Friday, May 13, 2011

Oil droplets as a primitive life form?

The origin of life is one the most fascinating problems of biology. The classic Miller-Urey experiment was carried out almost 60 years ago. In the experiment sparks were shooted through primordial atmosphere consisisting of methane, ammonia, hydrogen and water and the outcome was many of the aminoacids essential for life. The findings raised the optimism that the key to the understanding of the origins of life. After Miller's death 2007 scientists re-examined sealed test tubes from the experiment using modern methods found that well over 20 aminoacids-more than the 20 occurring in life- were produced in the experiments.

The Urey-Miller experiments have yielded also another surprise: the black tar consisting mostly of hydrogen cyanide polymer produced in the experiments has turned out to be much more interesting than originally thought and suggests a direction where the candidates for precursors of living cells might be found. In earlier experiments nitrobenzene droplets doped with oleic anhydride exhibited some signatures of life. The droplets were capable to metabolism using oleic anhydride as "fuel" making for the droplet to move. Droplets can move along chemical gradients, sense each other's presence and react to it and have also demonstrated rudimentary memory. Droplets can even "solve" a maze having "food" at its other end.

The basic objection against identification as primitive life form is that droplets have no genetic code and do not replicate. The model for dark nucleons however predicts that the states of nucleon are in one-one correspondence with DNA, RNA, tRNA, and aminoacid molecule and that vertebrate genetic code is naturally realized. The question is whether the realization of the genetic code in terms of dark nuclear strings might provide the system with genetic code and whether the replication could occur at the level of dark nucleon strings. TGD inspired quantum model of biology leads to a model for oil droplets as a primitive life form. In particular, a proposal for how dark genes could couple to chemistry of oil droplets is developed.

Intelligent oil droplets

New Scientist tells about a new twist related to the Urey-Miller experiment. Martin Hanczyc and his colleagues of University of Southern Denmark in Odense are doing research with a rather ambitious goal: the discovery of the recipe of life. The highly demanding challenge is to find candidates for the protocell that preceded the recent cell. What makes the task so difficult that it is not even clear what one should be searching for. For instance, what basic characteristics distinguishing living matter from inanimate systems protocell is expected to have before one can speak about primitive life form? And if one accepts the dogmas of standard biology, one encounters also the nasty hen-egg question which came first: metabolism or the genetic machinery.

Hanczyc and his colleagues have been experimenting with simple candidates for primitive life forms: oily nitrobenzene droplets doped with oleic anhydride immersed in alkaline aqueous solution (alkalinity is by definition an ability to reduce acidicity). They have found that these systems have some attributes generally associated with life. The recent experiments replaced oleic anhydrite with the black tar consisting of complex branched and fractal looking hydrogen cyanide (HCN) polymer produced by Urey-Miller experiments and found that also now the droplets exhibit lifelike behavior: they sense and respond their neighbors and move towards "food" sources.

The earlier experiments using nitrobenzene droplets doped with oleic anhydridge immersed in alkaline solution began immediately to move along straight lines. What happened that the oleic anhydrite at the surface of the droplet reacted with the water spilitting to two oleic acid molecules by hydration. This dropped the surface tension of the droplet and by a kind of spontaneous symmetry breaking the reaction rate had maximum at some point of the droplet and a "hot spot" was generated drawing oleic anhydride from the interior of the dropled and generating a convective flow. A pH gradient develops along the surface. The oleic acid in turn moved along the droplet surface from the hot spot to the diametrically opposite side of the droplet (see this). The net effect was a linear motion. pH gradient is claimed to be essential for the generation of motion but I must admit that I do not quite understand this point. A primitive metabolism liberating energy is obviously in question. By momentum conservation the total momentum for the convective flow and flow of oleic acid was compensated by a center of mass motion of the droplet.

One could claim that this process belongs to the same class of self-organization processes as the generation of convection patterns as one heats liquid from below. Other researchers have however discovered that the oil droplets can also travel along chemical gradients, something known as chemotaxis used by many bacteria to find food and void threats. One oil droplet managed even to "solve" a complex maze containing "food" at its other end. Whether this kind of behavior can be regarded as a mere chemistry is far from obvious to me. To me this a achievement look like a genuinely goal directed intentional behavior.

Hanczyc has also found that when the oil droplets approach each other they change course to avoid collision, or can circle each other-like partners in Viennese waltz! Oil droplets seem to have even memory. By videoing the paths of oil droplets Hanczyc found that the decision to stop or continue was not random but the behavior at any point of orbits was affected by the earlier behavior. This is by the way an elegant experimental manner to show that non-deterministic behavior is not just randomness. The experiments have been also carried using instead of oleic anhydrige mineral oil consisting of a mixture of alkanes having as building block polymeres from from CH4 by dropping two hydrogen from each C as also lipids have (methane CH4 is the simplest alkane). What distinguishes mineral oil molecules from the oleic anhydride molecules are the oxygen atoms in the middle of the reflection symmetric linear molecule. Also now the droplets move although the process takes place with a slower rate.

The basic objections against the identification of the oil droplets as a life form is that they do not replicate and there is no genetic code. One must be however very cautious with this kind of statetments. Maybe the primary life forms are not the droplets and the behavior of droplets reflects the control actions of these life forms on droplets. Perhaps also genetic code could be realized at at totally different level. The recent findings of the group of HIV Nobelist Montagnier indeed suggest a new realization of genetic code in water closely related to to water memory and TGD suggests a concrete realization of this code.

