[Bored chemist]

my assertion is that the start of everything is a thought,

That's theology or nonsense. The two can be hard to distinguish.
Neither belongs on a science page

[VinnyMS (OP)]

my assertion is that the start of everything is a thought,

That's theology or nonsense. The two can be hard to distinguish.
Neither belongs on a science page

on earth the most intelligent thing is the human brain. it started with bacteria which is brainless. my theory is that the bacteria was created by a brain, the universe as a brain. by forcing a result the universe creates life forms. the universe is the brain of a mother creature "mother nature" that keeps forcing the creation of intelligence, the creation of its children's brains the most intelligent creation. we're the result of the universes forcing us to exist. the universe depends on what intelligence it creates to succeed. every time a brain is created it wins and adds more intelligence to itself by populating space with brains or sorts of brains (aliens also) that can be infinitely intelligent

the brain is the most intelligent thing the universe can create, we're the result of the universes force

[Bored chemist]

the brain is the most intelligent thing the universe can create,

... so far.
It's entirely possible that we will create computers with greater intelligence.
(I'm not getting into a debate about how likely, when or even how do we define intelligence).
It's also possible that aliens have already done it- or they may have evolved to be brighter than us.
They might read your idea ad laugh.

[puppypower]

The brain would be a tough act to follow since the brain's components are way more advanced than existing technology. For example, a synapse is loosely analogous to the binary switches of semiconductors that computers used for memory. However, synapses are more complex than simple on-off binary switches. Synapses are variable switches that can fire at different potentials using what are called neurotransmitters. The neurotransmitters absorb into the membrane of the synapse and can make the switches easier or harder to fire. This is 100 times more advanced than simple on-off.

This allows the brain to store memory as superimposed layers, so we can use all the brain for specific tasks, while shutting off parts of memory, so we can focus easier on a specific task. If you are hungry, your mind comes to focus for food and the rest of the worries of the day are blocked out. This is assisted by the writing processes of the brain. If we shift the brain chemistry, then other layers become more conscious. The young male fixated on sex becomes linear, yet can he can become creative and resourceful, since the entire brain functionality is useable because the layer is everywhere. 

One thing that makes the brain the gold standard in connected to what we are trying to achieve, called intelligent computers. Computers are trying to mimic that creative side of the human brain. The brain has certain natural tricks that make this possible. Neurons pump and exchange sodium and potassium cations to develop a membrane potential. Neurons use about 90% of their energy adding energy to the membrane. Neuron firing at synapses releases this energy. The brain is adding energy to all the neuron membranes, and as a given point, it will spontaneously discharge; background brain waves that shows we are not brain dead.

The clever part of this design is connected to the sodium and potassium cations. The energy used by the brain, segregates these two ions, one on either side off the membrane, thereby lowering the entropy of these ions. Left to their own devices the ions would want to blend; 2nd law. But the brain constantly lowers ionic entropy, thereby creating an entropic potential at the membrane and at the synapses. There is a need to increase entropy; creative change. When neurons do fire, there is a potential for the ionic entropy to increase using sodium and potassium currents in motion throughout the brain. This is the basis for our creative and spontaneous nature. The paths of least resistance can trigger new ideas that build upon older memory.

This basic design principle could be used to develop intelligent computers. Picture computer memory where the semiconductors are designed, on purpose, to be unstable for long term storage, We try to simulate the high energy membrane and memory; metastable and subject to spontaneous change  This type of memory would be subject to change while in storage. Some semi-conductors switches would flip, and the energy output could start a natural cascade of energy and entropy. This would occur independent of the human conventions we use to define memory as a function of the binary on-off states. It will appear as noise.

The brain is different in that its stores memory, based on how energy and entropy naturally flow and cascade, The random change for a computer memory simulation above, becomes naturally directed in the brain; Eureka! Nature been building this system from scratch, over the eons. We try to do this with software and logic and stable switches, but nature does it with metastable memory, placed in physical states, which are naturally optimized by the laws of physics.

Getting back to a machine simulation using metastable memory, we could have a secondary hard rive that does not change. It job is to compared the changes in the metastable memory to the unchangeable memory and then tests the changes to find any useful change. Then we resets the metastable hard drive, for another cycle, and repeat the analysis.

