User talk:DMR Sekhar

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Genopsych

"The theory of evolution by Darwin....does not explain why a species produce variant types." <-- The details of DNA, chromosome recombination and mutation were not known when Darwin was alive.

instincts.....procreation. Instincts have to have a genetic basis, but the link between DNA and the behavior of an organism is complex. DNA can provide instructions for how to construct a brain that will in turn produce certain behaviors.

"The fact that DNA molecules remember their structure suggests that they are conscious of their existance"...."DNA molecules might be having some thing similar to Mind" <-- I wonder if you have ever read any of the work of Stuart Kauffman.
--JWSchmidt 14:30, 14 August 2007 (UTC)

Genome , the primary Instincts, natural selection and thermodynamics.

DNA molecules are ordered and have special properties of retaining the order [self repairing / self assembling] and replication [production of identical copies]. These properties are suggested to have controlled the process of evolution of genome towards a highly ordered structure from randomly produced natural mutant DNA molecules.

Introduction

The design and creation of the world's first vacuum pump [known as Magdeburg hemispheres] by Otto von Guericke, in 1650 begins the history of thermodynamics. However thermodynamics as a modern science started after the publication of a discourse titled "Reflections on the Motive Power of Fire" in the year 1824 by Sadi Carnot who is regarded as the" father of thermodynamics" .

Charles Darwin[1809-1882 ] propounded the theory of evolution which says that all the life on earth developed gradually over millions of years from a few common ancestors.

Sigmund Freud [1856-1939] a physiologist, medical doctor is the father of psychoanalysis and psychology. He originated several concepts such as unconscious mind, infantile sexuality, id, ego, super ego, primary instincts etc. The plant kingdom is out of the arena of psychology as they are supposed not to have a brain.

Deoxyribonucleic acid or DNA is a long polymer chain of sugar and phosphate atoms fixed by units called nucleotides. DNA was first isolated by Swiss physician Friedrich Miescher in the year 1869.

All these subjects are studied independently as specializations. In the year 1927, JC.Bose in his address to thirteenth Indian science congress said "now, full scientific attention has not been given to the power of our will in controlling all bodily functions". He talked of nervous impulses in plants. Clearly all these subjects are about life forms and their development but are misaligned. One theory does not fit into the other. They are discontinuous, are not complimentary to each other and don’t work in tandem.

Thermodynamics

Thermodynamics is a subject of interest to all those dealing with energy in particular and to physicists, chemists, engineers and to biologists in general. Psychologists ignored this subject despite the interest shown by Freud.

The second law of thermodynamics is of importance in the context of evolution. The general version of the second law from classical point of view is stated as "The total entropy of any isolated thermodynamic system tends to increase over time, approaching a maximum value." Entropy is the measure of disorder. What the second law says is that systems show tendency to become disordered left to themselves. This law of physics is special in that it does not hold always, it has exception.

From the stand point of molecular statistics, all states have equal probability. That is an ordered state may result out of a disordered state. This special version of second law is stated ^[1] as "the self compressive gas is not absolutely improbable." A simpler example ^[1] is: we have a pack of 52 playing cards. Every time we shuffle and show [say in a second] we see a disordered arrangement. Is an arrangement probable such that all the four suits of the cards show up in seniority? Statistically yes. All arrangements have equal probability. Such an out come is probable once in 10 ³⁷ shuffles. This is a rarest of the rare event if realized.

Theory of evolution

Darwin a naturalist studied fossils of extinct animals that were similar to modern species of South America. These studies prompted him to propound the theory of evolution which is based on the mechanism of natural selection. The mechanism of natural selection is two staged, [1] a species produces variant types, [2] some of the variants that fit well into the environment survived. That is survival of the fittest. The fittest again produced variant types so that the environment selects the most fittest and thus evolution proceeded. Important point is that the fittest is selected by the environment. The species it self has no roll. The species merely produced variant types randomly. Caution: evolution has directionality ^[2] but is not predetermined /preprogrammed. Here, [1] what do we mean by random?[2] Why a species produces an offspring? [3] what prompted species to produce variants instead of producing clones [4] what are the reasons for the evolution of bisexual organism from unisexual organism?

Primary instincts

Sigmund Freud identified that all living beings have ^[3] two primary instincts [1] self preservation and [2] procreation. Freud a highly original thinker was also influenced by the idea of conservation of energy of Helmholtz a physicist. Freud conceptualized "psychic energy" and thought that human personality is also an energy system. What is psychic energy?

Intelligence

We relate intelligence to neo cortex which is known as the logical brain. The neo cortex is the organ responsible for our logical thinking. This author defines: intelligence is the property that empowers an organism to find a solution or a number of alternative solutions to a problem. Amygdala which is also located ^[4] in the head is the organ responsible for emotional behaviour and hence is called the brain of emotions. Reportedly ^[5] the enteric nervous system [ENS] acts as brain of tubular animals which as such does not have a head. ENS is said to be responsible for gut feelings. The bacteria E.Coli changes the surface property ^[6] of its outer skin from hydrophilic to hydrophobic when exposed to 5% sodium chloride solution. As E.Coli does not have a formal brain it is imperative to think that the DNA might have guided its behaviour intelligently. Since long it is known ^[7] that plants do show intelligent behaviour. Now there is renewed interest ^[8] in this subject. The intelligent behavioral responses influenced by neo cortex and DNA /genome may be quite different. Neo cortex based intelligence is nurtured intelligence where as DNA based intelligence is native intelligence. The structure and operating mechanism of neo cortex and genome [DNA] are quite different. The construction and operating mechanism of NP junction diode and thermo ionic diode are quite different but their function is same, one way flow of electrons.

