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Author Topic:   Self Replicating molecules
axial soliton
Inactive Member

Message 9 of 25 (14464)
07-30-2002 2:22 AM
Reply to: Message 5 by Tranquility Base
07-29-2002 9:49 PM

What are the attributes of the threshold between molecules that don't self-replicate, and those that do? This threshold must have some local charge morphology or charge gradient basis (I speculate). Are there known phenomena at work?
This message is a reply to:
 Message 5 by Tranquility Base, posted 07-29-2002 9:49 PM Tranquility Base has responded

Replies to this message:
 Message 10 by singularity, posted 07-31-2002 8:14 PM axial soliton has responded
 Message 11 by Tranquility Base, posted 07-31-2002 10:20 PM axial soliton has not yet responded

axial soliton
Inactive Member

Message 12 of 25 (14715)
08-02-2002 2:23 AM
Reply to: Message 10 by singularity
07-31-2002 8:14 PM

Thanks for the reply. There has to be some thermodynamic solution that works in certain molecular configurations and charge gradients (environments) because we know DNA works. Salt doesn't replicate itself. it just precipitates out of solution. Between the two is a vast thermodynamic landscape. I was asking for some "signposts". The fundamental quantum mechanical phenomena are already known, just not how they apply in this case. For example, I personally had a suspicion that certain metals retained a spin state because of their bonding configuration in biological molecules when their subshells participated in binding sites. This spin state could be a factor in determinine when an enzyme acted, when DNA unfolded, etc.

We saw self-ordering in our lab in simple nickel lattices and believe it has to do with strain between crystal structure planes changing the bond lengths and angles between the lattice atoms. This might also be predicted by band models now, however our results were in advance of mainstream theory. So, I am trying to learn about what TB said using solid-state work as a starting point. There is an answer to this in physical chemistry. It is a bad idea to bet against physicists.

[This message has been edited by axial soliton, 08-02-2002]

This message is a reply to:
 Message 10 by singularity, posted 07-31-2002 8:14 PM singularity has responded

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 Message 13 by singularity, posted 08-03-2002 11:59 PM axial soliton has responded

axial soliton
Inactive Member

Message 14 of 25 (14818)
08-04-2002 2:44 AM
Reply to: Message 13 by singularity
08-03-2002 11:59 PM

Arbitrary! For me, that word really blasts through in your message. There has to be some underlying system to this. Maybe it is the worst type of many-body problem, but why not break the phenomena at work here into pieces by time and type. Following what you said, viruses might be the minimalist entity one gets to when minimizing the complexity of cells. Maybe today's viruses are the spores of some extinct cells that have themselves evolved through natural selection because evolved cells endowed the viruses with modified base pairs now and then (freely associating here).

I'm in a learning situation here, but arbitrary is hard to take. It is easier to find data to joust with creationists in every other technology field, it seems, than this one. It doesn't look like any creationists are readily offering their types of opinions here, and one of them keeps flaming out, so maybe we can just proceed without them.

Carbon is the base molecule for life as we know it. Each of its idiosyncrasies are tools that can be used to figure out why self-replicating molecules make dopplegangers. What I think I know is that the 2p carbon subshell bonds covalently with other carbons. Nothing else does that. Not even silicon (sorry Horta). It is a light atom. Ionization energy of the 2p electron is 11ev. There is an unusual range of bond angles and lengths that are stable for carbon. Hybridization of orbitals is endemic. I feel this is due to the shape of the subshell compared to the number of nucleons, 6 neutrons and 6 protons. The diameter of carbon is the smallest of the series on the table at 0.15nm. Lithium, Beryllium, and Boron, are all larger with fewer electrons. The 2p subshell is non-magnetic and this matches psi^2 predictions for lobe size and shape. Hexagonal lattice structure seems to be the preferred one for carbon. Carbon can bond with any element not inert. Carbon is made early in the life of suns, so it is plentiful in the Universe. Though not a metal, some forms of carbon superconduct at room temperature and higher (we achieved 10^8A/cm^2, sustained from a multi-walled carbon nanotube. Absolutely incredible to see. Just incredible.). Other forms of carbon have a wide band-gap and do not conduct.

