The primacy of DNA as a unit of life

DNA and Genome

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Abstract

The primary properties of DNA molecules viz self repairing/assembly and replication are analogous to and are the genetic basis of the primary instincts self preservation and procreation. It is the self programming property of DNA molecules that lead the creation of new information and programs in the genome which in turn drove the process of evolution of species by natural selection. Life forms are self programmed which is a biological property that is applicable to all living systems from DNA molecules [genome] to human societies. The recent studies indeed suggest that the DNA molecules/ genome might be having the stored internal electrical energy. Further Venter’s experiment proves that genome alone can build its cell under favourable environment. It is well known that information flows from DNA to RNA to protein which results into an expression or work function.

 
 

Introduction

It is said1 that biology has four great problems remaining unsolved which are (1) the nature of the molecular regulation of development of cells and organs (2) the understanding of macro evolution and eco system construction from the first principles of micro evolution (3) the mind/ body problem and (4) the genetic basis (if any) of cultural evolution.
The problem of mind/body is atypical in that a proposed model should be coherent and fit, several observations in the fields of chemistry, physiology, statistics, thermodynamics, genetics etc. on the one hand and psychology on the other hand. Mind/body problem goes beyond the study of neo-cortex (the brain) for even plants show2 aspects of intelligence. Tubular animals (earthworms for example) do not have neo-cortex, but can we say that they are unintelligent or they are mindless?

Adaptive responses of organism are explained as those “not consciously decided” and are due to “genetic means”. The creativity of evolution, the geneticists say3 does not mean “purposefulness’ in human sense. The problem with genetics is that the natural mutations of genes (that drove the process of evolution) are understood as errors! As errors cannot lead to, intelligence or creativity, evasive terms such as “genetic means”, “purposefulness in human sense” are resorted to, which preclude further investigations.
 

 
Second law of Thermodynamics

The second law of thermodynamics in its general version is stated as follows. For all spontaneous processes the entropy (disorder) of a system always increases. This is from the classical standpoint of thermodynamics. However, from the standpoint4 of molecular statistics this law is stated as “the self compression of a gas is not absolutely impossible” as all states have equal probability. The thermodynamic probability of such a state however may be very low. Thus statistical thermodynamics permit the occurrence of a self ordered state, although realization of such a state is very, very rare or rather rarest of the rare. Even if such state is formed, [as all states have equal probability] the same will be transient and highly unstable.

In simpler terms ‘ water always flows from [say hill] top to bottom’ as per the general version of second law of thermodynamics. However’ the flow of water from bottom to top is not absolutely impossible’ as per molecular statistics!? Molecules in a body of water move in all directions randomly. Is there any probability of all the water molecules in the water body move just upward? Indeed such probability exists at least theoretically. Even if that [water moving up spontaneously] happens it can only be a transient phenomenon which is not sustainable.
 

 
Evolution and the Properties of DNA

How, highly ordered molecules such as DNA first appeared out of a chaotic environment is not very clear so although the following stages that led to the origin of life are envisaged/explained5, (1) formation of primary amino acids from methane, ammonia, water vapour and hydrogen (past on electric discharge) (2) formation of large protein molecules and interlinking of these molecules, with “order” (3) followed by formation of very large molecules that form and disintegrate due to dissolving forces which may still take original shapes and sizes under favourable conditions. These large molecules may break into smaller ones and may start growing again.

