paths for the transmission of photons or light quanta and ions.

It is perhaps here worth stepping aside to address the proposed arrangements.  As is well appreciated, living systems have long been a source of fascination for physics because of their seeming to contravene the second law of thermodynamics and to at least briefly buck the general trend of energetic dissipation to the heat death or, more interesting, to the energetic chaos that is the microwave background.

As it happens this construction in fact offers us a direct means of interpreting the theoretical sorting mechanism held to be responsible for the physical contrariness of living systems and for a while known as 'Maxwell's demon'.  The standard texts would tell us that the theoretical 'demon' is a mechanism by which atoms of differing masses and velocities might be selectively sorted so as to create a disequilibrium by the separation of states.

What is being suggested here is that the water transport and the nucleolar arrangements effectively achieve this via a sort of atomic filtration.  Bound water effectively 'captures' and contains the free ion - all in a very calm and reasonable manner - whilst the sub-nucleolar volume, on which the five short arm centromeres (x2 for the diploid condition) impinge, creates a novel quantum environment that enables the 'sorting' of captured ions and their subsequent passaging into the centromere lumen. 

Whether this is a 'free' sorting or is ordinated by the incident centromeres of the chromosome system is, of course, not known, but either way presents a far more reasonable means of working than the Maxwellian demon having to capture atoms of 'unknown' mass and velocity and effect their separation.

As we will see later, it would seem that the system has moved on from man's primitive model of the 'demon' to the system working on the base of 'calm capture', only later working around the mass, momentum and quantum properties of the atom to derive energy and inform biological working.

THE CENTROMERE AS PROTON/ION STORE?

The unique thing about the centromeres of the human genome is their uniqueness, by which it is meant that there has been much research into, and yet consistent failure to find, any means of relation between the different centromeres or to defining any sub-groups.  Later we will see that this is to be expected. 

What they do have in common, however, is the occurrence of satellite DNAs, multiple iterations of non-coding sequences such as the ALU 171 base pair sequence.  Again, we will need to come back to these later in the model.  In the meantime we can at least work along the lines that, much as in the case of the condensed arms that in part form the nucleolus itself, highly iterated DNA sequences then physically present as periodic regions and, therefore, as potential photonic crystal.

That the centromere might act as a photon or ion store can be best illustrated when we look at the internal arrangement of the DNA helix in cross-section below with reference to the chromosome arm. 
      

THE ARM AS PROTON/ION ACCELERATOR?

We can readily find a means to model the physical functionality of the chromosome arm.  First indication of the validity of the analogue is that - as you might just be able to make out from the Millikan cartoon - the accelerator requires an immense system of resistors and in our biological realm these would equate with the DNA associated proteins - and, indeed, the whole transcriptome and proteome beyond.  It seems that we perhaps should regard proteins as flexible resistors or energetic sinks/stores - mobile quantum capacitors if you like - although, as Miller reports, 'proteins and nucleic acids appear to have average atomic heat capacities at STP even lower that the already-low values predicted merely on the basis of their elemental constituents (Miller, 1990) - 'amazingly low' as (Cochran, 1971) exclaims 'so low that it is very difficult to imagine any substance as complex as proteins that could have lower heat capacities' (Miller, 1991).  Is there then in this implication that while the diversity of organic molecules serves to offer a wide array of pathways or channels for quantum passaging, their own minimal capacities in this regard will act to assist in rapid energetic transfer?  Or is it the case that organic systems self-organisation acts to minimise the range of quanta that might be carried whilst developing an enhanced capacitance in particular modes or wavelengths? 

Whilst it has generally been asserted that proteins and nucleic acids are not characteristically different from other molecules, it would seem that these molecules do empirically seem to hold a unique status.  'Wolf et al., (1976) found 'fairly conclusive demonstrations' (Sutherland et al., 1978) of fractional SCS in six specially prepared bile cholates and their acids' as evidenced by 'diamagnetic shifts with temperature, sudden decreases in conductivity, remnant magnetism and even samples busting out of their containers in a moderate magnetic field.  The concentration of SCS domains was estimated to range from 10² ppm - 10⁵ ppm' (Miller, 1991).

Above are illustrated the three main DNA forms of interest - types A, B and C, 11, 10 and 9 base-pairs per right hand turn respectively - and below the cross-sectional and longitudinal views of B-type DNA, the form believed to be required for transcriptional activity.

In order to address the possibility of the chromosome arm acting as an accelerator we naturally need to move to a more physical interpretation of the arrangements we find.