I almost hate to mention this, because of the baggage, but carbon has 6 protons, 6 electrons, and 6 neutrons. If I spread the numbers out, it won't be discovered with a text search. I am thinking that the nucleus also has a-polar orbitals due to this pair of sextets. The implied hexagonal duet of nucleons could have interesting shape qualities in that 6 circles of one size fit in a plane precisely around a void having the same diameter as the circles. This happens exactly once in the range of geometry.

What else is important about carbon? It forms graphene sheets readily. Is it also a catalyst for some biological interactions? Is there a relationship between carbon and the helicity of DNA? When DNA folds, there must be strained bonds at the folds. Are there carbon atoms there? Would it help to compare the de Broglie wave length of subshell electrons to bond length? That might help where the morphology of a receptor area on an enzyme couples to something. Maybe metal ions in a chain can be strained enough to be magnetic. Polaiity could determine whether coupling between molecules fits, or not.

If some first-order rules can be hacked out, it is at least a first step.

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 Message 13 by singularity, posted 08-03-2002 11:59 PM singularity has responded

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 Message 16 by singularity, posted 08-07-2002 12:35 AM axial soliton has responded

axial soliton
Inactive Member

Message 17 of 25 (14976)
08-07-2002 4:34 PM
Reply to: Message 16 by singularity
08-07-2002 12:35 AM

Fascinating. In my experience, the most interesting and useful phenomena occur at edges or boundaries. So, my inclination is to start there. There are molecular and structure self-assembly phenomena galore, from which to learn in nature. My intuition is that there is a boundary/edge that can be defined by unique phenomena that lead to self-replicating molecules. There may be more to it than just self-replicating, such as successor levels with certain numbers of base pairs, or that code for a minimum of replicated molecules or of replication activities. As time allows, links such as http://mbe.library.arizona.edu/data/1991/0806/7mccl.pdf shed light on your use of "ambiguity" for me.

On the nucleons, the point would be that this specific number of protons causes a particular size and shape nucleus, that leads to a particular set of stable size and shape 2p lobes for carbon. Neutrons change the band energy levels slightly, but the space charge changes caused by changes in the number of protons is far more significant. There is something about carbon's 2p subshell size and lobe structure that make it the basis of life, and not, say, silicon and its 3p2.

Some explanation of my questions and speculation are in order. Digging the hole deeper... I discovered a relationship between the room temperature current carrying capacity of multi-walled carbon nanotubes and their phonon frequency. The IV curve pancaked at 130uA for MWCNT for longer structures. It seems to me that the carbon-carbon bonds in the graphene sheets of the CNT sheaths are so tensile that phonon frequencies yield phase lengths in the quantum regime. Phonon phase length comparable to local molecule dimensiona creates modes that can drive or control molecular behavior. This opens a new technology arena in solid-state physics that may already be in use in biotechnology (Is this being studied?). Both the number of electrons conducted per second and the phonon frequency were about 10^14. So, while we could strain many metals to become ferromagnetic, ho-hum, carbon never ceases to amaze. There may be a relationship between carbon's ability to form complex self-assembly structures with such amazing uniformity, mechanical, and electrical properties and self-replicating biological molecules. (The FORCE on the end of a 50nm CNT emitting 100uA ought to be science fiction.) Ballistic conductance at this quantum scale is the only rational mechanism for charge flow. Consider free electron density over volume! The charge distributes itself along the CNT by phonon phase. Thus, there are alternating regions along the molecule where constructive and destructive interference between the phonon frequency and the ballistic current flow exist. The charge is uniformly distributed by this mechanism, and the electrons gain a fascinating "coherence". The CNT is far more tensile and stronger than steel. The DNA molecule is floppy over the long range. It seems to have regions of variable charge. I surmise this due to the 4 molecular components having preferential bonding (2 groups of 2). Long range, the molecule is likely to be flexible. Short range, and perhaps between certain numbers and combinations of base pairs, it is likely to be more tensile. I have not looked up anything on DNA phonon frequencies, but there are probably complex modes over the long range made up of primary modes in the short tensile lengths. Individually, charge distribution and elactic bonds can each be important in molecular behavior at the femtosecond scale. Both are present here at the same time and in the same place. Natural selection may work to cause the sizes and placements of genes and introns due to these mechanical end electrical properties (caused by carbon). Does this further confuse, or elucidate?. Apologies to those bored by the above.

