Enthalpy/Entropy Associated With Transcription and Mitochondria
Biochemistry and Cryptanalysis for Psuchê
F. Bell, Jr.
(Greek kryptos for hidden, graphos for written) is the
study and practice of hiding written or spoken communication.
To hide the information to be communicated, a ciphertext must replace
the plaintext of the commonly understood lexicon used. The cipher
(code) is transferred from the sender to the receiver over platforms.
Cryptographic platforms range from paper(s) to computers and are called
use elliptic curves from algebraic structures. Auguste Kerckhoffs'
(1835-1903) principle, assumption, axiom or law stated that a cryptosystem
should be secure even if everything about the system, except the key
of course, is public knowledge. Claude Shannon (1916-2001) said
the enemy knows the system.
nonmilitary strategies should find the débouché and balance between
keeping the process simple and maintaining the security of the system.
As with all things, entropy or a state of energy loss effects cryptosystems
(in a closed system). Encrypted papers deteriorate and the information
is degraded. Computer systems cannot hold the imputed ciphertext
indefinitely. Geoffrey Chaucer (c. 1340/44-1400) stated in
The Frankeleins Tale of The Canterbury
"your trouthe kepe and save, Trouthe is the hyeste thing that man
may kepe." The scope of cryptanalysis must include the parameter
of entropy in appropriating ciphers in cryptosystems.
and Mitochondria of Human Biochemistry
is the study of the chemical compounds and processes occurring in living
organisms. Monomers and polymers are a structural basis of cellular
components of the four macromolecules of carbohydrates, lipids, proteins
and nucleic acids. Monomers are smaller molecules that form macromolecules.
Polymers are macromolecules created by the synthesized monomers where
the two molecules undergo dehydration synthesis.
have monomers called monosaccharides which include deoxyribose (C5,H10,O4),
glucose (C6,H12,O6), and fructose (C6,H12,O6). Water (H2,O) is
produced when two monosaccharides undergo hydration synthesis.
As we can see, carbohydrates contains carbon (C), hydrogen (H), and
oxygen (O) and functions as energy storage and structure.
usually composed of a molecule of glycerol and other molecules.
The main lipid or triglyceride has one molecule of glycerol and three
fatty acids. The saturated or unsaturated fatty acids are the
monomers. Lipids range from vegetable cooking oils to cheese and
butter. Lipids may have a polar characteristic that is not water
resistant as well as have a nonpolar characteristic that does not react
well with water.
large molecules and have monomers of 20 kinds of amino acids.
When amino acids combine they form a peptide bond and become a protein
or polypeptide. Proteins perform structure roles (e.g. skeletal)
as do carbohydrates. Proteins can be seen as chains of amino acids
with a carbon atom bound to four groups; an amino acids group (NH2),
a carboxylic acid group (COOH) which under physiologic conditions are
NH3+ and COO- respectively, a hydrogen atom (H), and (R) which is different
for each of the 20 amino acids.
are named for their prevalence in cellular nuclei. It is a heavy
molecular macromolecule composed of nucleotide chains that convey genetic
information. The most common nuclei acids are DNA and RNA.
Their monomers are nucleotides such as adenine, cytosine and guanine
which occur in DNA and RNA, and thymine which occurs only in DNA, and
uracil which occurs in RNA. Nucleic acids serve as genetic information
for all living cells and viruses and form the base molecule for adenosine
triphosphate which is the primary energy carrier molecule for all living
Both of the
DNA and RNA sequences use the same language. Transcription is
the synthesis of RNA language/information to another molecule under
the direction of DNA. A complementary nucleotide RNA strand is
produced when the DNA sequence is enzymatically copied by RNA polymerase.
The produced messenger (mRNA) carries a genetic message from the DNA
to the protein synthesizing machinery of the cell.
of DNA transcribed into the RNA molecule is a transcription unit.
The transcription unit that is translated into protein contains sequences
that direct and regulate protein synthesis and code the sequence translated
into protein. Prokaryotic transcription occurs in the cytoplasm
alongside translation. Eukaryotic transcription is largely localized
to the nucleus where it is separated from the cytoplasm by the nuclei
membrane. The translation occurs when the transcript is transported
into the cytoplasm. Rodger D. Kornberg won the 2006 Nobel Prize
in chemistry for his work concerning eukaryotic transcription.
has five stages. The first is "pre-initiation" where the RNA
polymerase binds to the DNA and with cofactors unwinds the DNA.