The Origin of Life

The events that lead to the origin ^[9,10] of life are as follows: [1] Formation of primary amino acids from methane, ammonia, water vapor and hydrogen past on electrical discharge. [2] Formation of large protein molecules and inter linking of these molecules with order. [3]appearance of very large molecules that form and disintegrate due to dissolving forces which still take their original shapes under favorable conditions. [4] Living organisms need continuous influx and outflow of matter and energy, without which it dies and rapidly disintegrates. [5] No new physical laws are required to explain the building of molecular order that characterizes living system. It is important to note that the statement [5] needs scrutiny. We know that DNA molecules show three extraordinary properties [a] they repair themselves [b] they produce their own replicates [c] some times during replication they produce variant types. The two properties, self repairing and replication of DNA are analogous to the primary instincts self preservation and procreation.

DNA and the Genome

DNA molecules have ^[2] adenine-thymine [AT] and guanine-cytosine [GC] nucleotide pairs fixed as sequences along the twisted double helix. G is bound [triple bond] more strongly to C than A to [double bond] T and hence we expect the presence of more GC pairs as favored by chemical thermodynamics which surprisingly is not the case. If GC and AT pairs are sequenced randomly then we expect GC and AT pairs to be at 50% each. This is also not the case. In fact the GC pair content in higher organism is in the range of 40% to 45% only which goes against the general version of the second law of thermodynamics .

Let us look ^[11-16]at the organization of the genome. The genome of mammals and birds are reported to have a GC content varying from 30% to 60%. Further the genome may be classified into [putative] isochors [regions or fragments] with varying content of GC pairs. The isochors are non randomly arranged i e the genome is structured from the point of view of isochors. With stable [GC rich fragments] and unstable [AT rich or GC poor fragments] states the genome resembles an information processing device.

Gene complexes bi thorax , BX-C and antennapedia, ANT-C are reported ^[17,18]to play a central role in programming the development of organism. Biological rhythms in an organism are due to gene clocks ^[19] which are automatically aligned with the external planetary rhythms. The alignment of bio-rhythms with planetary rhythms suggests that the gene clocks in fact sense the external environment.

Variations

Statistical process control (SPC) techniques are widely used ^[20-22]in quality engineering to maintain and improve the quality of products. Quality may be defined as fitness for use. SPC techniques are based on the idea that random variations in the characteristic of a product follow normal (Gaussian) distribution curve which is bell shaped, symmetric and the mode, median and mean (μ) coincide. 99.73% of the area under the normal distribution curve fall under the range μ + 3 σ (σ is standard deviation) and μ + 3 σ, μ - 3 σ are the control limits. A process is said to be under statistical control if the variations of the product quality are within these control limits.

Controlled processes

The variations in the quality characteristic are of two types (1) random variations, which are due to chance causes and (2) non- random variations which are due to assignable or special causes. Random variations can not change the direction of a process because of which the process is under “statistical control” whereas non random variations change the quality of the product. Common [random] causes are many and show feeble effect on the quality whereas assignable causes are few and show significant effect on the product quality. Processes under statistical control are Gaussian processes or centered processes.

Not all process are Gaussian, for example, variations in the grade (quality characteristic) of mineral concentrates (produced by floatation process) though above the minimum specification limits may not follow Gaussian distribution as the variations are non random. They may show (1) a skewed distribution with dispersed mode > median > mean > minimum specification limit, or (2) a multi modal distribution ²² each mode representing a changed “process setting”. Processes whose product characteristic do not follow normal distribution despite being fit are driven (positive direction) processes or non-Gaussian processes. Process settings include (1) internal characteristics of the material undergoing the process (2) process parameters, and (3) a control mechanism that (a) accepts or rejects a product, or (b) that allows or prevents the formation of a product. Processes are entropic in that left to themselves without control they deteriorate (negative direction) resulting unfit products.

Evolution as a process

The subject of SPC does not deal with intricacies of a particular process, rather it is about the statistical behaviour of any process and the characteristics of the product, the outcome of the process. Hence the concepts of SPC are also applicable to the process of evolution/ natural selection. The mechanism of natural selection is a two stage process viz. (1) appearance of variant types, and (2) survival of the fittest. Further Fisher’s theorem states ^[23] that the greater the genetic variability upon which selection for fitness may act, the greater the expected improvement in fitness. It is generally presumed that variant types appeared randomly and the fittest was selected by the environment in which the variant types were living and the selection is directional improving the fitness.

The cranial capacities [ in CC] of species from anthropoid apes to homosapiens (Chimpanzees and Gorillas 325-650, Australopithecus 450-650, Java man 800-1000, Peking man 900-1000, Neanderthal and recent man 1200-1600) indicates that the distribution of cranial capacities of all these species will be multi modal indicating that (1) evolution of these species is a process driven (non-Gaussian) under varying process settings (series of modes) and (2) populations of each species must have survived (as indicated by corresponding mode and ranges) under “statistical control” (a Gaussian process). May see this link :http://en.wikiversity.org/wiki/Image:Cranial.jpg

It is instructive to think that a change in the morphological character, for example cranial capacity of a species must be preceded by a corresponding change in the genetic material. According to the principles of SPC, a random genetic change may show a feeble effect on the cranial capacity i.e. stabilizing selection. However, shifting of the mode is due to non random variations (directional selection) and the genetic change that preceded must also be non random leading to a shift or change in the setting of intra genomic processes.

Some of the products of random genetic variations in the genome are better ordered while some others are lower ordered. The genetic products with low order will disintegrate due to entropic lead while those genetic products with better order retain their order due to genopsych. Continued accumulation of better ordered genetic products in the genome will lead non random structural changes in the genome.