Some key ideas of TGD inspired quantum biology

Before proposing a model for intelligent oil droplets as a primitive life form its good to list some of the basic ideas of TGD inspired quantum biology.,

  1. The basic hypothesis is that the dark matter at the magnetic flux tubes of the magnetic body assignable to any physical system serves as an intentional agent controlling the behavior of the ordinary matter (see this). Dark matter can correspond to just the ordinary particles- at least electrons and protons- in a phase with non-standard large value of Planck constant forming macroscopic quantum phases. Also biologically important ions could form this kind of phases.

    TGD inspired nuclear physics (see this) allows also the bosonic counterparts of fermionic with same nuclear charge so that every fermionic ion could be accompanied by exotic bosonic ion so that Bose-Einstein condensates could become possible.

  2. The model for dark nucleons as entangled triplets of three quarks (see this and this) leads to the identification of the counterparts DNA, RNA, tRNA, and aminoacids as three-quark states and one can identify also vertebrate genetic code. DNA sequences correspond to dark nucleon sequences - dark nuclei - in this correspondence. The proposal is that dark proton sequences in water form dark nucleons with so large a Planck constant that nucleon size corresponds to size of singe DNA codon. There is indeed evidence that in attosecond time scale (time scale for corresponding causal diamonds) water obeys effective chemical formula H1.5O as far as scattering of electrons and neutrons is considered (see R. A. Cowley, Physics 350, 243-245, 2004 and R. Moreh et al, Phys Rev. 94, 2005)).

    This would suggest that 1/4 of protons are in dark large Planck constant phase in the experiments. This proportion is expected to depend on temperature and pressure and should explain the rich spectrum of anomalies of water by regarding it as a two phase system (see this). Perhaps these protons could form dark nucleon sequences realizing genetic code. These sequences could replicate and evolve and could define at least the analog of DNA or RNA. Maybe even DNA-mRNa-aminoacids translation processing could take place. If a translation machinery transforming exotic DNA to ordinary has developed during evolution, this fundamental realization of genetic machinery might make possible kind of Research&Development making possible to experiment with different genomes. Evolution would not be a random process anymore (see this).

  3. The proposal is that the ordered water layers associated with polar molecules dissolved in water are attached to the magnetic body of the molecule induced in water environment and that this magnetic body mimicking the original molecule is an essential element of this primitive life (see this). The self-organization processes of these layers induced by external perturbations could be the predecessor of processes like protein folding and de-folding. The mechanism of water memory could be based on dropping of the magnetic bodies of molecules as a result of repeated shaking involved with homepathic procedure inducing a sequence of catastrophes driving the evolution of these primitive life forms. One can also ask whethert these magnetic bodies could define the analog of proteins providing one realization of dark matter genetic code.

  4. If dark nucleons have been the predecessors of chemical life forms, one can circumvent the hen-egg question about whether the genetic code or metabolism came first. In zero energy ontology negative energy signals propagating in the direction of geometric past would in turn provide fundamental mechanism of intentional action, metabolism, and memory. If this is the case, evolution would have only led to a refinement of the fundamental mechanisms of life already existing: there would be no need to pull anything out of hat. The mechanisms for chemical storage and utilization of energy are needed and moving oil droplets would provide a primitive realization of these mechanisms.

  5. The notion of negentropic entanglement makes sense if one accepts the role of p-adic number fields and the vision about life as something residing in the intersection of real and p-adic worlds (see this). Entanglement probabilities for negentropic entanglement must be rational or algebraic numbers in the algebraic extension of p-adic numbers involved and there is unique prime for which this entanglement entropy is maximally negative. Negentropic entanglement makes possible new kind of many particle states which is not based on binding energy but the fact that negentropic entanglement is stable against state function reduction if Negentropy Maximization Principle determines its dynamics also in the case of negentropic entanglement. This makes it possible to have bound state like many particle states in which composite particles are in well-defined sense free and binding energy is formally negative. The proposal is that the mysterious high energy phosphate bond corresponds to negentropic entanglement and carries both metabolic energy and information (see this). In this framework ATP-ADP cycle has also information theoretic interpretation as a transfer of conscious information.

The model for DNA as topological quantum computer (see this and this) led among other things to an identification of magnetic flux tubes connecting bio-molecules as a basic building bricks of living matter.

  1. Flux tubes are assumed to connect DNA nucleotides to lipids of the nuclear and cell membranes. Flux tubes could begin from =O in the double bonds R=O or from negatively charged oxygens. In the case of DNA R would correspond to the basic unit in phosphate deoxiribose backbone consisting of aromatic 5-cycle and PO4 containing one =O and one O-. The lipid end would would contain =O and -OH and the flux tube could end to either of these or possibly -OH ionized to -O- by a transformation of proton to dark proton.

  2. The braiding of flux tubes makes topological quantum computation like processes possible (see this). The contractions and expansions of flux tubes induced by phase transitions changing the value of Planck constant would be a basic control mechanis allowing to understand how two biomolecules (say DNA and its conjugate) can find each other in the thick soup of organic molecules. The reconnections of the magnetic flux tubes would be second basic control mechanism and ATP→ADP process and its reverse would represent standardized reconnection.