That creates an initiation bubble so the RNA polymerase has access to
the single stranded DNA template. Second, "initiation" starts
and the first phosphodiester bond is formed once the complex has been
opened. Third, "promoter clearance" is after the first bond
is synthesized and the RNA polymerase must clear the promoter which
has a tendency to release the RNA transcript and produce truncated transcripts.
Those abortive initiations cease occurring once the transcript reaches
around 23 nucleotides. Four, "elongation" occurs as one strand
of DNA (the non-coding template strand) is used as a template for DNA
synthesis. The RNA polymerase traverses the template strand and
with base pairing that complementary with the DNA template creates an
RNA copy. Lastly, "termination" is when the strategy to stop
transcription has been adopted.
(singular from Mitochondria; Greek mitos for thread and khondrion
for granule) is a membrane enclosed organelle found in many eukaryotic
cells. Mitochondria generate most of the cell's supply of
adenosine triphosphate used for energy. Mitochondria are also involved
is signaling, cell differentiation, the cell's cycle and function, and
content) is a description of the thermodynamic potential of a system.
That information can be used to determine the work obtainable from a
closed thermodynamic system under pressure and entropy. The International
System of Units is abbreviated SI from the French Le
d'Unités. SI is the modern
form of the metric system and the source of the measures below.
in joules) = E (energy of the system) + p (pressure in pascals) V (volume
in cubic meters)
In the absence
of an external field the following may apply.
H = U (internal
energy in joules) + pV
the state at which all things in a closed system move to a state of
less order since the times of Adam and Eve (Gen. 3:1-24). Moses
recorded after the flood that the maximum lifespan for mankind was 120
years (Gen. 6:3). Later, King David noted that humans live 70
to 80 years (Ps. 90:10). King Solomon wrote (Prov. 3:1-2, 10:27)
that the lifespan potential could be realized by complying with Natural
Laws of Freewill (NLF). It is evident that people that conform
to NLF, such as to not drink alcohol to excess, live healthier and longer
lives than people that violate NLF.
We know that
DNA and RNA are subject to entropy. Mitochondria DNA is associated
with diseases and may play a role in the ageing process. Mitochondrial
diseases have unique characteristics due to the way they are inherited
and their importance to cell function. Some viruses, such as HIV
which is the cause of AIDS, have the ability to reverse transcription
of RNA to DNA. The complementary DNA strand (cDNA) is integrated
into the host cell's genome via another enzyme causing the host cell
to generate viral proteins which reassemble into new viral particles.
As a result, the host cell undergoes programmed cell death.
human intervention can hasten DNA/RNA entropy. Recently, vaccines
for youngsters have been credited with needlessly triggering autism
and other mitochondrial disorders. Strains of pathogenic bacteria,
such as salmonella, may in time be becoming resistant or not susceptible
to antibiotics. (The lack of complete understanding of human
biochemistry and entropy was echoed by Rodger Kornberg to Dallas F.
Bell Jr. in an email exchange in July, 2008.)
of the behavioral entropy of DNA/RNA in humans and linguistics of cryptosystems
is apparent. Niels K. Jerne, the 1984 Nobel Prize laureate in
medicine and physiology, used Noam Chomsky's generative grammar components
for protein structures in the immune system.
that the antibody molecule is less like a word and more like a sentence
or phrase. The immune system is a lexicon of sentences which is
capable of responding to any sentence expressed by the magnitude of
antigens which the immune system may encounter. He emphasized
that the sentences representing antibodies possess partial mirror images
of an antigenic sentence. Those antibodies are not echoes of the
invading antigen, but were already available to the host in its repertoire
of B cells before the antigen arrived.
of humans is a collection of DNA/RNA programs and do not seem to have
freewill. Those molecules react to their environmental input and
potential. (The subject of monozygotic and dizygotic twins'
similarities and differences who were raised together and apart was
broached in the paper titled Behavioral Genetics:
Weltanschauungs of Natural Law, Crime and Identity.) The element
of human consciousness with the biochemistry exerts choice from freewill
on their biochemistry by their spirit or soul. It is thus concluded
that humans are autonomous moral (compliance
or noncompliance with NLF) agents.