[puppypower]

The key to life is water. One important observation that suggests this is the simple system of water and oil. If we mix water and oil, and then agitate, they will form an emulsion; lotion. If we stop the agitator, the emulsion is not stable but rather will reverse to reform two layers; water and oil

Life is composed of organic materials. Since these are all dissolved in water, the water-oil affect is in affect at various levels throughout all aspects of life. The result is the water-oil affect will force the organics to separate, merge and compartmentalize. In the earliest days before life, turbulence due to waves, for example, would agitate the water and primal organic soup, then water would take over and merge things.

The drive to separate an emulsion into water-oil is connected to the surface tension of the water, which water seeks to minimize. Water is the majority component in life and is the big dog in terms of surface tension. In life, if the surface tension is not minimized, locally, the organic-water surfaces become more active. The surface tension will also provide potential for evolutionary change; potential to try/add new things. The DNA itself is an organic surface in contact with water.

One may argue that other solvents could do the same thing. However, most other solvents that are theorized to support life, do not phase separate as thoroughly as water and oil. Ammonia, for example is a good emulsifier for oil and organics. The push to separate is much smaller,  leading to less potential to force organic merger compliance, so evolution can build upon a solid foundation in tension.

[puppypower]

What makes water so special is hydrogen bonding. Molecules such as water and DNA, are both held together by strong covalent bonds, between the atoms of the molecules. When similar molecules interact with each other, they will bind with weaker secondary bonding forces. DNA will form a double helix using one version of secondary bonding; hydrogen bonds.  After that, the secondary bonding forces, remaining, are not conducive for hundreds of DNA molecules to pile up in a stack. Each individual DNA molecule will tend to stay separate. This is due to the negative charges of the phosphate groups; different secondary bonding forces, on the surface of the DNA double helix. These repel each other.

Water is different in that its secondary bonding forces are all very strong and all based on just hydrogen bonding. Water can secondary bond  four neighbors, each of which can then bind to four neighbors, to form extended dynamic structuring in liquid water. This is energy favorable and very stable. When we add oil to water and agitate to form an emulsion, the extended structures of water are disrupted. Once we stop adding agitation energy, water will counter this and reform the extended grid, pushing the oil out. The oil will need to find other oil molecules to bind with its weaker Van der Walls forces. The secondary binding of water is the big dog, since hydrogen bonds are the strongest secondary bonds.

When water is around the DNA, water forms extended structure attached to the DNA that then further extends into the water. The water can bind to the negative surface charges on the DNA to help its out own energy needs. This water binding allows the DNA to be less self repulsive of other DNA in water.  In cell cycles, there is two DNA for a brief time, but at steady state each daughter cell will have one, since DNA stills wants to repel other DNA.  The phosphate is a strong acid so the hydrogen bonds of water to the phosphate are not permanent.

The reason the water can cause the DNA to put aside repulsion, long enough for cell cycles, is became the DNA does not disrupt the extended order in the water, the same way as oil. The DNA was designed by nature to assist water and thereby be under the water's radar. DNA is extremely hydrated, meaning it is surrounded by lots of hydrogen bonded water both within the double helix, on the surface and then outward, into the bulk water. The water can use DNA, in almost the same way as being near other water, in terms of lowering its potential. This minimal organic surface potential, relative to water, was a goal of evolution, from day one. You could not design a better molecule to be in harmony with the extended secondary structure needs of water. The DNA goal also turned out to be a very useful template molecule.

The DNA is transcribed or copied to form mRNA. The mRNA have similar hydrophilic properties as  the DNA, and are in therefore also under compliance to the needs water . RNA is actually even more compliant, to the needs of water, due to its more oxidized sugars and one of its bases being less reduced. The mRNA is used as templates to form proteins.

The translation of mRNA, into protein is performed at common ribosomal apparatus. The rRNA content of ribosomes add compliance and stabilize the ribosomes in water. The output protein, on the other hand, have different side groups, some of which are heavier on the oil side of the water-oil analogy. This causes the water, for its own local energy needs, to immediately pack protein in a way that allows the water to achieve it own minimize energy potential. This leads to the same proteins always packing same, always with perfect folding. Even with perfect water compliant folding, there is usually some residual surface tension and potential at the water-protein interface of enzymes. This is designed for catalytic actions.

[Bored chemist]

However, most other solvents that are theorized to support life, do not phase separate as thoroughly as water and oil. Ammonia, for example is a good emulsifier for oil and organics.

If they form an emulsion then the two phases are separate.

[puppypower]

However, most other solvents that are theorized to support life, do not phase separate as thoroughly as water and oil. Ammonia, for example is a good emulsifier for oil and organics.