  3. The flux tube ends would contain quark and antiquark (u,d and their antiquarks are involved) coding for the four DNA letters A,T,C,G so that also dark quarks and their antiquarks would provide an elementary particle level realization for the codons. Note that topological quantum computation does not necessitate genetic code and therefore also the repeating DNA sequences regarded as junk could be used for topological quantum computations.

General ideas about oil droplets as a primitive life form

It is interesting to see what one obtains if one takes the dark nucleon realization of genetic code, the mechanism of water memory realized as magnetic bodies attached to the ordered water layers associated with polar molecules, the model for DNA as topological quantum computer, and the ideas about magnetic body with dark matter as fundamental bio-control as basic ingredients of the model of intelligent oil droplets.

  1. A process resembling spontaneous symmetry breaking occurs for the droplet molecules as the hot spot is formed. The interpretation as a generation of magnetic body of approximately dipolar magnetic field is attractive. The magnetic body would control the droplet. The change of the direction of the motion of the oil droplet would correspond to the change of the orientation of the magnetic body and would thus reduce to a motor action of the magnetic body.

  2. The flux tubes of the magnetic body would be most naturally parallel to the direction of the nitrobenzene polymer strands. Oleic anhydride molecules and the hydrogen cyanid polymers would be transferred along the magnetic flux tubes of an approximately dipolar magnetic field entering to the hot spot from interior and the oleic acid molecules could move along the flux tubes continuing along the surface of the droplet to the diametrically opposite point. The migration of birds along magnetic field lines is a fractal analog for this.

  3. The dark matter at the magnetic body would give the oil drop its "intelligence". The dark nuclear genome could be realized at the magnetic body and the magnetic bodies might define the replicating life form as in the TGD based model of water memory for which the magnetic bodies represent molecules as far as low frequency electromagnetic fields characterized by cyclotron frequencies are considered. One could see intelligent oil droplets as a manifestation of control actions of a life form defined by dark matter at magnetic flux tubes and the first step in the process eventually leading to a complex control and coordination of the behavior of ordinary matter.

  4. The ability of droplets to react to the presence of other droplets would be due to the communications between magnetic bodies based on low frequency photons at cyclotron frequencies but having energy above thermal energy if the value of Planck constant is large enough.

At least oleic anhydrite, hydrogen cyanide, and mineral oil can serve as a fuel of oil droplets and this raises the question what might be the common property shared by them. Certainly this property must relate to metabolism and the model for ordinary metabolism suggests that this property is shared also by the high energy phosphate bond.

  1. Oleic anhydrite is a lipid formed by as a fusion of two oleic acids consisting of a sequence of CH2 units and the characteristic (C=O)-(O-H) group at its end. The burning of the molecule splits it to two oleic acids by hydration meaning utilizing one water molecule. The formation of oleic acid in turn involves dehydration so that the burning process is analogous to depolymerization of DNA or aminoacid sequence by hydration.

  2. Mineral oil is also a lipid and looks like oleic anhydride locally. In the ideal case however the crucial ..(C=O)-O-(C=O)-.. portions are lacking. Oxygenation could however produce this kind of defects to the mineral oil molecules so that the mechanism of burning would remain the same.

  3. Hydrogen cyanide HCN involves valence bond of valence 3 between C and N. The polymers are constructed from H-C-N sequences with single valence bond between both C:s and N:s of two subsequent horizontal H-C-N units, which one can think of as being obtained from (H-C)-(H-C)... sequence and ..N-N-N... sequences with N and C connected by horizontal bonds. This polymer replaces oleic acid as a "fuel" reacting with water and liberating metabolic energy. These polymers -which would serve as primitive analogs of proteins- would be transferred along the magnetic flux tubes and burned at the hot spot by hydration. HCN has been proposed to have been a primitive precursor of both amino acids and nuclei acids. With motivations coming from the general vision about quantum biology, tt will beproposed that also hydrogen cyanide polymers contain in their C-backbone ..(C=O)-O-(C=O)-.. portions as local defects due to oxygenation so that the burning would occur via hydration in all three cases.

What are the prerequisites for metabolism and topological quantum computation like processes?

The basic question is whether metabolism interpreted in TGD framework as negentropy transfer and thus requiring the analogs of high energy phosphate bond and ATP-ADP cycle is possible. The high energy phosphate bonds make also possible flux tube structures serving as a prerequisite for topological quantum computation like process. Both oleic anhydride, hydrogen cyanide and mineral oil can serve as a metabolic source and one should identify the common property of them making. This property should be the analog of high energy phosphate bond.

  1. High energy phosphate bond carries metabolic energy. This bond is poorly understood and I have proposed that high energy phosphate bond carries negentropic entanglement identified as the basic characteristic of life (see this. In the middle of oleic anhydride there =O-O-=O structure and its splitting in hydration liberates energy. This suggests that this structure also now carries the negentropic entanglement and the metabolic energy. The splitting process of oleic anhydrite occurring at the hotspot would be analogous to ATP→ ADP process involving splitting of PO4 molecule from ATP.

  2. Oleic acid is a lipid containing at its second end the characteristic (C=O)-OH group assumed to serve as a terminal for the magnetic flux tubes in the model of DNA-cell membrane system as quantum computer. In the presence energy feed one could imagine that the inverse process transforming oleic acid to oleic anhydride takes place and a primitive version of the metabolic cycle involving photosynthesis and cellular breathing can be imagined. Metabolic and quantum information processing would be very intimately related. By DNA as topological quantum computer analogy the magnetic flux tubes connecting oleic anhydride molecules would make be responsible for primitive topological quantum computation if present in the system.