Discussion

What might cause a change of process setting in the genome? There is evidence to say that adaptive responses [ say of bacteria] are not a direct consequence of a change in the environment [ for example ^[23] resistance to streptomycin or phage] and thus the forces/ factors that lead to a change of the process setting of genome are internal, that is to say, the change is self- organized/ ordered. The structure of genome is congenial for creation and processing of new information leading to the production of ordered states. It is important to note here that the first appearance of an ordered molecule such as DNA is via the special version of the second law of thermodynamics. Also these molecules should not have continued their existence in the face of the [general version of] second law of thermodynamics. However they not only continued but also replicated themselves. This phenomenon can't be explained with the known laws of physics or chemistry. We need to assign special properties to the DNA molecules. The fact that they remember their structure tells us that DNA molecules are memory molecules. Also the fact that they replicate themselves suggests that they are aware of their existence and are struggling to continue their existence. Thus it is instructive to think that DNA molecules have [the basis of] both the primary instincts [1] self preservation [self repairing] and [2] procreation [replication] and hence the production of variant types the first step in the mechanism of natural selection. We also noted ^{[17, 18]} that the development of the body parts of an organism is programmed at genetic level which means that, not only DNA molecules but also their complexes/ net works [the genome as such] are self ordered or self programmable, a special extensive property which may be termed as genopsych that operates counter to entropy. It is the genopsych that [1] gave directionality to the process of evolution [2] caused non random variations in the genome, indicating creation of new information [3] is the basis of native intelligence of the plants, microorganism. [4] It is genopsych the extensive property that distinguishes live DNA molecules from other matter molecules.

Laws of the origin and evolution of life

The laws of the origin and evolution of life may be stated as: [1] The formation of an ordered molecule such as DNA is not absolutely improbable.[2]The properties of self repairing and replication of DNA molecules are same as or similar to or the basis of the primary instincts self preservation and procreation of living organism. [3] DNA molecules and their complexes/ net works/ genome are 'self programmable' a property termed as genopsych.[4] Random genetic variations result into stabilising selection where as non random genetic variations lead the directional selection,that is speciation.[5]Evolution of genome is due to[a] the random production of variant DNA types and [b]the survival of the better ordered / better programmed.

References

1. Yeremin, E.N., 1983, Fundamentals of Chemical Thermodynamics, MIR Publishers, Moscow.

2. Volkenshtein, M.V., 1983, Bio physics, MIR Publihsers, Moscow,

3. Ernest Jones, 1960, Life and work of Sigmund Freud, Vol. 2, Basic Books Inc. New York.

4. Daniel Goleman, 1996, Emotional Intelligence, Bantam Books , New York.

5. Michael. D, Gershon, Alcmene Chalazonipis, Taube. P, Rothman, 1993, From Neural Crest to Bowel: Development of the Enteric Nervous System, Journal of Neuro Biology, Vol. 24, No. 2.

6. Gaudin , AM, 1962, Flotation of Micro Organisms, Froth Flotation, 50th anniversary volume, Ed. D. W. Fruestnuea, AIME, New York.

7. Bose,J.C. 1927, The Unity of Life,[ as reproduced in], Every man's Science , Vol.XXXIX,NO.4,Oct.-Nov.2004.

8. Anthony Trewavas, 2003, Aspects of Plant Intelligence, Annals of Botany 92:1-20.

9. George Wald, 1980, The origin of life, Molecules to living cells, W.H. Freeman and Company, San Francisco.11 - 19.

10. Philip C Hanawalt, 1980,Simple molecules to complex free - living cells , ibid.3 - 9.

11. Bernardi, G., et al, 1985, The mosaic genome of warm blooded vertebrates, Science, 228: 953-958.

12. Bernardi, G.,2000, Isochores and the evolutionary genomics of vertebrates, Gene, 241: 3-

13. Arndt, P.F., Hwa, T., Petrov, D.A., 2005, Substantial Regional Variation in Substitution Rates in the Human Genome : Importance of GC content, Gene Density, and Telomere-Specific Effects, J. Mol. Evol. 60 : 748-763.

14. Cohen, N., Dagan, T., Lewistone and Graur, D., 2005, GC-composition of the Human Genome :In search of Isochores, Mol. Biol. Evol. 25 (5) : 1260-1272.

15. Galtier, N., Piganeau, G., Mouchiround, D., and Duret, L., 2001, GC-content Evolution in Mammalian Genomes : The Biased Gene conversion Hypothesis, Genetics. 159 : 907-911.

16. Meunier, J., and Laurent Duret, L., 2004, Recombination Drives the Evolution of GC-content in Human Genome, Mol. Biol. Evol. 21 (6): 984-990.

17. Lewis, E.B.,1978, A gene complex controlling segmentation in Drosophila, Nature, Vol.276, 565-570.

18. Lewis, E.B., 1992, Clusters of Master Control Genes Regulate the Development of Higher Organisms, JAMA, Vol. 267 No. 11, 1524-1531.

19. Okamura, H.,2006, CIRCADIAN AND SEASONAL RHYTHMS – integration of mammalian circadian clock signals: from molecule to behavior, Journal of Endocrinology, 177, 3-6.

20. Zaidi, A. , 1995, SPC concepts, Methodologies and Tools, Prentice-Hall of India Pvt. Ltd., New Delhi.

21. Sekhar, D.M.R., Meena, R.K., Sriniwas, D.M., and Dhiraj Kapoor., 2000, SPC Techniques as Applied to Flotation Process, Indian Chem. Engr. Sec B, Vol.42, No.4,252-255.