The first appearance of DNA molecules might be possible as a matter of rarest of rare chance, a possibility similar to that of self compressive gas. It is surprising to note that DNA molecules not only continued to survive but also developed (evolved) into more complex organism instead of being in an expected unstable and transient state followed by their disappearance. This might be due to the remarkable and outstanding properties of DNA molecules such as (1) self repairing, (2a) replication and (2b) mutation [sometimes] during replication.
DNA molecules have5, 6 self repairing capabilities i.e if some part of it is damaged, DNA reassembles itself to its original form. That way they are “memory” molecules that have “self healing” capability. DNA molecules replicate themselves. These two properties remind7 us of the two primary instincts of all living things i.e self-preservation and procreation. The self repairing capability of DNA molecules is a way of self preservation. That is procreation (replication of DNA molecules) is an outcome of its struggle to preserve itself. Self-repairing capability and replication of DNA molecules are two faces of “will to survive”, the latter being a consequence of the former.
It is known8,9 that genetic material is responsible for the time sense of all living organism, in that they not only control internal biological clocks but also synchronize these clocks with external planetary rhythms ( for example, day and night cycles which are location specific).
DNA molecules are capable of not only replicating themselves but also can change their structure (sequencing of amino-bases) during the process of replication, a phenomenon known3 as natural mutations. We know that the point mutations of genes (change in the sequence of paired amino bases for example A-T and G-C) can happen spontaneously or naturally. However if these mutations are due to random causes only, the content of A-T and G-C pairs in DNA should be by an equal probability i.e. 50% each. But that is not the case. G-C pair is thermodynamically more favourable than A-T pair (G is bound more strongly to C than A is to T) because of which G-C pairs should have been predominant, which of course is also not the case. In higher organisms the G-C content (in DNA) is stabilized10 at the 40-45 percent level. Science explains this as ‘the evolutionary formation of a “G-C organism” is biologically meaningless, for triplets that do not contain A and T, code only for few (one fifth) of the amino acid residues’. This is an untenable explanation. Some of the natural mutations of DNA must be due to special causes and not random causes (the concepts of statistical process control are developed based on special and random causes11 that influence the outcome of a process) which should not be interpreted as errors. The DNA molecules are well programmed. The random undirected mutations are reorganised by genomic processes such as recombination, DNA- repair etc. Who programmed them? A careful examination of the properties of DNA molecules suggests that they are self programmable.
The other name of the extensive property ‘self programmability’ is genopsych. Thus genopsych is neither matter nor energy but an extensive property of DNA molecules that imparts self ordering nature to DNA molecules and their net works.
 
  

The Mind

There are situations where the role of mind can be perceived as distinct from the brain (neo-cortex). The study12 of placebo effect is one such case. For example 70% of people in treatment group (suffering from depression) get better after they are administered with an anti depressant drug which causes a change in the brain chemistry. If one looks at the control (matching) group (also suffering from depression) 35% get better, who were administered just with placebo (an inert sugar pill). Both groups are unaware of what they were given. While treatment group was given the actual medicine, the control group was given just hope which cured 35% of the patients. What should we conclude? Mere hope can cure 35% while medicine may cure another 35% and hence 70% in the treatment group got better. Placebo is an effect of hope, i.e. positive psychology (thinking).

Hope (the will to survive) belongs to mind. It is said12 that placebo effect is associated with an increase in the endorphin level. Thus the mind, an abstract thing can cause a change in the brain chemistry. The point is that brain has ”self healing” property/capacity (or self ordering property), which is due to the “will to survive”. Depression is the disorder (entropy!) of brain.
Those in the treatment group who believed that medicine may not help them remained uncured and this is known as nocebo effect. Negative aspects can be noted even at genetic level for example3 the existence of lethal genes, the phenomenon of genetic death and programmed cell death [PCD as it is known] etc. Thus the effect of psychology [putting together placebo and nocebo] works out to 65% where as the effect of medicine is just 35%.
The state of hypnotic sleep where the subject’s behaviour is controlled by mere suggestions by words is another instance that suggests the existence of mind, as during hypnotic sleep, the free will of the subject is frozen and the words (of the hypnotizer) act as stimulants so much so that they can cause physiological change in the subject, for example develop a blister on the body (not caused by burn!). The brain of the subject is run by the external suggestions (i.e. by the mind of the hypnotizer) by words. Placebo effect may be understood as “auto suggestion”.
 

 
The Primacy

Recently it is shown13 that the designed and synthesised genome of Mycoplasma mycoides if replaces [transplanted] the genome of Mycoplasma capricolum in the body of Mycoplasma capricolum will result into the reproduction [or evolution of] of Mycoplasma mycoides and not Mycoplasma capricolum. These studies indeed suggest that genome and genomic processes are primary over cell structure and cell processes.