  3. Also when the tar from Urey-Miller experiment replaces oleic anhydrite small amount of oleic anhydride was used to build a film around oil droplet to lower surface tension. This suggests that the oleic anhydride has a deeper purpose and defines the analog of cell membrane and make possible for the magnetic flux tubes from the interior of the droplet to attach to the lipids? This could occur at least in the hot spot and at point opposite to it so that magnetic flux tubes would connect the diametrically opposite points of the droplet. Oleic anhydride would therefore serve a dual purpose serving both asa metabolic resource and a building brick of the protocell membrane: metabolic energy would be accompanied by information. Also in real life lipids -about which fats are a special case- have this double role.

  4. The process occurs for both for hydrogen cyanide and mineral oil and and this raises obvious objections against the model since the energy and information carrying =O-C-O-C=O structures making also possible the flux tube connects are not present in the ideal situation. One must however remember that the situation in real life is far from ideal and the most obvious idea is that the polymers as such are not enough: oxygen is the basic metabolic resource and oxygenation serving as the loading of metabolic batteries might be the crucial element.

    1. The backbone of both lipids and of mineral oil polymers is CH2 sequence. If some fraction of mineral oil polymers contain (C=O)-O -(C=O):s serving as carriers of metabolic energy and information the situation reduces to that for oleic anhydride apart from effects caused by the fact that the density of metabolic energy per volume is expected to be lower, which would explain why the motion is slower.
    2. Also in the case of hydrogen cyanide polymers one can imagine the presence of similar defect structures due to oxygenation. A portion of ...(H-C)-(H-C)-(H-C).... sequence would be replaced with ....(H-C)-(C=O)-O-(C=O)-(H-C)... with three carbons lacking. The nitrogen sequence ...N-N-N-N-N.. would split to ...N-OH and OH-N... so that three nitrogens would be lacking.

Under these assumptions the model explains all three cases using hydration as the basic mechanism of metabolism as well as the conditions required by DNA as topological quantum computer model. Note that the process consumes oxygen just as the ordinary breathing.

What about genetic code and counterpart of DNA?

Consider next the possible realization of the genetic code. The first thing to notice is that even in the case that genetic code is not realized the braiding would make possible topological quantum computation like processes and a realization of memory in terms of braiding patterns. Furthermore, chemical realization of the genetric code is not possible so that dark nucleons remain the only possibility in TGD framework. The challenge is to try imagine whether DNA like structures having flux tube connections with the counterparts of lipids in the cell membrane could exist. The following suggestion is a product of free imagination based on analogies and reflects my amateurish skills in biochemistry.

  1. Aromatic rings are an essential element of both phosphate deoxiribose backbone of DNA and of DNA letters itself. Nitrobenzene molecule obeys chemical formula (C6H-5)-NO2 and contains benzene ring to which NO2 nitro group is attached. The oily character is due to the benzene ring. Benzene rings could serve as a counterpart for the hydrocarbon 5-cycles appearing in phosphate deoxiribose backbone. Note however that in deoxiribose ring one carbon is replaced with O and two hydrogens with OH. Moreover, single benzene molecule would correspond to the counterpart of DNA triplet rather than single nucleoside. One could however argue that only a backbone is in question so that the differences might not matter.

  2. One would naively expect that both nitrogen and phosphorus have same valence equal to three. In PO4 phosporus has 5 valence bonds as a rule and the interpretation is that phosphorus tends to donate its valence electrons to get empty shell. This kind of states are known as oxidation states and are possible also for nitrogen: hydroxylamine NO2H is one exmple of this kind of state. In fact, from the from structural formula of nitrobenzene one finds that nitrogen gives one electron to second oxygen so that also this state can be regarded as an oxidation state. This inspires the idea that nitrogen takes the role of phosphorus at least partially.

  3. If one does not allow oxidation states, the simplest manner to construct the analog of phosphate deoxiribose backbone is as structure ...X-X-X..., with X= R-O- (R1-N)-O, where R denotes oleic anhydride and R1 is for benzene residue. The bridges connecting benzene rings would be reflection symmetric. The breaking of reflection symmetry is however essential since it determines the reading direction of DNA.

  4. If one accepts oxidation states, the simplest option is that in benzene-NO2 complex NO2 is replaced with (N=0)-O and the counterpart of phosphate deoxiribose backbone would have the structure ...X-X-X-..., X=R- (R1-N=0)-O with R denoting oleic anhydride and R1 benzene. Oleic anhydride has valence bond to N so that N has 5 valence bonds as phosphorus in phosphate. Also the crucial =O is present. The units connecting subsequent benzene rings are not reflection symmetric anymore as indeed required. There is however no charged oxygen as in the case of ordinary DNA. Note that the analogs for AMP, ADP, ATP make sense since one can single replace P by N phosphate PO4.

