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Author Topic:   Self Replicating molecules
singularity
Inactive Member


Message 16 of 25 (14933)
08-07-2002 12:35 AM
Reply to: Message 14 by axial soliton
08-04-2002 2:44 AM


I meant arbitrary on the basis that it always comes down to someone subjectively deciding if something qualifies as life (including ourselves on our more philosophical days ), to which there will always be differing views. It is like trying to define the difference between a fried egg and a scrambled egg. Sure we all know what the traditional definitions are but it is quite easy to imagine everything in between. Names apply to extremes and continuitites underlie everything we describe. To clarify I am not saying that the nature of life is arbitrary- just the borders of what should be considered as living or nonliving.

Carbon is an exceptional element, but the 6/6/6 observation isnt the key to its adaptability and intergrity to living systems. For instance bacteria are routinely grown in 13C containing media (six protons, six electrons and seven neutrons) and 14C media (six, six and eight) with no major effects except from the low level radioactivity of the latter. The versatile bonding and redox behaviour of carbon adequately explains its utility in living systems. I don't think the question about folding DNA makes sense- there is carbon throughout the molecule so of course it is involved at folding sites, along with oxygen and phosphorous primarily. Your enzyme question is also very confusing.


This message is a reply to:
 Message 14 by axial soliton, posted 08-04-2002 2:44 AM axial soliton has responded

Replies to this message:
 Message 17 by axial soliton, posted 08-07-2002 4:34 PM singularity 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.


This message is a reply to:
 Message 16 by singularity, posted 08-07-2002 12:35 AM singularity has responded

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

  
singularity
Inactive Member


Message 18 of 25 (15020)
08-08-2002 5:27 AM
Reply to: Message 17 by axial soliton
08-07-2002 4:34 PM


Hi Axial

My instinct is after reading your theory that it sounds like a long shot (but what good is instinct?! ). It brought up memories of a few papers I have seen on DNA conducting electricity over short distances (a tunneling effect from memory) and some recent observations that proteins vibrate in a manner which is seems to be part of the basis of their catalytic activity. Sorry no detailed references- it was a long time ago and only in passing. I am not familiar with conductivity in carbon nanotubes, but expect that their expectional properties will not be applicable to biomolecules even over short distances.

I agree that there probably is a boundary between life and nonlife, but as I think it will be polydimensional and dependent on definitions and assumptions (and therefore in my mind artificial). The article you cited on retrosposons being wide spread was interesting, but they arent definitive proof an "RNA world" ever existed.

From my lessons on chemical bonding I remember being told that carbon's versatility is a product of its variable hybridisation and oxidation states and efficient orbital overlap (small nucleus effect I guess). Sulfur for example is also capable of catenation but is less versatile and the bonds are weaker because of the same factors. It is nice to imagine silicon based organisms but the truth is that life here already deals in it to a limited degree and would probably have utilised it if it was worthwhile. It is simply too happy being silicon oxide.

Where I loose faith in your theory is where it is implied that carbon-carbon bonds are essential to the phenomenon, yet DNA doesnt contain a continuous chain of C-C bonds. The basic units of the backbone are liked through phosphates (O-P-O) and even the bases and the sugars are separated by an oxygen.

There is aromatic pi electron stacking through the nucleobases in a manner not dissimilar to the packing of graphite sheets. I still don't understand what the resonance you talk about it actually supposed to *do*. Proteins interacting with DNA and RNA are dependent on local sequence and conformation only- as far as I know there is no unexplained influence of sequence at a distance that would require a different mechanism to explain. Interactions within DNA and RNA is mediated by complementary hydrogen bonding, which again acts locally.

Perhaps you can clear up some of my possible misinterpretations....

Shane


This message is a reply to:
 Message 17 by axial soliton, posted 08-07-2002 4:34 PM axial soliton has responded

Replies to this message:
 Message 20 by axial soliton, posted 08-10-2002 4:06 PM singularity has responded

  
Quetzal
Member (Idle past 3981 days)
Posts: 3228
Joined: 01-09-2002


Message 19 of 25 (15024)
08-08-2002 6:46 AM
Reply to: Message 8 by John
07-29-2002 11:04 PM


John:

Just a quick comment. I have to agree somewhat with TB here wrt protein replicators (although not really for the reasons he gave ). Basically, one key factor in identifying the first biological replicator is that - for abiogenesis to be true - it must not only be autocatalytic (which the protein is in this case), but also mutable. The underlying problem with protein as first self-replicator is that it can only create exact copies of itself: any addition or deletion of amino acids removes it's autocatalytic properties. It isn't, therefore, mutable. On the other hand, both pyranosyl-RNA and PNA replicators are mutable - beyond a certain point you can add/remove base pairs as much as you want without effecting the self-replicating capability (I think Schleigman went from 4500 bp to 220 bp pRNA over 70 generations or so and still had a replicator). Meaning you can have new features added to the original chain, and hence variation, and ultimately evolution by natural selection. Once you've set up the nucleic acid replicators, coopting amino acids and catalysing their production, glomming on to lipids, etc is just chemistry.