22. Sen, P., Ghosh. J., Prabhulingaiah. G., and Sekhar. D.M.R., 2006, Internal morphology of SMS grade limestone samples,Trans, Inst, Min. Metall. C, Vol. 115: 127-131.

23. Strickberger, M.W., 1996, Genetics, Prentice-Hall of India Pvt. Ltd., New Delhi.

Comments

Origin of life. I'm interested in the idea that there is a natural way for non-biological chemical reactions to produce a non-trivial polymer. If we trace back through life on Earth towards its origin, we see only DNA and RNA, but there may have been one or more other important polymers before RNA and DNA. So, I think that continued searching for polymers that might have bridged the gap between non-life and our DNA/RNA form of life is a viable research area. I do not think that the laws of thermodynamics represent a barrier from the non-living to the living.

Genopsych. It is an interesting question: how complex is the information processing that operates at the level of the human genome? I'm comfortable with calling some computer code "intelligent" in the sense that it responds to non-trivial environmental challenges with adaptive responses. However, I am not comfortable with freely using the terms "mind" and "consciousness" to refer to any system that displays adaptive behavior. We could expand our definition of "mountain" to include a 1 centimeter high ant hill, but doing so does not really help us understand the geology of mountain building. Animals have an interesting multi-level process by which genes are used to "program" cells with different phenotypes. The different cell types then self-organize into tissues and organs (such as the brain). A human brain can then construct a mental model of the world. And, of course, there is another "layer" of psychological analysis that humans can add on independent of any knowledge about genetics, embryology or neurobiology. In my view, this layering of processes/theories can constructively be understood by specialists who study DNA, cells, brains and behavior. Yes, entire careers can be played out at just one of these levels, but eventually we can synthesize all of the specialized knowledge from the seemingly isolated "layers" of analysis and construct a coherent understanding of all the layers functioning together as a unified system. Such a synthesis can be facilitated by conceptual exercises such as studying particular examples of how changes in gene expression relate to changes in cell phenotype, how changes in cell phenotype result in changes in brain morphology and function, how changes in brain structure result in changes in cognitive functions and how an available set of cognitive capacities constrains a species to particular patterns of adaptive behaviors and flavors of consciousness. The term "genopsych" points towards an alternative "short cut" for understanding that bridges from the "level" of complex human behavior to the "level" of genetics in a single bound. It is, of course, tempting to look for such a "super theory" that can leap over the tall building of the human mind in a single bound, but I am skeptical. I have no problem with the idea that there is a link between molecules and mind, but I do not think there is a trivial formula or algorithm that can be used to describe that link. The relationship between molecular events and mental events is complex and we need to keep track of the fussy details at the cell and organ level. The devil is in the details, I'm afraid, and many of the details are still being discovered by the various specialists.

I think we should start a Wikiversity page where we can begin a complete and careful discussion of the issues you have raised.
--JWSchmidt 15:40, 1 July 2008 (UTC)

Thanks for the link. I still think it would be useful and constructive to start a Wikiversity page for discussion of your interests. Maybe something like a reading group. --JWSchmidt 14:05, 26 November 2008 (UTC)

"how to start?" We have Consciousness studies. Maybe there could be a "reading group"/"discussion group" for the topic of "consciousness studies". We could format some discussions like a debate such as: "Can a DNA molecule have consciousness?" --JWSchmidt 16:22, 30 November 2008 (UTC)

Self Programmable

Unfortunately I am not aware of the work of Stuart Kauffman directly. But now I saw a review by Ronald F. Fox of the book by Kauffman titled “The Origins of Order: Self- Organization and Selection in Evolution".

The terms Self Ordering, Self- Organization ^[24] , Self Interpreted Dynamic Base of Information ^[25] , and Self- Programmable ^[26,27],self activating ^[28] are now being used while discussing the process of evolution. As these researchers are not from the same area of specialization it may take some more time to understand each other’s point of view.

I think the following subjects are relevant, to understand genopsych [1] plant neurobiology and intelligence [2] intelligent behavior of microorganism ^[29] [3] intuition and instinctual behavior [4] physiological changes due to psychological[ hypnosis, placebo effect and phenomenon like autotomy ] decisions [5] self assembling materials , memory metals etc [6] entropy to creation of new information [7] brain processes [8] information processing within genome [8] random and non random variations , statistical process control [9]Shannon Entropy.

[24] Ronald F. Fox, Biophysical Journal, Volume 65, December, 1993,2698-2699

[25] Manolis Kamvysselis, Evolution with a Purpose, http://web.mit.edu/manoli/evolution/www/evolution.html

[26] Sowerby S.J.; Stockwell P.A.; Heckl W.M.; Petersen G.B, Origins of Life and Evolution of the Biosphere, Volume30, Number 1, January 2000, pp.81-99[19]

[27] Sekhar DMR, Integration of the Laws of Thermodynamics, the Properties of DNA molecules, the Primary Instincts and the Mechanism of Natural Selection, in the proceedings of 22nd Indian Engineering Congress,14-16,December,2007, The Instituion of Engineers [India].

