Cells and entropy

[Billy T]

... It's fundamental to math and science, including thermo. ...

That is a good point. Perhaps even stronger than you know. I am almost certain ALL of thermodynamics follows from the Ergodic theorem, probability (statistics of random processes) and possibly conservation of energy (but that is assumed in the ergodic theorem)

 

[Billy T]

... I am looking beyond the DNA so it does not look as random to me. ...

Yes, as I noted earlier, you need to tear down "random" before there can be "intelligent design."

Be more honest - don't throw out a lot of nonsense that you don't even understand as there is no sense in it such as: brains being in love "optimize the release of free energy and lowers their combined entropy." etc.

I.e. just honestly say you believe in ID or one of the religions.

 

[wellwisher]

Let me prove that changes on the DNA are not exactly under random. If we took a six sided dice and threw it, each side has equal probability, such that over time each side will appear in the same proportions. If changes on the DNA were completely random, each base pair and/or each gene would have the same odds to mutate. Therefore, if it was random no aspects of the DNA, would be more likely to mutate, than a six sided dice will prefer only certain sides.

Correct me if I am wrong. Don't certain aspects of the DNA mutate faster than other aspects. While certain aspects are more conservative. This is not random relative to the entire DNA. If the DNA were dice, the DNA dice would be loaded. I told you what the weight is that is loading the DNA; free energy.

I suppose we can narrow our point of observation and treat the narrow set of genes that do mutate, more often, as doing so in a random way. This will allow us to use the black box so we don't have to think why is the entire DNA is not in the scope of this assumption. The dice are loaded but the politics needs to deny this.

.The misunderstanding that constantly follows me is just because I think in terms of free energy does not mean i don't believe in evolution. I just don't fully except everything in the current explanation for evolution because certain things violate free energy such as the random DNA.

What tends to happen is if you don't fully believe the dogma of evolution, lock, stock and barrel, you are automatically lumped into creationisms. This is a political trick or smoke screen to banish one if they point out flaws in the dogma. This is how you discredit truth to protect dogma.

The DNA does not mutate uniformly, so it cannot be completely random. Some areas of the DNA changes much faster than others. The dice is loaded. Evolution, as is, has been playing with loaded dice calling it a fair game. I don't think it is cheating, but more like they just haven't been smart enough to recognize the dice were loaded, in a world considered random to them.

I have no problem with Darwin, since he points to a consistent outcome called natural selection. He didn't know how to explain this consistency in terms of laws of science, but left it nebulous but intuitive.

 

[billvon]

You need to extend the concept of efficiency to more than just biochemistry. The tail of the peacock has an impact on the female at the level of the brain; appeal. The brain is at the top of the hierarchy in terms of the animals overall control system. Optimization changes in the brain can lead to overall system efficiencies.

And can lead to extinction when the environment changes. Which from an evolutionary standpoint is the opposite of efficiency. Again, evolution does not give a shit about overall system efficiency. It only cares about reproduction.

The idea of those traits preserved and amplified does not explain where the energy and entropy comes from to do this?

Nope. Energy comes from sunlight, which is used directly by plants and indirectly by animals. The only exceptions are a very few extremophiles that can use temperature differentials and dissolved minerals to generate energy.

It relies on a nebulous version of energy in the ethereal world of chaos. I am trying to get past that subjective veil.

Word salad.

There are parts of the DNA that are conserved and parts that are more subject to change during DNA duplication. This, by itself is not implicit of random.

Correct. DNA replication is not random. MUTATION is random. Most of those mutations destroy the cell or render it incapable of reproducing. Thus the only DNA changes that are conserved are the very rare ones that allow the cell to survive.

There is no need to change that which is already optimized.

Mutation doesn't care. It changes DNA anyway. If the new organism is less optimized it dies.

How the DNA know which is which so it can restrict some genes more than others?

It doesn't. We just see the results of the "good" changes more than the results of the "bad" changes.

It has to do with free energy and that which is more or less favorable for entropy.

DNA could care less about free energy.

 

[billvon]

Let me prove that changes on the DNA are not exactly under random. If we took a six sided dice and threw it, each side has equal probability, such that over time each side will appear in the same proportions. If changes on the DNA were completely random, each base pair and/or each gene would have the same odds to mutate. Therefore, if it was random no aspects of the DNA, would be more likely to mutate, than a six sided dice will prefer only certain sides. Correct me if I am wrong.

You are wrong. The changes are random but the changes we OBSERVE are definitely not - because they have been filtered. The more deadly changes have already been removed.

Let's take your example. I give you 500 boxes, each carefully handled so as to not disturb the contents. In each box is a dice that has been rolled. You open them all and see approximately 100 dice that have rolled to 1. Approximately 100 have rolled to 2, 100 to 3, 100 to 4, and 100 to 5. None have rolled to 6. You might then conclude "these dice are not random! They never roll a 6."