  5. An interesting question is whether the nitrogen based metabolism could be realized as a primordial metabolism. Nitroglycerin is analogous to tri-phosphate although the nitrates are not arrranged linearly as in ATP and is used as both heart medicine and as an active incredient of explosives. The latter use conforms with the idea about the presence of high energy nitrate bond in NO4.
  6. The two mirror image branches of oleic anhydride molecule consist of 15 carbon atoms and the structure is rather long as compared to the basic unit of phosphat edeoxiribose backbone so that the distance between subsequent benzene units would be rather long- of order 10 Angstroms. On the other hand, 10 DNA codons correspond to 10 nm length in a good accuracy so that one codon would take 1 nm length also in this case. If double strand is formed, twisting is possible so that the scales could be the same. The size scale of the dark nucleon representing single DNA codon should correspond to the size scale of single oleic anhydride molecule and the required value of Planck constant would be of order 106 as the ratio of this scale and nucleon size of order 10-15 meters.

  7. The counterparts of DNA nucleotides forming a linear structure should join to the benzene rings. Dark nucleon sequences remain the only possibility if one wants a realization of genetic code. Each dark codon represented by dark nucleon would be connected by three flux tubes with quark and antiquark at their ends to single unit of the proposed structure. There would be three =O:s per single benzene ring. Since single benzene ring corresponds to single DNA codon three =O:s are indeed expected. Therefore =O:s could indeed correspond to terminals for flux tubes coming from single dark nucleon representing single DNA codon.

  8. The division of oil droplet would be the analog of cell replication and would involve at the deeper level the replication of dark nucleon sequences. This requires the analog of DNA double strand and the analogs of DNA codons would be dark nucleons. Genetic codons could be realized in terms of flux tubes connecting dark nucleon sequences to the oleic acids or oleic anhydrides at the surface of the droplet. It remains to be seen whether the division can be achieve in real world.

To sum up, this model is rather direct application of TGD based vision about life and the killer test is whether the mineral oil oil molecules and hydrogen cyanide molecules are not ideal but actually contain the (C=O)-O-(C= O) pieces carrying energy and information and serve as terminals for the magnetic flux tubes.

For background see the chapter Evolution in Many-Sheeted Space-time of "Genes and Memes". See also the article Oil droplets as a primitive life form?

28 Comments:

At 9:13 AM, Blogger ThePeSla said...

Matti,

In terms of a hierarchy of p-adic distances (presumably some as a dark analogy) what sort of such distances are described here and can it be measured in theory at least?

Of course given a unified theory what in the physics or cosmos may correspond on a deeper level with the gene environment.

Interestingly the oil drop experiment to measure a single electron charge was a little adjusted for the expectations of the experimenter. But we can learn a lot directly or indirectly from say a single electron and its behavior.

If there is some sort of memory, metaphorical or not, in a real sense as in clay dimmers, these oil droplets do replicate and perhaps seem to be aware.

Certainly structures are possible from that early tar soup with things not explained, say to build RNA by such methods and it not be able to replicate even atom by atom (this may have been resolved in the last decade) as to what is this mystery called life. In any case we are not that far from how a paramecium behaves.

Clearly, the number of objects or bacterium have to reach a threshold for things like collective phosphorescence. And i is clear that the mechanism of flagellum is one of random left or right to escape in a random manner, or just right spin to find a food source. Again issues of what is chiral memory over some time or distance.

There are a few more ideas we need to resolve in this more geometrical philosophy. But the chicken egg thing is a pointless question that should not be so avoided by biologists- life can arise anywhere, even spontaneously or so it seems in the concrete memory of the universe. Your questions of purpose is a good one in these applications of symmetry and the chiral direction of life that so reacts to the universal cosmic code.

PeSla

 
At 1:44 PM, Blogger Ulla said...

http://www.sdu.dk/staff/martin.aspx

Publications.

 
At 1:57 PM, Blogger ThePeSla said...

Matti,

A comment is on my blogspot in case it does not reappear here.

I also looked a little more at the 89 and 107 idea.

The PeSla (www.pesla.blogspot.com)

 
At 1:58 PM, Blogger Ulla said...

http://www.nature.com/news/2011/110223/full/news.2011.118.html

Video about the pH movements.

 
At 8:36 PM, Anonymous Matti Pitkanen said...

The comment of Szostak is interesting. He argues that the oil droplets represent oil based life. This is misleading.

The oil droplets move in water. And oil is one special case of lipids and all life involves lipids in an essential manner. In the proposed model oleic anhydride (oil) is used both as fuel (also fat molecules are lipids and serve the same purpose) and to form layer to the surface of droplet serving same functions as cell membrane.

If one takes seriously the new realization of genetic code, the experiments of Szostak and Hanczyk do not differ so dramatically.

 
At 12:30 AM, Blogger Ulla said...

There is an interesting overview over the primitive protocell at http://flint.sdu.dk/research/protocell.html
Follow the links.

If we think that life evolved deep inside earth the oxygen must also be questioned. oxygen was used first when mitochondria was captured into cells, before it was a poison (reactive as in free radicals). The most primitive metabolic steps were anaerobic, producing methane? From where came methane? Or could methane be used in other ways, as building blocks for organic chemistry? The cyanide is also interesting, because it offers a link to N. Then there are the two ends (-COOH and N) of receptors already there. CN is linked to acids?

Carbon as a quasiparticle or BE-condensate is interesting for why C is the building block of life.

 
At 2:33 AM, Anonymous Matti Pitkanen said...

There are underearth water reservoirs and one can quite well consider the possibility that oxygen came from this water.