[28] Frederic Peters, http://precedings.nature.com/documents/2444/version/1

DMR Sekhar 08:31, 4 August 2008 (UTC)

[29]Yuriy V. Pershin et al. Memristive model of amoeba’s learning, http://precedings.nature.com/documents/2431/version/1

DMR Sekhar 19:49, 31 October 2008 (UTC)

[30] Eric D. Schneider and James J. Kay : Order from Disorder: The Thermodynamics of Complexity in Biology , http://www.redfish.com/research/SchneiderKay1995_OrderFromDisorder.htm

[31] http://sciconrev.org/2007/04/consciousness-in-the-single-neuron/

86.108.58.254 17:27, 8 November 2008 (UTC)

Stuart Hameroff and Roger Penrose wrote³⁵,"Objective Reduction is taken as an instantaneous event-- the climax of a self organising process in fundamental space-time"

[35] http://www.quantumconsciousness.org/penrose-hameroff/consciousevents.html

DMR Sekhar 10:51, 21 September 2009 (UTC)

Consciousness

It is probably correct that "genpsy is to genes as the mind is to brain" in that genpsy and Mind play similar organizational roles in relation to their respective mediums: cognition plays the same ordering role vis a vis the body as DNA does vis a vis the morphology of the organism. But this does not mean that DNA is cognitive nor certainly consciously cognitive. Cognition has to do with using representations to move the organism, not constructing the organism at the molecular level. And conscious cognition is a special kind of representational mentation involving specific content and a particular way of processing that content (http://www.wwwconsciousness.com/Consciousness_PDF.pdf ).

The fact that DNA molecules have the capacity to reconstruct their structrure does not mean they cognitively "remember" their structure, and thus it is not possible to suggest that DNA is in some sense "conscious" because it remembers.

However it would be correct to say that the capacity to reconsrtruct structure is analogous to cognitive memory, which involves a capacity to reconstruct perceptual scenes.

I think that the comparison of DNA capacity to that of cognition tells us that DNA is lot more "intelligent" that we give it credit for, where "intelligence" = capacity to respond to sensed changes in the environment. But intelligence thus defined isn't necessarily based on cognition (which uses representations of the environement to generate and guide movement through the environment) and most certainly is not conscious.

Having said that, some scholars would agree with your equation. Panpsychism is apparently now making a comeback as witnessed in a recent report about the Tucson Conference on Consciousness June 2008. (http://tantranand.gaia.com/blog/2008/4/toward_a_science_of_consciousness_tucson_2008_conf_review)

Insyte 22:51, 1 November 2008 (UTC)

Well Insyte, I will define consciousness as: A system is conscious if it is self programmable. A system can programme itself provided if it [1. can sense itself, time and location [2. is intelligent [3. has memory. Self programmable includes self updating / improving of the programme.

94.249.13.81 10:52, 20 November 2008 (UTC)

A bird in flight

May refer to the section on DNA/ genome. As is mentioned AT nucleotides pairs are more than GC nucleotide pairs in the genome of higher organism despite the fact that formation of GC pairs is thermodynamically more favorable as G is triple bonded with C where as A is double bonded with T. Triple bonds are more stable than double bonds. Formation of a less stable state is probable according to special version [molecular statistics] of second law of thermodynamics as a transient phenomenon but such a state can’t persist as it is unstable. It requires a conscious effort to maintain an unstable state.

Let us see the following example. An air plane on the ground is more stable than an air plane in flight. It takes a conscious effort to keep the air plane flying. An air plane in flight consumes fuel and requires a pilot. Well an unmanned air plane can also fly if suitably programmed [by some body] consciously. A bird in flight is conscious.In other words an unconscious bird can not fly. May see this: Sekhar Dmr. Random Birds: Unconscious self programming is impossible. [Internet]. Version 1. dmrsekhar. 2009 Oct 31. Available from: https://dmrsekhar.wordpress.com/article/random-birds-3ecxygf1lxcn2-22/

Who programmed the genome [of higher organism] to maintain more unstable AT pairs? The answer is “the genome is consciously self programmed.” An unconscious self programming [of genome] is impossible.

DMR Sekhar 19:04, 3 November 2008 (UTC)

Certainly Not Random

As DMR Sekhar explains in his discussion points, the notion that changes to DNA chemistry are random should be reconsidered. We may begin our reconsideration of these principles with an excerpt from one of Richard Feynman’s many thought provoking books on physics; QED (Quantum Electro Dynamics) 1985:

“It appears that all the ‘particles’ in Nature- quarks, gluons, neutrinos, and so forth- behave in this quantum mechanical way. So now, I present to you the three basic actions, from which all the phenomena of light and electrons arise. ACTION #1: A photon goes from place to place. ACTION #2: An electron goes from place to place. ACTION #3: An electron emits or absorbs a photon. Each of these actions has an amplitude- an arrow- that can be calculated according to certain rules.”

Feynman goes on to say that these three actions are responsible for the entire field of chemistry. This would include biochemistry, which means that life-forming chemical reactions are not random; they follow quantum mechanical rules. A unified theory of evolution will explain how these quantum mechanical rules are related to the rest of nature and the development of life.

- J. Patrick

Photon

Looking at the process of evolution from the starting point of photons will be really exiting. After all, life forms consume energy/ matter for survival.

DMR Sekhar, 09:17, 5 November 2008 (UTC)

Forms and Levels of Consciousness.

The term consciousness is generally being used with respect to the consciousness located in the human brain / mind. I think consciousness related or located in the brain / mind may be termed Consciousness Proper or brain consciousness or just CoP. What about the living organism that do not have a formal brain? Are they not conscious? Reportedly ^[5,32] the enteric nervous system [ENS] acts as brain of tubular animals which as such does not have a brain. ENS is said to be responsible for our [human] gut feelings. May kindly see ^[29] this: It was shown that a large amoeba-like cell Physarum polycephalum subject to a pattern of periodic environmental changes learns and changes its behavior in anticipation of the next stimulus to come. Are organism such as Physarum polycephalum without consciousness? To resolve these questions I state that a self programmable system is conscious. The above approach permits me to arrive at genomic consciousness as genome, as a system is self programmable. A system is self programmable if the system has programmed it self without an external programmer. The first condition for a system to be self programmable is that it should be aware of its existence. Thus I note consciousness may be operating from different levels or in different forms, say genomic consciousness [or genpsy], Physiological consciousness [through ENS and other systems within the body of an organism] or just Cophy. And there may be different degrees of consciousness at sub levels in each of the three forms.