Then I reveal that I have removed all the boxes that rolled a 6 before giving them to you, and that there were about 100 of them. Would you change your mind?

 

[Billy T]

... If changes on the DNA were completely random, each base pair and/or each gene would have the same odds to mutate. ... Correct me if I am wrong.

No one is claiming random means all parts of the DNA suffer equal probability of being changed.

... Don't certain aspects of the DNA mutate faster than other aspects. While certain aspects are more conservative. This is not random relative to the entire DNA.

true.

... If the DNA were dice, the DNA dice would be loaded. I told you what the weight is that is loading the DNA; free energy.

No "free energy" which you need to define in this context, would not be important compared to the local structure. Loaded dice tend to favor some result over others - random DNA changes is not doing that. It is more about what part of the DNA is changed not what will be the favored result.

... The misunderstanding that constantly follows me is just because I think in terms of free energy

OK -define what you are speaking of by "free energy" (Or is it some buzz words you read in a thermo book where perhaps constant temperature or pressure were required for the definition?). You speak of free energy changes in the brain when one falls in love, etc. - let see you tell how many ergs that is or how measured or even how to know if it goes up or down (without circular reasoning to fit it into your ideas).

 

[Aqueous Id]

The DNA does not mutate uniformly, so it cannot be completely random. Some areas of the DNA changes much faster than others. The dice is loaded.

The uniform distribution is but one of a veritable plethora of random distributions. Besides, why not expect a normal distribution, since that would be, after all, normal.

What tends to happen is if you don't fully believe the dogma of evolution, lock, stock and barrel, you are automatically lumped into creationisms. This is a political trick or smoke screen to banish one if they point out flaws in the dogma. This is how you discredit truth to protect dogma.

Since creationism typically denies all kinds of facts, evidence and human discovery, its anti-evolutionary stance, including some of the points you rely on, are generally regarded as false dogma by both religious and scientific communities. You may feel tricked or banished or sense smoke, but until you come to grips with what science is teaching, which renders your premises invalid, you will probably never understand how or why you (and similarly situated folks) are regarded as political tricksters blowing smoke.

I could help you understand if you are interested, but I also understand you may not be receptive to my help.

I have no problem with Darwin, since he points to a consistent outcome called natural selection. He didn't know how to explain this consistency in terms of laws of science, but left it nebulous but intuitive.

If by "law" you mean "entropy", then Darwin is correct in ignoring it, since it only applies to closed systems. I can help you understand your error in stating this if you wish.

 

[wellwisher]

If you look at other candidate solvents for life, such as alcohol, if we burned them in O2, water will be one of the final products of this combustion along with CO2. What that means is the potential between energy rich cellular components and water is higher than any other solvent. Water gives the best bang for the buck.

If we used an alcohol for life, the alcohol would be the lowest energy state we could create in that cell. If we exceeded that alcohol state, we would start to burn the cell's solvent as fuel. With water, we can burn an alcohol or any other solvent, all the way down to CO2 and water and gain far more energy. Water is a very stable bottom state in terms of the cell's energy economy; cell can't burn it.

There is another consideration with water and the organics of life, which can be understood with a simple example. If we mix water and oil, and shake these, they will separate out into two layers with oil on top. This will lower the free energy of the water-oil system; lowers the surface tension. Life is composed of organics. The presence of water will result in a slight push of the organics away from the water, toward other organics, due to various amounts of surface tension This constant push helps combine organic things in water. Organic solvents would do the opposite and have a pull that will slightly separate organics more into solution.

For example, If we put phospholipids in water, the water pushes this into a bi-layer membrane, fully assembled and ready to go for step two. This is like oil and water separating out but with charged oil via phosphate. If there were other organic things in the water, the water will push them into the membrane. Now we are ready for step three. Organic solvents are not quite as strict as water so step two and three would form much slower.

Water is held together with hydrogen bonding. This is also the most important secondary bonding force in life. The DNA double helix uses hydrogen bonding. The organics defining DNA, as they evolved, had to conform to the free energy constraints within water. The inclusion of hydrogen bonding in the DNA, is sort of like the old saying, if you can't beat them (water) join them.

Water is tough and strict and not to be taken lightly by the organics. It can also self ionize and use that to make sure the organics conform via chemical changes. A different solvent would push the genetic material to evolve a different bonding strategy to define lower free energy in that solvent. This minimal energy strategy may not be as good as hydrogen bonds, since these are the strongest secondary bonds used by life. The genetic material could have a harder time be a consistent template with weaker organic template bindings.

Besides also that, water is the second most abundant molecule in the universe, only behind H2, with is number one. The energy difference between H2 and H20 just so happens to define the limits of all the energy states of life. It was meant to be.