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 Message 16 by singularity, posted 08-07-2002 12:35 AM singularity has responded

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 Message 18 by singularity, posted 08-08-2002 5:27 AM axial soliton has responded

axial soliton
Inactive Member

Message 20 of 25 (15165)
08-10-2002 4:06 PM
Reply to: Message 18 by singularity
08-08-2002 5:27 AM

I wouldn't go so far as to call what I am thinking out loud about DNA, a theory. There is a toolbox of critical phenomena in molecular mechanics. In the larger scheme, nature does not re-invent, it "merely" reuses. So, I speculate on properties of DNA, based upon the new physics my group and our peers have observed with our own eyes in another macromolecule; the carbon nanotube. The problem with textbooks in magnetism (my main area) is that the front edge of discovery is in the sci-fi realm by comparison. You might understand how no one wants to be first to publish a paper on the quasi-coherent ballistic conduction of electrons in CNT. A hundred million Amperes per square cm is just too star trekish, and requires the writer to explain why this trashes long-standing rules of thumb. That is hard work. Maybe the same is happening in your area.

Some groups are doping and bending carbon nanotubes to make "transistors", NAND, and NOR functions. Incredible, but true. Check out Phaedon Avouris (sp?) at IBM in Yorktown. Phosphorus is an n-type dopant in today's semiconductors. I think it might not be a stretch to look for conjunctions between electrical and mechanical properties in DNA over the short and long range, as well. Some atoms could be the donors and others could be the holes. I am quite sure that a specially outfitted AFM (probably with a 9nm closed-end single-walled CNT as the probe) is needed to study the electrical characteristics of DNA. We used a proprietary ferromagnetic tip in AFM mode of our Digital Instruments multimode microscope (nanoscope 3a) to study surface electrical and magnetic characteristice. Such methods developed to study a surface might be applicable because the macromolecule is "only surface". Has anyone done studies using any of the newer advanced band simulations? These might shed some light on this. You know, tunneling implies a use for the band gaps....

I have always wondered why DNA comes in only 1 handedness. Has this anything to do with supporting properties of replication?

I do not think the characteristics we, and others, have observed only happen in HOPG, single-walled CNT, Multiwalled-CNT, fullerenes, diamond-like structures, on and on. Groups are only now infringing the boundaries of adding other atoms as dopants or lattice position replacements to carbon structures, and how to make nanotubes from other elements (like boron), morphology, etc. carbon uses both hexagonal and pentagonal dimers in self-assembling into nanotubes. These change chirality of the tube, its quantum impedence, and more. Incredibly, just by varying the diameter of a nanotube, one can observe resistance from practically zero (superconducting) to wide band-gap like diamond. Same carbon atoms and dimer, just different diameter. Oxygen specifically changes electrical and magnetic properties of conducting ions it oxidizes. By example, the difference between Fe2O3 and Fe3O4 is BIG. A French group discovered 25% strain between 3 atomic layers of Fe on Ir[100] and thought their measurements were wrong. So they went about publishing a paper 4 years later that addressed their "errors". By that time, a hundred groups had discovered boundary strain in a thousand other places (including us). I guess it is a French thing. Anyway, you should see the internecine warfare over chromium oxides! The variety of observations is astounding. One day, all will become tools in our toolbox. Pick an element involved in biology, and there are surface and solid-state physicists diligently sparring over it. While I am not going to have the time in this life to become an expert on DNA, it seems like physics is chomping away at the other end of the same candy bar. It would serve all well to meet in the middle.

The "resonance" can lead to different phenomena depending upon shape, size, charge, spin-state, charge gradient, ... of a molecule or local structure. For example, a conducting structure could be an artificial atom due to its size and trap an electron in an energy band. The trapped electron would then torque the local structure from its previous alignment relative to the remainder of the molecule. This bend is a way to reflect phonons, increase impedance to the flow of current through the molecule, insert a kink in the charge gradient, or simply change the shape preference of a receptacle from one type of structure to another. These are the fundamental tools. From them one can engineer atomic structures for specific duties. In the case of a self-replicating molecule, there might be a narrow band of phonon energy or feequency at a bonding site where a second molecule normally plugs in. If extra phonon energy is channeled to the area of the plug point by modifying the phasing in the phonon mode, the plug is turned off. A destructive interference point in phonon characteristics is symetrically on the other side of this band and will result in the same turn-off. Or maybe there is yet a new difference to discover there. One can imagine temperature-sensitive enzymes based upon this.