I think sleep walking man is at the lower degrees of CoP. Let us take the example of Coma ^[33] where a patient in coma is assessed by gauging the level of consciousness. A coma patient may die, or may go into vegetative state [brain dead but not dead Physiologically] or may come back into CoP. What brings a coma patient back to CoP? I think consciousness in the physiological and genetic forms / levels struggle to realign with CoP by reprogramming the mind/brain. The body of a man in coma is self programmable at the physiological level and hence is alive even when brain is dead fully or partially .I believe that genome is conscious. A system is conscious if it is self programmable. A system can programme itself provided if it [1] can sense itself, time and location [2] is intelligent [3] has memory. Self programming allows self upgrading of the programme. Thus we can measure consciousness in terms of the information in the genome. The three aspects of first condition about consciouness are adopted from the views of Frederic Peters ^[28] .

[5] Michael. D, Gershon, Alcmene Chalazonipis, Taube. P, Rothman, 1993, From Neural Crest to Bowel: Development of the Enteric Nervous System, Journal of Neuro Biology, Vol. 24, No. 2.

[29] Yuriy V. Pershin et al. Memristive model of amoeba’s learning, http://precedings.nature.com/documents/2431/version/1

[32] Sandra Blakeslee, There is a brain behind gut feelings, Times of India, 5, Feb., 1996.

[33] http://en.wikipedia.org/wiki/Coma

[34] http://knol.google.com/k/dmr-sekhar/genpsy/3ecxygf1lxcn2/1#

DMR Sekhar 09:51, 29 November 2008 (UTC)

It may make things easy to understand if we presume that consciousness may exist in different forms as CoP, CoPhy and Genpsy the same way energy exists in different forms such as light, heat,sound, etc.

DMR Sekhar 10:25, 30 November 2008 (UTC)

Evolution of Consciousness

Let me propose a model based on some simple assumptions [if the assumptions are false then the model will be false and if the model can’t explain many other observations then both the assumptions and the model may be false.] and test the model if it can answer some questions of relevance.

First: I will accept Frederic Peters ^[28] description of consciousness that is I-ness, Now-ness and Here-ness. In his words: As the primary reference frame of active waking cognition, this recursive I-here-now processing generates a zone of subjective self-awareness in terms of which it feels like something to be oneself here and now. This is consciousness. Second: Let me assume that consciousness exists at three levels such as genetic, physiological and psychological. The forms in which the consciousness exists in these levels may be different in a way similar to the different forms of energy say light, heat, electricity etc. Genpsy, CoPhy, and CoP are the forms of consciousness at genetic, physiological and psychological levels respectively.

Now the argument: We know that sun rise and sun set are specific to a particular location. We also know ^[19] that all living beings [biological systems] have bio rhythms such as sleeping. And we also know that bio rhythms are synchronized with planetary rhythms. This is achieved by gene clocks. Thus now-ness [time sense] and here-ness [sense of location] comes from genome.

We know that genome contains a variety of programmes for example ^[17] the programmes that control the development of body organs. These programmes are not incorporated into genome by any external agency, rather these programmes evolved. Thus genome is self programmed. Further genome [higher organism] contains more AT pairs than GC pairs despite the fact that GC pairs are thermodynamically more stable. To maintain this ordered and its relatively unstable state genome consumes energy/ matter that is genome is self controlled. It is true that living systems increase entropy out side of the system to compensate the increased order [read as additional information or a new programme]inside the system and this however does not mean that genome is not self programmable. To be self programmable and to be self controlled genome [for that matter any other system] should be aware of itself. The I-ness of Frederic Peters definition belongs to the Brain.

We generally attribute consciousness to the brain. We know that the brain and the body developed from embryo a single cell. In a sense genome is the brain of the embryo. If the brain has consciousness, it also must have developed / evolved along with the brain. That is consciousness also should have a precursor form at the level of genome of the embryo and that is what I call genomic consciousness. If the I-ness belonged to the brain then genome may be expected to have i-ness, the spring head of I-ness. Entropy is applicable to both physical and biological systems where as genpsy is an exclusive property of biological[read living] systems. Only living systems are self programmable and self programmable systems are conscious.

[28] http://precedings.nature.com/documents/2444/version/1

[19] Okamura, H., 2006, CIRCADIAN AND SEASONAL RHYTHMS – integration of mammalian circadian clock signals: from molecule to behavior, Journal of Endocrinology, 177, 3-6.

[17,18]a. Lewis, E.B., 1978, A gene complex controlling segmentation in Drosophila, Nature, Vol.276, 565-570. and b. Lewis, E.B., 1992, Clusters of Master Control Genes Regulate the Development of Higher Organisms, JAMA, Vol. 267 No. 11, 1524-1531.