The most primitive could have been based on photons: to get energy system send negative energy phase conjugate photons to get energy: quantum credit card. This idea is now in firm theoretical basis (zero energy ontology). This mechanism would be still at work.

In this framework the problem of metabolism reduces to a much easier problem of how chemical storage of metabolic energy evolved. The storage mechanism might have emerged much later in evolution.

One can imagine many options. For instance, UV radiation liberated in the fusion of two molecules in interstellar space could have served as metabolic energy source. The light from nearby star would induce the decay of the molecule and this would give rise to a cycle analogous to photosynthesis-respiration cycle.

 
At 3:19 AM, Blogger Ulla said...

Maybe something like this?

http://www.sciencedaily.com/releases/2011/05/110512150731.htm

 
At 9:48 AM, Blogger ThePeSla said...

Ulla,

Compare this to other article as to what is energy and so on.

http://www.newscientist.com/article/mg21028125.400-graphene-may-reveal-the-grain-of-spacetime.html

"So how about the electron's intrinsic spin? It cannot be a rotation in the ordinary sense, as electrons are point particles with no radius and no innards. Instead, like pseudospin, it might come from a lattice pattern in space-time itself, says Regan. This echoes some attempts to unify quantum mechanics with gravity in which space-time is built out of tiny pieces or fundamental networks (Physical Review Letters, vol 106, p 116803)."

Things are going at a rapid pace and in some ways the blogger hiatus of may 12 broke the continuity of dialog.

Matti,

If there are levels of Planck's constant- would there not be a wider concept of Zero-point energy? especially if these clouds without innards or radii as the electrons in the article seem to default to a grounding where the energy gain is at best zero from a qm vacuum? Such effects would still be distant to see. But why would there have to be an energy source to kick start life if it is part of the overall topological dynamics?

The PeSla

 
At 10:36 AM, Blogger Ulla said...

http://www.mitpressjournals.org/doi/pdfplus/10.1162/artl_a_00002
Chemical Basis for
Minimal Cognition.

We propose how this system may be useful in the study of minimal perception and cognition. The system consists simply of an oil droplet in an aqueous environment. A chemical reaction within the oil droplet induces an instability, the symmetry of the oil droplet breaks, and the droplet begins to move through the aqueous phase. The complement of physical phenomena that is then generated
indicates the presence of feedback cycles that, as will be argued,
form the basis for self-regulation, homeostasis, and perhaps an extended form of autopoiesis. We discuss the result that simple chemical systems are capable of sensory-motor coupling and possess a homeodynamic state from which cognitive processes may emerge.

Note, homeostasis is a pure physical state. It needs feedback loops and what may be called memory.

I simply missed this interesting guy.

 
At 11:03 AM, Blogger ThePeSla said...

Ulla,

Homeostasis and feedback seem a little outdated to me as once powerful fresh ideas. Minimal cognition is a reasonable question but I do not think we can reach the deeper explanation of consciousness as pure chemistry alone, nor base the deeper properties of memory on it.

While it is good to consider what happens in oil drops, especially the math of surface phenomena and what may be going on in its restrained innards... How does one explain that sometimes a quantum pool of Helium will not boil while
it is being watched? Or that our watching objects of a certain diameter can add to the order of things despite popular ideas?

In any case, an older theory suggests that clay is a catalyst for life involving its dimmers as if interlocking circles.

Sometimes I think it is better to go back to the drawing board than to be burdened with ever more growing obsolete ideas.

Yet, learning somehow maintains a memory over our awakening.

The PeSla

 
At 11:03 AM, Blogger Ulla said...

Also the clayor dust are important (for darkmatter/energy?)
http://www.usf.uni-osnabrueck.de/usf/literatur/beitraege/texte/033-fellermann.pdf

http://cshperspectives.cshlp.org/content/2/9/a002212.full

 
At 11:22 AM, Blogger Ulla said...

PeSla
No, homeostasis and feedback loops are not outdated. They are very much the essence of what is life and memory. But we always think homeostasis is something containing in life. Instead it is thermodynamics and entropy, purely physical.

The idea here is exactly to minimalize consciousness/memory and perception, because if we find a functioning recipe, then we have solved almost every other kind of measurement in living matter too.

I have the opinion that every fact must be involved. Now and then the drawing board is always necessary. But the problems cannot be solved at the drawing board. We need experiments and proofs too, to exclude false assumptions. Otherwise we soon have an M-theory of biology, which we don't want.

Life use superconduction to regulate the energy. It is absolutely necessary, otherwise life would be impossible? It would gather heat (dissipation)?

 
At 8:22 PM, Anonymous Matti Pitkanen said...

To Pesla,

graphene electron's pseudospin is just a formal notio. If I remember correctly the spin states correspond to two opposite directions of momentum. It has has nothing to do with real spin. The idea about spin emerging from lattice structure fails because it forgets symmetries. This just he everyweekly hype. At least 99.9 per cent of articles about theoretical physics are pure hype in New Scientist and other popular journals as well as blogs since the only criterion is that the proud father of the new theoretical idea speaks native American english. Twistor amplitudes represent the only really new and brilliant idea in official theoretical physics for decades.


For the hierarchy of Planck constants scaling the zero point energy of say harmonic oscillator scales like hbar just as energy. Zero point energy as infinite source of energy is nonsense and reflects one of the shortcomings of quantum field theory. It has no place in TGD.