It is not possible
to create a flawless behavioral power law of a biochemical and environmental
stimuli and an exactly predicted behavioral effect. Good people
(compliant with NLF) can return evil with forgiveness and bad people
(not compliant with NLF) can return good with evil. However, a
range of behavioral possibilities can be predicted using the enthalpy
energy models, such as when the government violates NLF and takes private
property. The victims of that violation of NLF could range from
civil disobedience to armed revolution. (The difficulty with
power laws of terrorism specifically was discussed by Dallas F. Bell
Jr. and both Neil Johnson of Oxford University and Michael Spagat of
the University of London during May and June, 2006.) It is
well documented that prolonged stress (S1, S2 and S3) releases hormones
for self-defense and leads to many biological problems if not resolved
out that in this realm energy and mass (matter) are the basic forms
of existence. Mass can become energy and energy can become mass
under favorable conditions. An empirical psuchê
(Greek for soul; Hebrew for nephesh) proof could be as follows.
--A soul is
equated to the known existence of consciousness.
is not mass or energy.
is not mass or energy, yet still exists by consciousness.
disproof would entail using mass and energy to create consciousness.
soul proofs would include the two anthropocentric groups of humans and
The Bible contains
revelation of the existence of the nonmaterial human soul and its eternal
destination in heaven for the saved (Rev. 20:4) and its eternal destination
in hell for the unsaved (Prov. 23:14). Jesus' statement on the
cross to the repentant sinner was that the sinner was to be with Jesus
in paradise that day (Luke 23:39-43). The Bible is singularly
used as the reference for human souls because it perfectly describes
the omniscient God of the first cause of all effects and passes the
perjurer's test (false in one false in all) concerning all epistemological
aspects. It must either be accepted or rejected. If it is
accepted the following is to be believed. The soul is created
by God and joined to the immediate biochemical result of conception
(Luke 1:41). The soul belongs to God (Exek. 18:3-4) and is immortal
(Matt. 10:28). The soul believes (Heb. 10:39), gets wisdom (Prov.
19:8), can love God (Deut. 6:5; Luke 10:27), sins (Mic. 6:7), and can
keep God's liberating law/word (Deut. 11:18, 26:16). The human
soul leaves the body in death (Gen. 35:18) and has memory of this biochemical
realm (Luke 16:19-31).
If saved (John
3:16) the soul is infused with God's Holy Spirit energy and can give
up the biochemical life to live or if not saved can loose the biochemical
life by trying to live (Matt. 16:24-26). The soul is temporally
limited to individual biochemistry, such as the number of healthy neurons
in the brain for IQ or affected by diseases like Alzheimer's.
There are examples of supernatural intervention by God beginning with
the creation itself (Gen. 1:1-27). It is recorded that the shadow
on the sundial turned backward (2 Kin. 20:11). Jesus turned the
water into wine (John 2:1-11) and raised Lazarus from the dead (John
was biochemical and since the soul is nonmaterial yet can love God,
the human biochemistry would mirror the aspects of the soul's characteristics
of intellect, emotion and freewill, and is how demons
communicate with witches (1 Sam. 28:7-25). The body is to be the temple
of the Holy Spirit for the saved but can be influenced by demons (Acts
5:1-9). Supernatural possession of the soul means the freewill
control of the body is yielded to the supernatural spirits of either
the demonic (Matt. 8:28-34, 9:32-33, 12:22-23, 15:22-28, 17:14-21; Mark
1:23-26, 16:9) or the Holy Spirit. The soul is eternally secure
if saved because greater is the Holy Spirit within a person than the
demonic in this world. The saved are not to quench the Holy Spirit's
control (Eph. 4:30; 1 Thes. 5:19) or loss of discernment and fruit will
The four categories
of nonhumans are natural nonliving things (e.g. rocks etc.), human made
nonliving things (e.g. computers etc. but does not include natural life
from artificial means), non animal living things (e.g. plant life etc.),
and animal life. The first three categories do not reflect the
potential for consciousness which is required for souls.
biblical arguments for animals having eternal souls based on passages
that all that have breath praise God (Ps. 150:6) and all living things
have souls (Job 12:10). Worms are said to be part of the eternal
torment of hell for the unsaved (Mark 9:43-48), but people with an unbiblical
agenda may interpret eternity to animals (Is. 34:11-17). Biblical
language includes methods of common discourse, such as (1 Sam 15:10-11
and 29) where God is said to have repented but a few verses later it
is noted that God is omniscient and is never surprised and need not
repent. Taken in context, the first verses described God's dissatisfaction
and that meaning is expanded on in the later verse.