 

[wellwisher]

Here is one possible scenario. Since the person can drink water in the form of fruit juices, but can't use plain water, this suggests the skin, like the fruit juice water, is slightly acidic, since fruit juice tend to have an acidic pH.

Tap water is neutral to slightly alkaline due to water hardness (minerals in water). Maybe the difference in pH, between acid skin and neutral water, when the two neutralize, will cause a slight energy output. The skin;s nerve endings may be sensitive to this pH input (like warm or cold) causing an amplified sensory and feedback reaction in the brain.

One way to test this theory and gather data is to put fruit juice on the skin to see the reaction. Next, dilute the juice with water, in several stages, to slowly raise the pH, until they start to feel something. This will give a sensory pH threshold. Then they can adjust bathing water pH to be able to use water.

 

[origin]

Here is one possible scenario. Since the person can drink water in the form of fruit juices, but can't use plain water, this suggests the skin, like the fruit juice water, is slightly acidic, since fruit juice tend to have an acidic pH.

Tap water is neutral to slightly alkaline due to water hardness (minerals in water). Maybe the difference in pH, between acid skin and neutral water, when the two neutralize, will cause a slight energy output. The skin;s nerve endings may be sensitive to this pH input (like warm or cold) causing an amplified sensory and feedback reaction in the brain.

One way to test this theory and gather data is to put fruit juice on the skin to see the reaction. Next, dilute the juice with water, in several stages, to slowly raise the pH, until they start to feel something. This will give a sensory pH threshold. Then they can adjust bathing water pH to be able to use water.

You do realize that in this entire post you did not use the term entropy. You might want to go back and amend the post.

 

[wellwisher]

Entropy would be behind the generic change that made this sensory feedback connection. It is also behind differences in pH. Acids have extra H+, which are very mobile in water. These H+ is a source of higher entropy in acids. If we neutralize the acid, the entropy of H+ falls, releasing energy.

 

[origin]

Entropy would be behind the generic change that made this sensory feedback connection. It is also behind differences in pH. Acids have extra H+, which are very mobile in water. These H+ is a source of higher entropy in acids. If we neutralize the acid, the entropy of H+ falls, releasing energy.

Whew... My equilibrium has been restored, as well as my faith in the pseudo-scientific method.

 

[wellwisher]

There is a phenomena called cooperative hydrogen bonding, which not only occurs within water, but also within bio-materials and within composites of water and bio-materials. What cooperative hydrogen bonding essentially is, is the team is stronger than the sum of its parts.

For example, say we had ten hydrogen bonds in a cooperative, the cooperative acts like a team which makes all the hydrogen bonds stronger. The way this teams acts is the cooperative will shift resources to make sure there is no breech in the cooperative. This makes normally weaker hydrogen bonds (individuals) have the strength of the team.

This team strength is typically true, only for breaking the first hydrogen bond somewhere along the cooperative. Once the first hydrogen bond is broken, the cooperative breaks up and the superman bonds of the team go back to normal individual Clark Kent bonds.

I suppose the transition into cooperatives, because of their stability, means there is energy given off during formation. It is almost the hydrogen bonding version of resonance. It takes a strong force to break the cooperative, such as an enzyme. The breaking of the corporative can result in a large increase in molecular entropy. It might be possible for sensory system to pick up one or both of these effects and then feedback an overreaction.

The DNA double helix forms cooperative hydrogen bonds. The unzipping enzymes are used to break that first team bond, then unzipping is easy as the individuals leave the team, up to the stop codon cooperative.

 

[wellwisher]

Cancer represents a state of heightened entropy compared to normal cells. Cancer cells have more degrees of random freedom compared to normal differentiated cells. Cancer treatments, which try to disrupt cancer, do so by a further increasing cancer entropy; dissociation all the way to death. However, this often causes an entropy increase in normal cells leading to mutations and birth defects in future generations.

There is another approach, which addresses cancer treatment in the opposite way. Since cancer cells define higher entropy than normal cells, theoretically, if we took a "lower the entropy of cancer approach", this would theoretically change active cancer into an inert state, while doing little or no harm to healthy cells.

In radiation treatment, the radiation impacts the DNA of both cancer and healthy cells. The healthy cells can repair the damage better, since they exists at lower entropy; try to move back to equilibrium order. The cancer, being at higher entropy, favors disorder and can't shift equilibrium in the needed direction.

Both affects is done via configurational equilibria, where the organic configurations within the cell or cancer define a state of dynamic equilibrium. The idea would be to alter this equilibrium in cancer in the direction of normal cells. Cancer which disappears on its own, tends to go backwards into the order of the body.

Here is how I look at this. The human body is a complex organic machine which loses efficiency when we get cancer. The loss of efficiency means more energy is lost into entropy, such as cancer. The growing cancer gains entropy as the body lowers efficiency making more wasted energy available for the cancer entropy. We need to shift the balance back the other way into less entropy.