If they form an emulsion then the two phases are separate.

This is true at the micro-scale, but not it is not true at the macro-scale, as is displayed by water-oil and two phase layers. The separation of the two phases all the way to the macro-scale, by water and oil, implies higher starting surface tension at the micro-scale of the emulsion. This higher tension and potential is useful for evolution, since there is free energy available for change. This potential will increase as we agitate in the direction of the emulsion.

Water is very stable. Water is one of the terminal products of combustion, if we were to burn any organic material found in any modern or ancient cell. Because of the chemical stability of water, the surface tension and potential at the phase boundary between water-organic cannot be easily reduced by chemically altering water, since water is so chemically stable. The burden of change is placed on the shoulders of the organics. The organics will need to makes changes to lower the potential; evolution.  Water is like an ancient bookend of life. The other organic bookend is still evolving towards the goal of no tension.

[puppypower]

Water chemically binds to the DNA using hydrogen bonding. The degree of hydration will determine the 3-D chemical structure or conformation of the DNA.

The organized hydration extends to several nanometers from the surface. The strength of these aqueous interactions is far greater than those for proteins due to their highly ionic character [542b]. The DNA double helix can take up several conformations (for example, right-handed A-DNA pitch 28.2 Å 11 bp, B-DNA pitch 34 Å 10 bp, C-DNA pitch 31Å 9.33 bp, D-DNA pitch 24.2 Å 8 bp and the left-handed Z-DNA pitch 43Å 12 bp) with differing hydration. The predominant natural DNA, B-DNA, has a wide and deep major groove and a narrow and deep minor groove and requires the greatest hydration.

Depending on how much water is chemically bound to the DNA will determine the layout of the DNA in 3-D space. The most common DNA conformation; layout, is (beta) B-DNA, which, not surprisingly, has the highest degree of hydration. This was a goal of evolution, as set by the water bookend from day one.

What scientists have shown is when DNA is hydrated to a lessor degree, different water-DNA hydrogen bonds have different energies, with some stronger and some weaker. On the other hand, as the hydration increases, all the hydrogen bonds have similar energies. This affect is connected to a special version of hydrogen bonding, called cooperative hydrogen bonds. Cooperative hydrogen bonding will created extended 3-D structures similar to polymers of hydrogen bonded molecules. What carbon does with covalent bonds, water does with hydrogen bonds.  The water structures are weaker and easier to reverse and reform.

When a hydrogen bond forms between two water molecules, the redistribution of electrons changes the ability for further hydrogen-bonding. ... Cooperative hydrogen-bonding increases the O-H bond length while causing a 20-fold greater reduction in the H····O and O····O distances

Cooperative hydrogen bonding by stretching the O-H covalent bonds of the water molecules and compressing the secondary bonding distances of the hydrogen bonds, H"""O and oxygen-oxygen interactions, O""""O, causes the normal line between hydrogen bonding and covalent bonding to become somewhat blurry. The electrons within the cooperative can delocalize and start to share among the cooperative. The cooperative becomes a type of resonance structure induced by hydrogen bonding. B-DNA and water, due to the high level of hydration forms a cooperative between water and DNA which immerses the DNA into a type of hydrogen bonding induced election resonance.

Since the cooperative is so ordered, it represents a state of lowered entropy. This is useful to enzymes on the DNA, since within the cooperative is the potential for an enzyme to increase entropy and lower free energy. Enzymes and ATP when they bind disrupt the cooperative allowing the entropy to increase. The enzymes cash in and use this free energy for their various tasks. The cooperative quickly reforms for another cycle.

The processing of the genetic information within DNA is facilitated by highly discriminatory and strong protein binding. It has been shown that the interfacial water molecules can serve as 'hydration fingerprints' of a given DNA sequence

The primary driving force for the specificity of protein binding is the entropy increase due to the release of bound water molecules (estimated at 3.6 kJ ˣ mol-1 for minor groove water and 2.3 kJ ˣ mol-1 for major groove water, both at 300 K [1096]), c with the DNA sequence determining the hydration pattern in the major and minor grooves (see above). Less perfect (that is, weaker) binding involves mainly secondary hydration water loss and so would allow sliding of the protein along the DNA [1176], facilitated by the remaining primary hydration water molecules [889]. For example, about 110 water molecules are released on the binding of the restriction endonuclease EcoRI to its site GAATTC, leaving an essentially dry interface and firmly bound complex with binding constant ≈ 10,000 times that for nonspecific binding.