Now actually getting to pRNA or PNA outside a lab is a bit more chancy. Both require pretty stringent conditions. Guess where the creationist designer/god is currently located?


This message is a reply to:
 Message 8 by John, posted 07-29-2002 11:04 PM John has not yet responded

Replies to this message:
 Message 21 by singularity, posted 08-11-2002 4:11 AM Quetzal 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

  
singularity
Inactive Member


Message 21 of 25 (15178)
08-11-2002 4:11 AM
Reply to: Message 19 by Quetzal
08-08-2002 6:46 AM


I disagree totally that protein self replicators are necessarily incapable of mutation across generations. The interactions for catalysis are not simple yes or no propositions. Modifying single residues only changes the catalytic efficiency to some degree. The paper I cited made their catalytic system more efficient by making the peptides assemble less strongly, thus speeding up the rate of substrate exchange. Rates of nonspecific catalysis were observed for earlier model peptides...

I agree that peptides alone are unlikely candidates for first life, but they are no worse than any nucleotides or PNA. The biggest problem in abiogenesis is a big enough energy source to power catalysis. I was thinking about this recently and wondered if elemental iron and carbonates could react to give iron oxides and reduced forms of carbon- perhaps catalysed by iron sulfur complexes which still form the core of all biological energetic systems. I just found a good link which supports the basic idea:

http://www.nature.com/nsu/000224/000224-3.html

So much of the hard work of living systems is controlled by very inorganic looking systems, such as iron-sulfur in metabolism and metals in enzyme catalysis.

Any comments?

Now actually getting to pRNA or PNA outside a lab is a bit more chancy. Both require pretty stringent conditions. Guess where the creationist designer/god is currently located?

[/B][/QUOTE]


This message is a reply to:
 Message 19 by Quetzal, posted 08-08-2002 6:46 AM Quetzal has responded

Replies to this message:
 Message 23 by Quetzal, posted 08-12-2002 6:22 AM singularity has not yet responded

  
singularity
Inactive Member


Message 22 of 25 (15179)
08-11-2002 4:25 AM
Reply to: Message 20 by axial soliton
08-10-2002 4:06 PM


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

The handedness of DNA is due to the handedness of the sugars in the back bone. They simply wont bend the other way, but using the enantiomers of the sugars would give a helix with the opposite handedness. The chirality of life may just be a detail- there is no reason to believe why an organism cant be a molecular mirror image of itself, except of course that interactions are also chiral and it would have trouble living in a world with the opposite chirality. It may just be a convenience for organisms to deal in one kind of enantiomers for the basic building blocks- a metabolic common currency to support a free market

I still don't see DNA acting as a long range wire in vivo- for one thing there is no known plausable mechanism for providing the necessary electrochemical energy up and down the helix that I am aware of.


This message is a reply to:
 Message 20 by axial soliton, posted 08-10-2002 4:06 PM axial soliton has responded

Replies to this message:
 Message 24 by Quetzal, posted 08-12-2002 6:48 AM singularity has not yet responded
 Message 25 by axial soliton, posted 08-13-2002 2:16 AM singularity has not yet responded

  
Quetzal
Member (Idle past 3981 days)
Posts: 3228
Joined: 01-09-2002


Message 23 of 25 (15265)
08-12-2002 6:22 AM
Reply to: Message 21 by singularity
08-11-2002 4:11 AM


Hey, Singularity.

You may be on the right track inre iron sulfide catalysts (or at least templates). There's a group at Glasgow working on an OOL hypothesis based around inorganic templates at submarine volcanic vents (Russell, Hall, Rahman, Turner). Here's a link to their site: The Origin of Life at a submarine alkaline seepage. Earth as a photochemical battery... It's an interesting theory. Maybe you could check it out and see if they're missing something. I think they end up with something like PNA (although they only mention ferredoxins).


This message is a reply to:
 Message 21 by singularity, posted 08-11-2002 4:11 AM singularity has not yet responded

  
Quetzal
Member (Idle past 3981 days)
Posts: 3228
Joined: 01-09-2002


Message 24 of 25 (15269)
08-12-2002 6:48 AM
Reply to: Message 22 by singularity
08-11-2002 4:25 AM


With reference to why almost everything has the same chirality, I think you're probably correct. It's just a detail. Regardless of how it started predominating, once homochirality became the norm, anything that didn't match didn't make it. It could even be by simple stochastic processes - sort of like genetic drift randomly moving the frequency of alleles in a small population to one side of the equation or the other. After all, we're talking about the ultimate in founder populations, right?

A couple of papers showing different approaches:

A Sequential Scenario for the Origin of Biological Chirality (abstract from the Journal of Molecular Evolution 44:121-127 (1997))

Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality (full text, PNAS (2001))


This message is a reply to:
 Message 22 by singularity, posted 08-11-2002 4:25 AM singularity has not yet 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.


This message is a reply to:
 Message 22 by singularity, posted 08-11-2002 4:25 AM singularity has not yet responded

  
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