It is reported14 that double helical DNA can serve as a conduit for efficient charge transport reactions over long distances in vitro. The double helical structure adopted by B- form DNA, where a negatively charged sugar – phosphate back bone surrounds a Pi stacked array of heterocyclic aromatic base pairs, allows it to serve as an efficient medium for long range charge transport15. This chemistry has now been well established14 as a property of DNA. The transport of charge along DNA can be rapid and may cause16 chemical changes at a distance of 200 angstroms.
Pi stacking due to A-T and G-C pairs at the core of DNA is non polar17 which also means that the central core of the DNA molecule is neutral and hydrophobic. Being hydrophobic the central core may not only repel water molecules but also may induce some sort of structure16 similar to ice-1 in the nearest neighbour water molecules. Each A-T and G-C also has a dipole [due to London – Van der Waal forces] which may differ slightly with each other due to structural differences. Further in the given situation of DNA the charges in the dipoles are likely to be influenced by the negative charge in the back bone structure of the double helix in a way similar to the envisaged19 polarisation of heavy metal cations near sphalerite surface.
By visualising the negatively charged back bone structure of sugar phosphate double helix as outer circular plane and the Pi stacked non polar core as inner circular plane, we notice that the DNA has the features of a capacitor. A capacitor stores readily usable electrical energy. Thus DNA might be storing electrical energy which it can use independent of ATP/ ADP chemistry which is a necessary condition for a DNA molecule [or a similar or a precursor of DNA molecule] to evolve into a cell during the process of evolution of first set of living cells.
 
 

Confusion worst confounded

Let us see this statement: I am a liar. Indeed if I am a liar then I am telling the truth which proves that I am not a liar. If I am telling the truth then the statement is a lie which makes me a liar. The statement “I am a liar” is an inconsistent one in that it is not self explained. Standing before you if I state that I am existing, then it does not require any further proof as my statement is self consistent. At this stage I leave it to the sceptics to prove or disprove my existence. The inconsistency of the statement, “I am a liar” is generally quoted to explain Godel’s theorem of incompleteness which obviously is not applicable to the statement, “I am existing”. Similar confusion arises when one tries to apply the second law of thermodynamics as second law is applicable when we see an organism and its surroundings as a system where as the drive [programmed coordination of self controlled processes] of the internal processes of the organism can’t be explained by the second law as these processes are genopsychic and are not entropic. Stephen Hawking said20 ,” The second law of thermodynamics has a rather different status than that of other laws of science, such as Newton’s law of gravity, for example, because it does not hold always, just in the vast majority of cases”. Hawking’s statement is the most honest about the second law of thermodynamics.

The so called orthodox science is now accepting21 the truth of placebo though coyly saying,” belief is powerful medicine, even if the treatment itself is a sham. New research shows placebos can also benefit patients who do not have faith in them”.
Most of the confusion is due to the fact that science views life only through the physical laws. If it is not by genopsych then how can we explain the strange properties of DNA [self repairing, replication and self programmability], the organisation [non random structures] of genome, the genomic ability to create new information and the execution of genomic programmes, autotomy, instincts, intuition, and placebo effect through one single model?
 

 
Closing Remarks

Genopsych is the extensive self programming property of the genome. Self programmable may be understood as genome acting as both the programme and the programmer, i.e. genopsych is dual natured.

The self programming property of brain (neo cortex) may be termed as Mind. More clearly, mind an extensive property may be described as “self programmable software” that controls the brain. The self programmable nature is a property imparted to the mind by the genopsych the original mind.
The perception that mutations of genes during replication of DNA are just errors is untenable for errors [even a series of them] can not produce a biological system as complex as human beings. In fact an error in DNA causes disease for example haemophilia.
Recent research proves13 that genomic processes have primacy over cell processes.
 