B DNA in cross section

'Photo' of DNA

As can be seen this gives far more dynamic illustration than the usual ball-and-stick models.  Here we see the quantum continuum mapped like the flow of water, whilst the presence of powerful quantum or electrophilic traps, i.e., major atoms along the way, is signalled by the vortices they generate as a result of their own magnetic flux pinning and which then pattern the quantum flow dynamics.

From just such modelling a higher level of pattern can be seen to be generated (illustrated below) where the field that emerges as the result of the redox flow has been mapped over part of the molecule.  Pattern generates pattern. 

Field pattern from molecular pattern ...

Helical winding of the current in DNA in the spine generates a complex internal magnetic field

The proton stack or core that winds around the helix axis

Beyond the proton core winding around the helix axis, the bases themselves offer longitudinal paths

The coil and field illustration on the left shows the sort of arrangement that is proposed as emerging within and around the DNA once we accept the dynamic quantum continuum underpinning electron flow in the sugar-phosphate spine of the DNA.  When we model in this way the internal dynamics of DNA as being constituted by the quantum flow within the atomic array, the longitudinal electron flow along the helix spine means that the molecule then presents, in physical terms, a nano-solenoid and, as such, will generate a complex magnetic field within the DNA helix itself which percolates through the atomic arrays and bonds of the base pairs traversing the helix core. 

As we all know from school physics the magnetic field within the DNA is capable of moving mass and we can suspect that it is this which will act to accelerate any free ions or protons within the helix.

Given the nano-scale winding of DNA, which in the B form has a wavelength of ~3.4nm, the magnetic fields thus generated within the DNA will fall in X-ray range.   

It is of course definitive of DNA that the base-pairs that make up the 'rungs' of the DNA helix characteristically have either 2 (in the case of the A-T base pair) or 3 (as in G-C base pair) hydrogen bonds and in light of the above modelling we can see that these then constitute a proton core or stack winding around the longitudinal axis of the molecule. 

We can analogise from this arrangement to that of the classical electrical circuits that supply our homes with electricity.  Turning on the switch does not set free an electron from the source to zoom through to the electrical fitment, but of course actually acts to shunt the idling and effectively stacked electrons in the conducting wire to complete the supply circuit.  In the same way then we might suspect that the proton stack in DNA is similarly 'shunted' once electron flow is initiated in the DNA helix and the proton supply and flow is initiated with formation of the nucleolus.

As a nano-solenoid, of course, we are prompted to consider Dirac's proposal for the generation of a magnetic monopole and this arrangement would seem to indicate the possibility that the chromosomal array can generate magnetic monopoles at the telomere ends, the other 'pole' of such an arrangement then being buried within the centromeric material of the chromosome.  Evidence for this might be found in the sequence data for the two extremes of the chromosome arm and, indeed, a ten base-pair consensus sequence has been characterised within the centromere and this does have some accord, in inverse, with the sequence data of the telomere.  We will return to this later.

There is of course a quantum continuum that extends also across the bases and the hydrogen bonds of the base pairs.  One of the effects that also has to be considered in this arrangement is that the pi-orbitals of the bases, when mapped as resonant flow structures, would also constitute electro-magnetic mirrors or quantum state-splitters. 

In accord with this thinking it is notable that the B form of DNA, which we believe to be the transcriptionally active state, is such that the plane of the base-pair bond is at 90 degrees to the long axis of the molecule.  This would then imply that the base-pair plane is maximally exposed to the internally generated magnetic flux and the electric field then also operating at right angles to that flux will drive charge to the periphery of the core (a quantum Hall effect?), freeing up the proton flow and then also diverting power to the bases themselves.  The net resultant of these dynamics might then act to charge load the bases and thereby perhaps encourage helix melting and induce helix opening for the start of transcription or duplication.

X-rays running in DNA?  Seems weird, I know, but bear in mind that one of the first human hormones to be crystallised was the female sex hormone oestrogen and crystallographic analysis of the structure showed that oestrogen absorbs in the X-ray range.  This of course is widely known and the property of X-ray absorbance classically attributed to the protective role oestrogen is proposed to play in safeguarding the genetic material from the radiative danger of our natural environment.  Finding that in fact X-ray energies are generated within the DNA helix only makes the role of oestrogen more important. Indeed, if in the future this 'internal' role for the hormone is confirmed, it will require that much of the medical healthcare given to females in the UK, e.g., breast cancer screening or osteoporosis monitoring, will be realised as perverse and quite perfectly the opposite of what should be offered, i.e., young and old should only have ultrasound examinations whilst the oestrogen competent population is better able to cope with X-ray based methodologies.

We have now developed a reasonable model for how the nucleolus, centromere and chromosome arm might accord with our cartoon model of a cyclotron leaving only the last two required analogue components of the target atom and collector system to identify ...

> THE TELOMERE AS TARGET?