DMR Sekhar 11:35, 2 December 2008 (UTC)

self programming & evolution

self programmability of genome
Stuart Kauffman <-- I do not know if he has been able to establish an active work group in Canada. I've spoken to other theoretical biologists who are not enthusiastic about Kauffman's approach. I think part of the problem is linguistic. Like all specialists, biologists tend to have their own terminology and specialists in different fields can be isolated conceptually because of differences in how they use certain words, by which methods they use and by which concepts dominate their particular field. It is interesting when we are left wondering if progress in a field is limited by the habits of people in the field and their tendency to just keep using the same old approaches that they are comfortable with. I've also seen this problem in the fields of consciousness studies and artificial intelligence research where people such as Gerald Edelman have made interesting attempts to work at the boundary between biology and computer science....but their methods and approaches never seem to form the basis for a popular research trend that can be readily adopted by others.
I think it is safe to say that most biologists with an interest in genome evolution are not interested in consciousness and most biologists who are interested in consciousness do not concern themselves with consciousness at the level of the genome. It might be useful to start a Wikiversity page where an attempt is made to clearly define terms (self-programing, evolution, consciousness) and explore why it is that so few people tend to put all these terms together in a coherent sentence. --JWSchmidt 16:27, 19 March 2009 (UTC)

Definitions

[1]A system is self programmable if it can create new software on its own which in turn can build its own hardware with new features.

[2] A system is living if it can self preserve and procreate.

[3]Evolution is a process of procreation where the procreated has features distinctly different [a non random changes] from the procreator or procreators.

[4] conscious is self awareness. A “system” to be aware of it self must exist in two interacting/ communicating/ sensing states that can act in tandem . Genome eminently satisfies the criteria for self awareness in physical terms. Hence genome is the originator of self awareness in physical terms and hence is the real self. The brain generated “self” image/consciousness is ephemeral. Sekhar Dmr. Reality of the Self: Self, Reality and Consciousness [Internet]. Version 1. dmrsekhar. 2011 Mar 28. Available from: https://dmrsekhar.wordpress.com/article/reality-of-the-self-3ecxygf1lxcn2-81/

[5] It is intuitively obvious that living systems are self programmable and conscious.

DMR Sekhar 17:15, 28 March 2009 (UTC)

Transcience

My dear Prof. Schmidt Let me begin with your observations that limits of terminology and methodology often delimit The scope of exchange of ideas across the spectrum of a theme like Consciousness or Evolution. The overemphasis on formal research background normally impedes dialogue among intelligent and Educated scientists, despite their commonalility of interests. The ideas (Theories!) of Genopsych, Evolution and Consciousness are such examples which need to be debated among Evolutionary Biologists, Molecular Biologists, Statisticians, Mathematicians, Sociologists, Psychologists and Philosophers who have dwelled and contributed out of their concern and interest for integrating The Philosophy with Science with a passion to envision the path of Evolution of human societies. This fundamental exercise has a potential application in evolution of a reverential coexistence of Humanity with all biotic and abiotic components of planet earth.With this agenda in mind I am thinking to bring out an edited book on “Philosophy Of Evolution”. I invite you to join me as first Editor. As Editors we shall invite experts from diverse and seemingly unrelated fields to contribute articles, and shall strive to coordinate thoughts and explore coherence. While there would not be any hurry to draw conclusions, there would be a sincere effort to bring the ideas on a plinth of a round table. The tentative topics may be: 1.Self ordering and evolution 2.Plant intelligence and plant neurobiology 3.Plant signals 4.Genopsych, 5. Structure/organization of genome and measurement of genomic information 6. Thermodynamics and evolution with special reference to Human thermodynamics 7. The evolution of society with special reference to the human society 8. Consciousness from the points of view of Jain, Buddhist, Christian and Hindu philosophy 9. Bio-rhythms and evolution 10i. Origin and evolution and consciousness

The Blogs are doing a great service, but a book in print, would further complement the Effort to initiate a dialogue which can be transformed into an International Transcience Symposium Sometime during 2010.I request you to give your consent to become first editor. After receiving your consent we would be planning publication modalities.

I may be contacted at

ak_pur@sify.com

Thanking you, AK Purohit

Maybe the construction of such a book on “Philosophy Of evolution” could be facilitated by a project page here at Wikiversity. It sounds like the project would encourage a certain amount of original thinking and would not be welcome at Wikibooks. --JWSchmidt 14:38, 11 April 2009 (UTC)

Dear Schmidt,

I have been discussing the issues related to evolution with friends like Prof. AK Purohit. As the subject goes across several areas a face to face discussion will be more fruitful. AKP is of the opinion that it is time to invite all those interested to contribute their papers and publish them in print as very senior scientists may not be interested in web discussions. This should be followed up by an international symposium that may help the creation of a permanent platform [such as Transcience Society] competent enough to take up contradicting scientific views. I fully agree with Prof. Purohit. I request you to kindly respond to the invitation of Prof. Purohit. DMR Sekhar 03:48, 12 April 2009 (UTC)

Nonkilling

Dear DMR Sekhar,

I've just seen your message. Could your provide an email contact?

Best, --Cgnk 16:57, 27 April 2009 (UTC)

The equation of genopsych

The equation of free energy in thermodynamics may be re written in psychological terms as follows.

F = B + i G

Where F is the free will that imparts freedom to think creatively and take decisions, B is the bound will, the programs at Genetic, Physiological and Psychological levels / phases. For example blood circulation and heart beat are controlled by programs at physiological level/phase. Then i is the self awareness that imparts I-ness to us, measured in degrees of consciousness and G is the genopsych, the self programming property [similar to or same as entropy of physical systems,a measure of order of a state] of the living forms/ systems. At i tending to 0 or G tending to 0, F is approximately equal to G as in the case of a virus which is said to be sub living or at the boundary of living and non living. Needless to say that the free will and bound will of the species increased as they evolved into higher organism.May we call it geno dynamic equation?