The Bible addresses
man's relationship to animals in that man should care for animals
(Prov. 12:10) as man was given dominion over them by God at creation
(Gen. 1:27-30). If animals had eternal souls and thus freewill,
then animals could be expected to break God's laws such as to love
God with all one's heart, mind and soul (La) and love his neighbor
as himself (Lb). Then, like man, animals would need salvation.
Since man has dominion over animals and animals violate La and Lb by
killing the innocent, man would have the need to seek the conversion
of the animal's lost souls. There is no biblical reference of
that need nor were accommodations made for that circumstance.
Instead animals are said to perish at death (Ps. 49:12-15, 1 Cor. 15:31-33).
to animals is that He created them (Gen. 1, Ps. 104) and that they belong
to Him (Ps. 24:1). God cares for them (Ps. 147:9, Matt. 6:26,
1 John 4:16). Animals obeyed God by coming to the ark (Gen. 6:17-22),
frogs were sent against the Egyptian Pharaoh (Ex. 8:2-14), snakes were
used to judge the rebellious Israelis (Num. 21:5-9), lions did not eat
Daniel but ate his evil enemies (Dan. 6:16-24), killed the disobedient
(1 Kin. 13:24-26, 2 Kin. 17:25-26), the whale swallowed Jonah for three
days (Jon. 1:17, 2:1-10), and bears killed disrespectful children (2
Kin. 2:23-24). God used so-called lower animals of lice (Ex. 8:16-18),
flies (Ex.8:21-31), locusts (Deut. 28:38, 1 Kin. 8:37), worms (Deut.
28:39, Jon. 4:7, Acts 12:23), and caterpillars (1 Kin. 8:37).
On the other hand, God had to protect the Israelis from snakes and scorpions
(Deut. 8:15) meaning that not all animals always obey God.
obey God at times and do not obey God at other times, it indicates that
animals have freewill. Most people have witnessed animals exhibiting
emotion. Common examples of animal emotions are when cats and
dogs become sulky, jealous and angry when other cats and dogs receive
more attention. An ass was given an audible voice to speak to
Balaam (Num. 22:28-31) and showed anger as well as showed intellect
and freewill to save Balaam's life. Even an ox knows his human
owner (Is. 1:3). Seemingly, the fact that animals have freewill,
intellect and emotion could indicate the presence of a temporal soul
for God's communication purposes. Animals (i.e. hogs in Matt.
8:28-34) have been known to be possessed by demons.
It is possible
that some animals do only God's will and is the reason that they were
acceptable by God as a sacrifice for sin during the Old Covenant time
period, for example sheep. It could also be that sacrificial animals
were just a sign of the owner willingly giving the best offering in
public obedience and love for God.
do not have temporal souls, then they have uniqueness or uniformity
with the biochemistry of man regarding intellect, emotion and freewill.
Whatever the reality is, animals have no precedence for being given
governmental equivalence with the rights of mankind.
observes the enthalpy and entropy of the information of cryptosystems,
human biochemistry can be readily compared to those efforts. DNA/RNA
has a language that is deteriorating in all humans where the death rate
is 100%. That reality has proven the existence and character of
the God of the first cause of all effects described in the Bible.
math formula that artificially overrides rationality could falsely show
that God's existence is less than 100% of absolute and is a 99.999%
possibility. It could also be used to show that 2 + 2 = 4 is 99.999%
possible and not 100% since we have a finite understanding of infinite
math. No rational person chooses to not accept the sum of two
plus two as being four because of their recognized lack of having infinite
knowledge of math.
The human soul
is as real as the God who created it and is accountable to that God.
Proofs for this view abound in logic, empirical evidence and revelation.
It is then up to each individual to respond appropriately.
RIGHTS RESERVED © 2008 DALLAS F. BELL, JR.-----------------