Evolution Of Irreducible Complexity Explained

[Rade]

Good example of how constraint can be used to advantage by living systems:

 

==

 

http://www.physorg.com/news64046019.html

[HydrogenBond]

There is also another constraining factor. For example, the lipid bi-layer that comprises the background for the cell membrane, forms as it does, because of the impact of water. This shape just so happens to be the lowest energy shape in water. Once lipids began to appear, this lowest energy shape within water, came together, as if on cue. With water still able to permeate the bi-layer, this meant lingering potential in the water. One way to lower the water potential is to add proteins. Proteins can help to shield the water by binding with the internal hydrocarbons, while also lowering the potential of the water via their surfaces. As soon as we get proteins floating about, water already has a place to put them in an attempt to lower potential. Some do a very good job at this, such as the ion pumps, which were a premium to collect.

 

Enzyme shapes are also connected to lowest energy within water. Even before there were any such proteins, the basic shape was already in the works; hydrophilic out and hydrophobic in. This is not so much irreducible complexity, but irreducible simplicity. If we tweak an enzyme shape, so it does not form the lowest energy shape in water, we can store potential energy within the enzyme's structure. This can come in handy if we need our enzyme to have a little extra kick in water, when it needs it. One way for water to try to get rid of this extra potential, is to use something similar to what it did for the membrane. That is, try to add things to lower potential. The substrate adds, but the enzyme releases, after it renders it useless to reattach. The enzyme may win the battle, but the water is determine to win the war; keeps pushing.

 

The cell has a trick up its sleeve, but it will take energy. The cell could transport an enzyme into very hostile water, where the potential is even higher. The enzyme won't go there on its own, since the water will resist. But with energy, and a racket mechanism, the water has to acquiesce. Now what we have is an even higher potential to bind substrate. This can come in handy, when the cell learns to use the potential of water in its own favor. Now the cell can target aqueous potential to get diffuse focus for mutations.

[HydrogenBond]

If we compare DNA to RNA, there are a few differences. The net effect is DNA is more reduced than RNA. This means RNA has a lower potential in water than DNA. This is why the RNA has more flexibility with respect to shape shifting in water, such as a single or double helix. With the water potential to the DNA higher, the squeeze by the water defaults the DNA to the double helix, since any other shape will contain too much potential.

 

With respect to evolution, RNA was the first genetic material. The movement into DNA, meant that the genetic material became more reduced, increasing the potential between the water and the genetic material. The question becomes, why increase the potential between the water and the genetic material? Well for one thing, with everything else being equal, we have more water potential for everything. When we separate the DNA, the potential in the local water becomes higher than for RNA. This makes our template stronger. The water pushes harder in an attempt to lower the higher potential compared to template RNA. Maybe we get more accuracy.

 

The DNA is a huge molecule, with its huge bulk size, having considerable impact, on the water inside the nucleus. One way to lower this impact is to reduce the surface area that is in contact with the water. This is where packing proteins come in handy, lowering the surface area. If we unpack the DNA, just enough, we can increase the water potential to a specific level.To help lower this intermediate potential, we can add things to the DNA, such as enzymes. Some of these enzymes will separate the DNA double helix, thereby increasing the water potential locally. High potential zones means we need to bring in even lower potential enzymes to compensate.

 

If you compare making RNA to making DNA on DNA templates, making RNA will result in a lower water potential induction, than making DNA. Also, when we make RNA, the DNA stays packed at least in some areas. While when we make DNA, the entire DNA unpacks. Or highest potential DNA configurations makes the higher potential DNA, while lower potential or partially packed DNA configurations tends to make the lower potential RNA.

[HydrogenBond]

Another simple water effect, which helps the cell in a global way is connection to the cationic exchange at the membrane. The cell will accumulate K+ ions and will exchange and pump out Na+ ions, setting a membrane potential. The K+ are chaotropic meaning that they increase disorder in water relative to pure water. The disorder will increase the potential within water since water would like to hydrogen bond into order. The accumulation of K+, cranks up the water potential, globally, so everything above is amplified.

 

The outside of the cell membrane contains extra Na+ due to the ion exchange. There is also extra Na+ at the outside membrane surface due to the concentration gradient with the inside (there is less Na+ inside than in the bulk outside). The Na+ is kosmotropic, which means it increases the order in water relative to pure water. This order lowers water potential. Relative to organic food molecules outside the cell, in pure water they will create a given water potential. Since the Na+ lowers the water potential near the outside of the cell, the organics will migrate to the cell where their concentration can increase based on the potential formula; organic+pure water =organics + water + Na+. The higher Na+ is able to balance out a higher organic concentration allowing the cell to attract food.

 

The transport of material into the cell uses the energy within the membrane potential associated with the cationic gradient. Picture organics concentrating near the Na+. When the ion pumps reverse and K+ leaks out and Na+ leaks in, the local water potential changes. The K+ makes it too high, while the Na+ lowers the water potential inside, locally. The food follows the direction of lower potential and moves inward.

 

Although the K+ accumulates within the cell, the K+ concentration tends to be higher right at the cell membrane. The reason for this is the concentration gradient to the outside of the cell becomes higher than in the direction of inside. There is much less K+ directly outside, since it is mostly Na+, so extra K+ will tend to stay near the membrane trying to get out. What this simply trick does is create an internal gradient of K+ ions, which create a water potential gradient to the DNA, where the K+ is slightly higher at the membrane and slightly less at the DNA. What is useful about this gradient is it can help position material based on equilibrium. In the cell, many things know where to go because the water potential gradient tells them where their equilibrium sweet spot is. The modern cell then uses ATP energy to transport some material into non-equilibrium zones, to crank up the potential.

 

During cell cycles, the membrane will unsaturate allowing K+ to leak out easier, causing Na+ to leak in. This not only lowers the global water potential inside the cell, since the K+/Na+ ratio changes inside, but this also changes the gradient between the cell membrane and the DNA. This lower the global water tug on the DNA. Now the DNA is more free to duplicate, since the water potential rise needed to make DNA have been compensated by the increase in kosmotropic Na+. While the gradient change makes provisions for moving materials.