DMR Sekhar

Science of nonviolence

Dear Cgnk, I am sorry for the delayed response. Welcome. I think the science of non violence is covered under transcience effort being made by Prof. AK Purohit. My email ID is dmrsekhar@yahoo.com . Please contribute your article which you may send to Prof Purohit or to me to our email IDs. Thanks. DMR Sekhar 06:41, 17 May 2009 (UTC)

Very relevant topic. The behavioral traits selfishness and altruism are two faces of the same coin [the species] that help the survival of the species. Humans are probably evolving towards altruistic societies. Evolution of altruistic societies if true must have biological basis. Peaceful coexistence and cooperative living apparently are probable directions for the existence and evolution of human societies. 117.199.112.201 03:43, 19 May 2009 (UTC)

The third way

I again read the article of James A Shapiro. It is so convincing. He did not use the word genopsych but described it fully. You too may like it. Here is the link.But it appears that Dr Shapiro gives more importance to the cell than the genome and DNA. But the recent experimental evidence suggests that DNA/ genome and genomic processes may be primary.

[35] http://www.bostonreview.net/br22.1/shapiro.html

Thanks, DMR Sekhar 18:41, 6 April 2010 (UTC)

[36] Daniel G. Gibson, et al, Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome, / www.sciencexpress.org / 20 May 2010 / Page 2 / 10.1126/science

[37] Sekhar, DMR, . Life, Consciousness and Evolution: Evolution of species is a conscious process. [Internet]. Version 25. dmrsekhar. 2014 Dec 13. Available from: https://dmrsekhar.wordpress.com/article/life-consciousness-and-evolution/ DMR Sekhar

DNA Electronics

It appears that intra electronic structure of DNA permits it to not only to store usable electrical energy but also to sense the ionic environment adjacent to it.

May see this knol.

[38] Sekhar, DMR. Sekhar Dmr. Capacitor like electronic structures of DNA: DNA Electronics [Internet]. Version 1. dmrsekhar. 2010 Jul 24. Available from: https://dmrsekhar.wordpress.com/article/capacitor-like-electronic-structures-of-3ecxygf1lxcn2-33/ DMR Sekhar 17:47, 31 July 2010 (UTC)

Intra DNA Quantum computing?

Elisabeth Rieper, et al recently concluded ³⁹ by applying their model to DNA that entanglement may play a crucial role in explaining the stability of DNA double helix. Quantum entanglement explains ⁴⁰ Hameroff, is a weird quantum process where a single wave function describes two separate objects which effectively share the same existence, no matter how far apart they might be. Elisabeth et al closed their discussion saying, “what is the influence of entanglement for read out of DNA? Is there anyway to harness this entanglement?” Hameroff reacts to these questions with another question, “Is DNA a quantum computer?” Indeed future research needs to be directed to these questions.

39. Elisabeth Rieper, Janet Anders and Vlatco Vedral, “The relevance of continuous variable entanglement in DNA”, arXiv:1006.4053v1 [quant-ph] 21 June 2010, arxiv.org/abs/1006.4053

40. Stuart Hameroff, “Is DNA a quantum computer”, http://www.quantumconsciousness.org/DNAquantumcomputer1.htm

DMR Sekhar 13:31, 21 August 2010 (UTC)

Faulty explanation of evolution by natural selection

It is natural that the quality of products of any process natural or artificial will vary randomly which does not mean that the process itself is random that is directionless or purposeless. This applies equally to even the process of evolution of species by natural selection. The process of production [procreation] of variant types is not random but the variations in the morphological features of the variants are random and procreation is well driven/ directed process with the purpose of [self] preservation of the species, the life forms.

[41] Sekhar Dmr. The drive and the direction of evolution: The drive behind the process of evolution of species [Internet]. Version 1. dmrsekhar. 2010 Aug 15. Available from: https://dmrsekhar.wordpress.com/article/the-drive-and-the-direction-of-evolution-3ecxygf1lxcn2-34/.

DMR Sekhar 13:54, 21 August 2010 (UTC)

Gibbs ensembles and systems biology

The thermodynamic state of a living cell is analogical to that of grand canonical ensemble described by Gibbs but the living cell shows emergent system's properties such as self programmability, will and consciousness which cannot be reduced to myriad chemical reactions that go on in the cell.

[42] Reality of the self, http://dmrsekhar.wordpress.com/article/reality-of-the-self-3ecxygf1lxcn2-81/

[43] Living Systems, http://dmrsekhar.wordpress.com/article/living-systems-3ecxygf1lxcn2-84/

[44] Gene, Brain and Behaviour, http://dnadecipher.com/index.php/ddj/article/view/20

[45] Sekhar, DMR, Genome and Plausible Genopsych, Journal of Consciousness Exploration & Research, Vol 2, No 10 (2011), http://jcer.com/index.php/jcj/article/view/193

DMR Sekhar 05:38, 9 March 2011 (UTC)

International Journal of Applied Life Sciences and Engineering

May see the article on consciousness by Dr. Syamala Hari here: http://ijalse.org/Issues.php?vo=1&is=1

DMR Sekhar (discuss • contribs) 03:33, 15 February 2014 (UTC)

---

Life as a State of Matter

Life, Consciousness and Evolution

Life is a state of matter with primary emergent properties such as self- programmability (genopsych), consciousness and free will, the origin of which is traceable to the genome. What mind is to brain is as genopsych is to genome. If so it becomes instructive to think that the evolution of species driven by the genopsych is a conscious process.

Life, Consciousness and Evolution: Evolution of species is a conscious process. [Internet]. Version 25. dmrsekhar. 2014 Dec 13. Available from: https://dmrsekhar.wordpress.com/article/life-consciousness-and-evolution/

DMR Sekhar (discuss • contribs) 15:37, 9 January 2015 (UTC)