 

[wellwisher]

Complexity is often associated with entropy. Entropy, in turn, is also associated with inefficiencies, when it comes to work cycles. Irreduceable complexity is the minimal complexity associated with maximum efficiency; minimal entropy due to efficiency=less complexity.

In other words, if efficiency is high, entropy will be low since most of the energy goes into work and not entropy. Based on this low entropy, there will still be entropy= complexity, but the minimal amount of entropy=complexity needed to balance the level of efficiency.

This push toward efficiency, which is part of evolution, can not be random, since random would to maximize entropy and complexity and try to lower efficiencies. The current model of evolution is only half baked since it does not take into account the efficiencies that are globally evolving in all aspects of life; lowers complexity=entropy (lean mean cell machine)

The push toward lowered entropy=higher efficiency to produce irreduceabe complexity (minimal complexity), is lumped into natural selection. This is useful but does explain the chemical mechanism and how this impacts even the DNA. The result of this deficit are subjective false positives when it comes to the existing theory.

 

[origin]

The push toward lowered entropy=higher efficiency to produce irreduceabe complexity (minimal complexity), is lumped into natural selection.

Only in your mind. Natural selection could care less about entropy since the earth has an absurdly large excess of energy in the form of sunlight.

Animals evloved to eat grass which has hardly any nutritional value - very inefficient - so they have to eat huge amounts. It may be ineffient but since there is so much grass due to the outside energy from the sun why not utilize it?

This is useful but does explain the chemical mechanism and how this impacts even the DNA.

Entropy does not explain "the chemical mechanism and how this impacts even the DNA" because it has essentially irrelevent to the process.

The result of this deficit are subjective false positives when it comes to the existing theory.

There is no problem, other than your complete confusion on what entropy is and why it could have any affect on life in an open system like earth.

 

[Rhaedas]

That which evolves and survives isn't always the most efficient. It just is the one that reproduces and passes on those genes. There's plenty of examples of inefficiencies in life forms...it's another reason not to believe in the idea of a great designer. Unless it was design by committee.

 

[wellwisher]

Complexity has a connection to entropy with increasing entropy equating to increasing complexity. Entropy also has a connection to work cycles, with entropy associated with inefficiencies and the irretrievable energy that is lost. Entropy needs energy to increase. In work cycles, energy is partially converted to work and therefore not available for entropy. Entropy will only get the wasted heat energy due to ineffiency. As cellular efficiency increases, entropy falls and therefore complexity decreases relative to states of lower efficiency. It is simple math.

If we add this together, as life increases efficiency and therefore entropy lowers, (more energy into work and less into entropy), entropy=complexity lowers into irreducible complexity. It can still be complex but not as wasteful complexity, like if the system was more inefficient.

For example, the US government is very complex with a lot of redundancy. If we increased its efficiency we would lower complexity by removing the redundancy. This is lowering the entropy by placing more and more manpower energy into work efficiencies. This lowering of structural entropy into irreducible complexity is an aspect of evolution. There is a logical reason of this.

Cells are very efficient. If we drew a curve of cellular efficiency as a function of evolutionary time scale we would see a trend moving toward higher efficiency and less wasted energy left over for high entropy=complexity. Even the DNA reflects this with the evolution of proof-reading enzymes to make sure there is lowered DNA entropy to reflect the higher cellular efficiencies.

The current model of evolution lumps this into natural selection without any chemical mechanism that can show how this relates to the DNA.

 

[origin]

That which evolves and survives isn't always the most efficient. It just is the one that reproduces and passes on those genes.

Ding Ding Ding, correct answer.

You can learn this wellwisher, I know you can, it is not that difficult....

 

[wellwisher]

There is no problem, other than your complete confusion on what entropy is and why it could have any affect on life in an open system like earth.

If you could not control the entropy, within aspects of an open system, you could never make machines more efficient. An open system, in your opinion, would make it impossible to control the local entropy. This is done all the time. The MPG of cars has gotten better in this open earth system with waste energy=entropy going down. An engineer does this for a living. A biologists assumes random everything therefore throwing dice to engineer a car to be more efficient might appear impossible. That is not how it is done. There is a logic to it.

The cell is very efficient. If we assume 85% efficient, then only 15% of its energy goes into entropy. The other 85% percent goes into work. Cells were not always this efficient. If we assume starting without full cells the efficiency started close to zero.To gain cellular efficiency from 5% to 85%, cell entropy had to fall in the open system earth. It is not magic but simple math.

With car efficiency, to get better MPG, we need a logic path. You can't just throw the dice hoping this will happen randomly. To do this for thousands of enzymes in billions of cells you need a plan. Like Origin said, the open system wants to go the other way so random will not work. Life has a plan.