 
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  1. Aryanism: Arya Dharma
  2. Hindu in the Contemporary India
  3. Life, Consciousness and Evolution
  4. Bhil Nadu
  5. Engineering Education
  6. Unbound Intelligence – Review
  7. Laws of Biology
  8. Genopsych : collection
  9. Libet’s puzzle
  10. Survival strategies of living systems
  11. New Ideas
  12. घंटाघर
  13. चांदनी रात
  14. Colosseum
  15. ఇప్పుడు కాదండీ
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  17. ద్రోహి
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  24. సమయం
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  26. లోకం పోకడ
  27. శఫరి
  28. బానిసత్వం
  29. ఆలోచన
  30. గొంగళి
  31. సామి
  32. కాల భైరవం
  33. రాజకీయం
  34. స్వేఛ్చ కోసం
  35. గోగు పూలు
  36. పరిశోధన
  37. వైరం
  38. గాంధీ గారు
  39. Blind faith in old science
  40. వాస్తవం
  41. ఆనాటి శఫరి
  42. ప్రయాణం
  43. వైనం
  44. Conscious systems and the third law of biology
  45. గుగ్గిళ్ళు
  46. Sir JC Bose and the second law of biology
  47. Entropy and its dual nature
  48. Living Systems
  49. మాయం
  50. ఎడారి మయూరి
  51. మేఘ నిరసన
  52. రాగ రాగిణి
  53. వెబ్ లో తెలుగు సినిమా పాటలు
  54. పెద్దల మాట
  55. ఉలుకు పలుకు
  56. పునరాలోచన
  57. Reality of the Self
  58. నా కధ
  59. అనివార్యం
  60. ఒకనాటి కల
  61. మార్పు
  62. శేష దుష్ప్రభావం
  63. ఆటవికులు
  64. మట్టి దిండు
  65. వేకువ ఝామున
  66. శక్తి
  67. సమీక్ష
  68. లెక్కలు
  69. వెన్నెట్లో పూల పందిట్లో
  70. నిశ్చయమైన విషయం
  71. అధ్భుతమైన స్వప్నం
  72. నిన్నటి అందం
  73. Eddington’s Psycho-Syndrome
  74. అగ్ని ప్రక్షాళన
  75. వెర్రి వాడు
  76. వాన
  77. వర్షం
  78. తెల్లవారని తెలివి
  79. యశస్వి
  80. సునామీ
  81. యాక్ ఛి
  82. చింతన
  83. మర్దిన్చవే నా చెల్లీ
  84. హిందోళ
  85. స్వర్గం
  86. గుప్త చిత్రం
  87. దేవుడు లేని దగ్గర
  88. ఎడారి
  89. మహా మార్గం
  90. నేను, పర్వతం
  91. గోడు
  92. సన్న్ద్ది
  93. వెయ్యి దివ్వెలు
  94. అరణ్య రాజ్యం
  95. తీరని కోర్క
  96. భారతి
  97. వెన్నెట్లో దిగులు
  98. కాకి గోల
  99. విశ్వరూపం
  100. సింగూరు
  101. ఒప్పుకుంది
  102. ప్రియురాలి అందం
  103. శివరంజని
  104. కవితా వేదన
  105. దుమారం
  106. గావు కేకలు
  107. తాళం లేని ద్వారం
  108. అంతంలేని చోటు
  109. మృత సముద్రం
  110. కల్లుకుండ
  111. ఈత చెట్టు
  112. నేస్తాలు
  113. తను
  114. శఫరి
  115. The paradox of life
  116. Castes in the Court
  117. Genopsych
  118. The properties of living systems
  119. Plants and human health
  120. Evolution of Human Societies
  121. Sindollu
  122. Seetha Katha
  123. Venter builds Wald’s machine
  124. The primacy of DNA as a unit of life
  125. The drive and the direction of evolution
  126. Aryan, Arya and Ayyanar
  127. Capacitor like electronic structures of DNA
  128. Thorleif Wathne
  129. Random Birds
  130. Phosphates in agriculture
  131. Poturaju