Wouldn't it be a hoot to find out the DNA molecule is laced with molecular "transistors", boolean logic, and intrinsic memory! This might only be an engineering problem using the above tools, except that no one has asked these questions before.

How about we redirect ourselves at this juncture. Obviously, it is a lucky thing that only a few molecules around us self-replicate. We could make a movie! Attack of the self-replicating Toshiba printers!It seems to be a good place to start asking specific questions about what phenomena control gene operation and exactly how/when/why, what genes/interim sequences/etc. are needed by the minimum self-replicating molecule, what additional genes code for protein coats... Post 19 from Quetzal seems to indicate there is a minimum number of base pairs needed for a "smart" self-replicating molecule. "Smart" might be a bad word (like "spin" for the electron), but you know what I mean.

This message is a reply to:
 Message 18 by singularity, posted 08-08-2002 5:27 AM singularity has responded

Replies to this message:
 Message 22 by singularity, posted 08-11-2002 4:25 AM axial soliton has responded

axial soliton
Inactive Member

Message 25 of 25 (15337)
08-13-2002 2:16 AM
Reply to: Message 22 by singularity
08-11-2002 4:25 AM

Let me diverge for a moment and offer some comments and questions on the early life article you posted.
3rd and 4th paragraph. Though the mix of gasses around early Earth may have been different than the 1953 experiment, the young Earth mix then was not homogenous. There is the good possibility that a very similar mix was located somewhere, possibly at a thermal vent. Certainly there was more ambient energy then than now, and it too was not homogenous. It seems to me that the generation of the self-replicating molecules could have happened in countless pockets over time on the young Earth until a few of the pockets endured. Let's think of the next step as a probability density, psi^2. It means we don't exactly know which pockets, what time, or how long, but a simulation predicts a region (envelope) of probability for existence of the molecules and their species. Hope this makes sense to all. If so, then the next step is the equivalent of quantum tunneling. Part of the probability function is outside the box, so to speak. This means part of the self-replicating molecules self-replicate themselves into a new type of existence. This new existence could be a local environment changed by hordes of self-replicating molecules, better molecules, competing molecules, cooperating molecules and biological food molecules. By probability, an electron passes through a charge gradient that its initial parameters would have disallowed. In reality, there was a confluence of momentum/energy at the instant the electron was in the correct position in space to couple with it and, bang. The same could be true if these self-replicating molecules are thought of as a thermodynamic system. These self-starters may have self-started in thousands, millions, or trillions of pockets.

The same math used to engineer systems based upon quantum tunneling might be applicable to biological processes of mutation. As with tunneling, individual recorded events can be quite different from the average. If anyone wants to challenge this notion in surface science I will be very happy to oblige. Since nature reuses principals and phenomena, this approach might help.

Nanotubes have chirality. It is one of the factors that determines what the "band gap" is for a particular nanotube. The chirality can be caused by the uniform placement of pentagonal dimers in the graphne sheets forming the tube. Don't know why they can be uniform, but it happens. Also, dopants impact chirality. Probably there are papers now on the doping. There is a site run by David Tomanek of MSU that might show some links. On the current, I am not thinking the DNA is a long wire. A computer chip is not a long wire. I am thinking there are segments that can act like chemical gates and memory bits. All these effects are local to tiny regions on the molecule that might be only a few or a few hundred base pairs. The signs for this are the donor and hole type atoms included in the cross links, the chirality, the folding, the 2 groups of 2, and the carbon atoms. Charge in a quantum regime is bigger than a hydrothermal event (science joke). Also, there are numerous instances of metals catalizing interactions and phenomena. If magnetite played a part, then I wonder about the spin-state of the subshells (both catalyst and chemical) involved in the chain of interactions calalyzed by the magnetite. It's late.

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