Genomic Consciousness
sekhar dmr
Wednesday, 05 August 2009 16:47 UTC
Abstract.
Consciousness is generally understood as an activity related to the brain. If we consider brain as hard ware, mind is the soft ware that runs the brain where the psychological programmes are located. The placebo effect indicates the self programmability of the mind. Frederic Peters describes consciousness as, 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. The consciousness Peters referring is the consciousness related to the brain.
We know that the brain and body are developed from a single cell embryo. All the information / programmes required to develop the brain are in the genome [of the embryo] and genome expectedly interprets the information and executes the programmes that result into the development of the body and the brain. For example gene complexes bi thorax, BX-C and antennapedia, ANT-C are reported to play a central role in programming the development of organism. Further biological rhythms in an organism are due to gene clocks 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. Thus it is from gene clocks the organism senses the time [Now-ness] and its own location [Here-ness]. If brain has consciousness, genome must also have a precursor form of consciousness with genomic i-ness which is the spring head of the I-ness.
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 molecules have 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%. Volkenshtein notes The replacement of the pair A-T by G-C is evidently thermodynamically favorable since G is bound to C more strongly than A to T. If it were for thermodynamics alone, the relative G-C content in DNA should have increased during the evolution. Let us look 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 GC content in some putative isochors as low as 30%. 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. As having more AT pairs in the genome is thermodynamically unfavorable there must be conscious effort to maintain that state. Thus genome is consciously self programmed and the genomic consciousness is the spring head.
http://en.wikiversity.org/wiki/User_talk:DMR_Sekhar
Updated 05 August 2009 16:54 UTC
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Welcome Dr. Sekhar,
Thanks for the article.
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Dr Sekhar,
Many months ago when you first shared these ideas with me, I was intrigued by the un-favored ratio of GC to AT pairs in the genome structure. That which is required to maintain and grow the un-favored condition, along with self repair and replication is attributed to consciousness at the genome level. This idea is further supported as you point out, because the genome contains all the instructions necessary to produce a fully conscious living organism (such as a human being.)
In my own work, many of the processes exhibiting negative entropy and exponential energy throughput in living and non-living systems are attributed to principles of natural law. An example is the coupled pair reactions at the molecular level that enable a thermodynamically un-favored reaction by coupling it with one that is favored. These molecular arrangements ultimately lead to the complex molecules needed to build DNA molecules with properties of repair and replication, along with the capacity to promote an un-favored ratio of GC to AT pairs.
Dr Sekhar suggests a fascinating and rather compelling idea that these processes, specifically at the level of the fully developed genome, involve a conscious effort. I find this idea as intriguing today as I did many months ago. I am looking forward to reading and hearing more on the subject from Dr Sekhar in the near future.
John Patrick
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The quality of genomic i-ness (whatever that actually is) seems to be present in all living things. But how do we define this seemingly “conscious” and directional behavior at a genomic level? It certainly seems to be based on a recognition system.
And in the case of humans – how do the conscious ‘mental’ thoughts impact on genomic behavior? E.g. placebo/nocebo effects.
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Tina Ryan,
You wrote,
[1. The quality of genomic i-ness (whatever that actually is) seems to be present in all living things. But how do we define this seemingly “conscious” and directional behavior at a genomic level? It certainly seems to be based on a recognition system.Yes. I argue that genome has the capacity of self recognition a condition to its ability to self program.
[2. conscious ‘mental’ thoughts impact on genomic behavior?
Evolution is a genomic process and natural selection is not influenced by mental thoughts but genomic processes will influence mental thoughts. How ever scientists working in the area of epi genetics do believe that experiences [say mental thoughts] of an organism may influence the genomic processes. Epi genetics is a controversial area.
[3. I think that placebo effect is due to the self programming capacity of the Brain which is an extension of [or which evolved from] the self programming capacity of the genome.
Sekhar.
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Dear John,
What you are saying about coupled reactions may be true. But can we define life forms by a set of chemical reactions is the question.
May just see the following references.
1. Volkenshtein, MV, in his book 1 “Biophysics” writes, “The replacement of the pair A-T by G-C is evidently thermodynamically favorable since G is bound to C more strongly than A to T. If it were for thermodynamics alone, the relative G-C content in DNA should have increased during the evolution”. If it is not thermodynamics alone then what it is?
2. Stephen Hawking, in his book “A Brief History of Time” said 2 ,” 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”. This is a most honest statement.