About the question about energy gain. Energy as such is not any blessing for life. It is information, the character of entanglement , and metabolic energy accompanying negentropic entanglement which matter.

*If one accepts zero energy ontology and number theoretic negentropy and thus negentropic entanglement having interpretation as a correlate for conscious information. Information carrying entanglement is possible in the intersection of real and p-adic worlds. Negentropically entangeled particles are correlated since the binding energy is negative so that relative translational degrees of freedom are not frozen. Perhaps one could assign the conscious experience that we are used to call "love" to this kind of correlated behavior. Or experience of understanding, or something experienced as positive.

Negentropy Maximization Principle supports create life since it favors the generation of negentropic entanglement and stabilizes it. In any case, life as also free love;-) is a critical phenomenon, blade runner since the intersection is like the edge of blade. Living system must be able to stay at it and perturbations from environment- second law- tend to destroy it. The pessimistic vision is that second law still holds true. The generation of negentropic entanglement is accompanied by a generation of entropic entanglement with at least the same magnitude of entropy so that life unavoidably pollutes the environment. Looking what we have managed to do for this planet seems to support this view.

There is however the moment of mercy: next quantum jump beginning with a U-process allows to replace the polluted sub-Uniberse with a new one remaining for a short moment a paradize until Adam and Eve once again initiate the state function reduction cascade and good and bad emerge.

*The concrete connection between information and metabolic energy comes in the following manner. High energy phosphate bond (in the proposal of posting higher energy nitrate bond possible for so called oxidation states in which atom tends to make the electron shell empty rather than filling it, would represent negentropic entanglement. The ATP-ADP process is a highly standardized process of moving around packets of negentropy- maybe the exchange of this energy information packet is experienced as a friendly hug;-).

Facebook seems to be achieving similar standardization of social interactions: I do not like it but maybe it is best option after all.

*There is no need for drawing energy from vacuum: energy conservation holds in any case. What is needed transformation of energy to negentropic energy and at same time also entropic one.

 
At 10:31 PM, Anonymous Matti Pitkanen said...

To Pesla:

as Ulla says homeostasis and feedback loops are certainly there but probably emerge at later stages when system begins to regulate its behavior.

I do not believe that homeostasis reduces to physics only. Living system is like a dancer at rope. If you put on the rope a dead statue of the dancer no physics can keep it on the rope, intentional actions of the dancer are required and this is the essence of homeostasis. I would prefer explanation of homeostasis in terms of self hierarchy. Homeostasis would be analogous to flow equilibrium in society: competing tendencies at various levels of hierarchy take care of stability: when only one tendency remains, catastrophe results as the failures of communism and of market economy have taught to us (I do not refer to Lubos here;-)).

Homeostasis needs memory as Ulla notices and genuine memory requires consciousness so that physics in standard physics sense is not enough.


To me the finding that the time intervals between stops and starts of the oil drop are not random demonstrates the presence of genuine memory in the oil droplet system. I would say that this is an ingenious manner to demonstrate the presence of intentional action. Quite generally, fractal long range correlations combined with local randomness -something very difficult to understand in terms of pure physics- would be the signature of intentionality. It would have p-adic fractality as space-time correlate/mimicry.

 
At 10:46 PM, Anonymous Matti Pitkanen said...

I share the hope that theoretical biology would not reduce to a new M-theory. The experimental input which is still poorly understood is so immense that there is probably no fear about this.

The attempt to discover protocell is clearly something much more interesting than biology reduced to the study of possible correlations between genes and structure and function. This is important but as it has already turned out we cannot always trust gene-function correlations. I believe that that the neglected new level is magnetic body bringing in topological quantum computer programs as software to the hardware provided by genes. Only in this manner we can understand why organisms with practically same genome can represent so hugely different evolutionary levels.

My dream is that experimentalists would discover as many systems as possible demonstrating some key elements of life. Only their comparison and the attempt to see the common denominators can lead the guessing theorists to a safe ground.

For an imaginative theorists biology is intellectual El Dorado: practically nothing is understood and the only manner to proceed is creative imagination.

 
At 12:34 AM, Blogger Ulla said...

Homeostasis is a stress-response in which the stress is made to do work, and it strives for entropy, or low energy. Life recieves stress as perceptions (and dark metabolism) all the time, and this measurement is essential to life. Life creates new stability points at higher energy levels. But this is only temporal, as Lubos points out. A higher level of stress means higher level of stability points in biological tissues. This is the negentropic maximation, or self-organization at higher energy level, which at the end leads to diseases. So energy is basically no good for living tissues, but a certain amount is needed for the dance.

Opposite to homeostasis is allostasis, which creates more stress as a tool to achieve a new balance. The school example is to run, more free energy is created, and this force to higher pulse, more contractions etc. This is why much exercise is not good either.

The dance is between homeostasis (entropy) and allostasis (negentropy). A dead body has no inputs, and that was a bad example :)

Much of the pollution comes from needs to brace this organism, cool it down. Not even superconduction is enough :) We need food and water too. And much of other, more 'illusionary' (quantum negentropic entanglement to give a sense of not beeing alone) kinds, as love. Small babies dies without love, no matter how wellfeed they are.

WAU, Matti, is this a word-salad? Nice.

 
At 1:52 AM, Anonymous Matti Pitkanen said...