3. Second law of thermodynamics from the stand point of molecular statistics is different from its classical version which says that “all states have equal probability” that implies “an ordered state may be the out come of a disordered system by some probability”. This is stated as 3 the self compression of a gas is not absolutely impossible
[1. Volkenshtein, M.V., 1983, Bio physics, MIR Publishers, Moscow,
[2. Stephen Hawking, 1987, A Brief History of Time, Bantam Books, Toronto.
[3. Yeremin, E.N., 1983, Fundamentals of Chemical Thermodynamics, MIR Publishers, Moscow.The above plus the primary instincts and the properties of DNA molecules lead me to think differently, that is life forms are self programming. Now can any system program itself and update its programs without being conscious [aware ] of its own self? This necessitated me to the idea of genomic consciousness.
Thanks,
Sekhar. -
Sekhar,
You have posed the right question; “Now can any system program itself and update its programs without being conscious [aware] of its own self?”
Another question is; “Now can any system evolve from a state of unconsciousness to a state of consciousness, in accordance with ‘principles’ of physical natural law which can be defined?” These are the ‘principles’ that I am attempting to discover.
On the question of a “superior brain” there are three that I am certain of; which are my wife and my teenage son & daughter who out-smart me every time!
John
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John,
You wrote:
Another question is; Now can any system evolve from a state of unconsciousness to a state of consciousness, in accordance with principles of physical natural law which can be defined?I suggest reading: The origin of life, Molecules to living cells, W.H. Freeman and Company, San Francisco, 1980. And about self compressive gas from reference [3. in my previous reply.
As of now the first appearance of RNA/DNA molecules can be explained as a probability out of a set of reactions [coupled reactions? As you say] to the best of my knowledge. However recently some experimental work on self programmable matter is published by Sowerby, SJ et al which may give a clue.
I wish to pay a visit to your super brains at some point of time in future.
Thanks,
Sekhar. -
Sekhar,
Of course we hope you will be our guests when you come to the U.S.
John
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John,
Thanks. But it can happen in India too.
Sekhar. -
This is a provocative suggestion. Based on my limited knowledge, I can only disagree with you. Genome, the total DNA that constitute the entire chromosome set of an organism has no ability to perform any of the activities necessary to sustain life. Thus the DNA is packaged as chromosomes in highly coiled and condensed structures. These function of these structures are totally controlled by proteins that are associated with chromosomes.
“DNA molecules show three extraordinary properties [a] they repair themselves”
No, DNA has no self-repairing mechanism. Generally, misincorporation of bases heppen during replication, and an exonuclease is immediately employed to excise the wrong base. Other types of damages are repaired by different enzymes such as hOGG1.
“[b] they produce their own replicates”
This is also wrong. DNA cannot replicate itself, for this there are specific DNA polymerases and an elaborate reglatory mechanism to maintain fidelity. Helicases, RNA primases, DNA polymerases, Exonucleases, DNA ligases, Nuleases, and telomerases are some of the key component of the replication mechinary.
“[c ] some times during replication they produce variant types.”However, because of the proofreading mechanism during the replication process, these variations are very limited (10^-8 to 10^-10), however, these give rise to single nucleotide polymorphisms, and also gene mutations. Some areas of the DNA sequence are prone to more mutations than other regions. Another major source of genetic variability is the recombination.
“The two properties, self repairing and replication of DNA are analogous to the primary instincts self preservation and procreation.”
So, from the above facts it is clear that DNA lack these two qualities, eventhough it contains all the information for these qualities.
Rest of the facts about DNA GC content is debatable. Generally, prokaryotes has more AT in their genome than the eukaryotes. And in eukaryotes, some genes or even entire regions are specifically high GC rich. This is probably a regulatory mechanism, to control gene expression. How important is the GC content for the chromosome stability is not clearly known. In chromosomes, DNA is heavily packed by histones and non-histone proteins, that in fact stabilizes the DNA structure. It would be safe to assume that the AT rich prokaryotic DNA is probably the most favoured one because prokaryotes require fast DNA replication as well as transcription. If the genome is high in GC, it would require more effort and extra machinary to act fast. In eukaryotes the situation is different and a major part of DNA evolved into stable GC rich regions. However, these facts does not indicate in any way that the genome is capable of self-programming. So, the arguement that the genome has consiousness is a weaker one.
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