From Wikipedia I read that allostasis is the process of achieving stability in the sense of homeostasis.
Life is critical phenomenon and I would interpret homeostaisis as the ability to remain at unstable -that is critical- equilibrium point by (at some levels) intentional efforts. Standing at the edge of knife.

Consider as an example just simple looking action as standing still. One would fall down immediately without homeostasis. If stress is present it must be present at levels not conscious to us.

I am not sure whether I could see homeostasis as a stress-response although standing at the edge of knife might be pretty stressing;-). Wikipedia teaches me that stress is due to inability to respond adequately to mental, emotional, or physical demands.

 
At 11:21 AM, Blogger Ulla said...

Here quite a good article that tells what allostasis is about.

http://www.nature.com/npp/journal/v24/n2/full/1395603a.html

If you compare to the brainwaves homeostasis is the basic low energy level (4-7 Hz) that is disrupted by higher levels of 20-40 Hz and even higher 'rushes'.

http://www.ncbi.nlm.nih.gov/pubmed/9629234

"Adaptation in the face of potentially stressful challenges involves activation of neural, neuroendocrine and neuroendocrine-immune mechanisms. This has been called "allostasis" or "stability through change"

However, there are a number of circumstances in which allostatic systems may either be overstimulated or not perform normally, and this condition has been termed "allostatic load" or the price of adaptation. Allostatic load can lead to disease over long periods. "

Homeostasis is one thing very badly understood in biology.

 
At 1:49 PM, Blogger Ulla said...

These interactions are non-linear and very complex. What this non-linearity means is that when any one mediator is increased or decreased, there are compensatory changes in the other mediators that depend on time course and level of change of each of the mediators. Unfortunately, we cannot measure all components of this system simultaneously and must rely on measurements of only a few of them in any one study. Yet the non-linearity must be kept in mind in interpreting the results of any investigation that measures the biomarkers of allostasis.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474765/

This is a quantal effect?

 
At 4:15 PM, Blogger ThePeSla said...

Ulla,

If we have a little more complex geometry such as some sort of fundamental sheets of the topology very much of what we think as non-linear becomes linear in general or tendency or behavior (I assert) much as some have pictured the transition from zero to then dimensions as three generations of point line curve perhaps ending in point again.

BTW Leo's work has its own take on things and seems to miss the ground of or have some black hole physics ideas that are sound- I am surprised he has so many articles posted where the blogger publish on line if not in journals. I have thought a long time of varieties of black holes- and their behavior is akin to little oily spheres as much a our idea of billard balls and varieties of spin.

Matti,

especially for students in a subject I usually look to the original sources behind the popular magazines so they can cite it as a better reference- as in linguistics.

Are you sure if given a better theory in the details that genes although more complicated than we imagine are not reliable in themselves?

Wish we could talk somehow together and clear some of these loose ends up- seems a lot of new physicists are close but not quite there yet.

ThePeSla

 
At 1:25 AM, Blogger Ulla said...

ThePeSla
Sorry, I could not get your point or your question.

Fundamental geometry is many sheeted spacetime as Einstein saw it. Topology is a repetition of fundamental body structures beginning from the cell, or best seen in the fractal microsystems of the body. The fractality is wast. Everything essential is still in the cell, which itself is a many-sheeted spacetime.

A change in one microsystem will inevitably change all the others. ZEOs are many, very small inside the cell, and very big, including the environment. The boundary for our body is illusionary and temporal. In a year as much as > 90% of our body has been replaced from our environment. Compare to an amoeba with phagocytosis and excretion.

The binding structure (the bodyplan) is not changing so fast. One of the most fascinating areas to study this is morphogenesis.

 
At 1:43 AM, Blogger Ulla said...

Genes are not reliable structures.

http://neuroskeptic.blogspot.com/2011/05/theres-no-dna-in-disease.html?spref=fb

http://www.sciencedaily.com/releases/2011/05/110512150719.htm

Many cancer biologists now agree that changes in DNA methylation might be as important as genetic mutations in causing cancer. There are far more epigenetic changes than genetic changes

Also the same mutation can give rise to different diseases.

Genome is a chart for body plan, and protein-factory. But metabonomics and proteonomics are very complicated and it is simpler to go the other way - to magnetic body?

In fact, epigenetics is about methylation much. Is that a clue?

So the essential drive is in methane?

 
At 12:06 PM, Blogger Ulla said...

http://www.wired.com/wiredscience/2011/05/microbial-mats-oxygen/

 
At 3:33 AM, Anonymous Matti Pitkanen said...

Methylation might be important but I think that it is only a modification of the hardware. The really important modifications occur at the level of programs- that is magnetic body.

 
At 11:51 AM, Blogger Ulla said...

Methylation is the on-off switch and the eg. regulator. The genome is different in different parts of the body and in different ages.

http://rsif.royalsocietypublishing.org/content/6/36/575.full
Bud Mishra:
Intelligently deciphering unintelligible designs: algorithmic algebraic model checking in systems biology

 
At 3:16 AM, Blogger Ulla said...

http://www.neverendingbooks.org/index.php/penrose-tilings-and-noncommutative-geometry.html

 
At 8:55 AM, Blogger Ulla said...

http://neuroskeptic.blogspot.com/2011/05/free-will-is-in-brain.html
About Libet.

 

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