Cells and entropy

A better theory of evolution should be able to interface abiogenesis, with biological evolution and with the evolution of human consciousness, since this range is all about life. If a theory can only do one of the three, how do you know that theory reflects reality?

Here is an analogy. We will break the growth of a tree down into three stages of its life. We will then treat each stage as though it is independent of the other two stages and call that the best theory possible. I see that approach as flawed or at least over simplified.

Maybe those who like evolution, as is, can explain the logical assumptions behind dissociating that theory from the two bookends of life, that came before and after the evolutionary theory.

 

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A better theory for evolution would use the concept of entropy, as a central premise, instead of the premise of random changes. Entropy is very similar to random in many ways, but with the constraint that the randomness of entropy can be induced into an ordered path. Let me give an example of this effect within nature, then I will show how the cell establishes a parallel set of conditions.

If we expand a gas, the entropy will increase as the gas molecules gain additional degrees of freedom. Under the expansion, the gas will cool as the increasing entropy absorbs energy (energy conservation).

Say I had a large room of moist air. In the center, I will place a condenser which will take the water out of the air and turn it into a liquid. Going from vapor to liquid will lower the entropy of the water. Since the water vapor exerts a partial pressure within the air, the water condensation will lower the pressure (entropy) contribution of the water vapor. This will pull a slight vacuum near the condenser.

If you look this closely, the condensor will induce a zone of low pressure. This will cause the gas in the rest of the room, to expand toward the condenser (higher to lower pressure). The bulk room gas is gaining entropy (randomness), while also being give a sense of direction (move toward that tiny zone of lower pressure).

Relative to the cell, the use of ATP energy to pump and segregate potassium and sodium ions lowers the entropy at the membrane. The cations would prefer to be much more random within the water. This entropy lowering induction is very simular to our condenser, in the above example, with both lowering entropy.

The loss of entropy, at the membrane, will allow entropy to increase elsewhere (analogous to higher to low pressure) but in a way that directs the entropy to the conditions set by the low entropy (pressure) zone. The entropy on the DNA (mutations) is analogous to the high pressure gas expanding toward low pressure, with this apparent random genetic change having a sense of direction.

Selective advantage gives a sense of direction, but does so after the random. But the condensor example, shows that an increase in entropy can also be in response to a lowering of entropy. In the condenser example, for this to work continuously we need to constantly add energy to the condenser, or else the flow of entropy would stop working. The cell has to constantly add energy to the membrane for the same reason, with tweaks in performance altering the (pressure) gradient.

 

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It has been many years since I did thermodynamic analysis, so I will lets someone else correct many of your other errors. I will just note that the degrees of freedom of a gas are not related to its density as you assert.

BTW, When your start with ignorance and a false premise, normally you reach a false conclusion.

Monatomic gases like He have three translational degrees of freedom.

Diatomic gases like O2 have these three plus two rotational degrees of freedom (Not three rotational freedoms as the rotation about the line joining the two Os makes no change.)

Non linear molecules like H2O have 6 degrees of freedom, but linear triatomic molecules like CO2, sometimes written: OCO have the five degrees of freedom of diatomic molecules, plus two flex modes I will soon illustrate. (H2O also has at least one flex mode more, which I will not illustrate)

If you had greatly compressed the gas instead of expanded it some new degrees of freedom, "internal degrees of freedom" associated with the excitation of vibrational states start to enter. Then the picture gets more complex, and much more complex if you do it correctly with quantum effects included.

For example O2 only has the symmetric oscillation, which can be pictured as:
O--O ---> O-O ---> O--O etc. (some times called the "stretch mode")

But OCO has that plus the anti-symmetric mode (or degree of freedom) which can be pictured as:
O-C--O ----> O--C-O etc. and still more the flex modes in both planes, harder to picture but sort of like:

O......O
....C (ignore the dots they only hold spaces so Sciforum's computer does not drop them)

Half a cycle later becoming:

....C
O.....O

I.e. IN THE PLANE OF YOUR SCREEN, THE "C" oscillates across the line between the two "O"

Now I cannot even try to illustrate the corresponding mode where the "C" is moving out of the screen towards you and half cycle late is behind the screen farther from you than the two Os.

As you obviously don't know much about any of this, please tell, DEFINE, what is the entropy of gas and then support your claims with more than false words.

 

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When you expand a gas it will get cooler. Try this for yourself. Where is the energy going? The energy is going into entropy.

Relative to the expanding gas, it now has the extra freedom to diffuse in bulk.

By degrees of freedom, I am talking about more than just gaseous energy levels. A defect in a diamond provides additional degrees of freedom to a perfect crystal. Mutations have additional degrees of freedom beyond perfect base pairing. Random events add addtional degrees of freedom to an ordered path. These are also examples of entropy.

The point remains, when we lower entropy in one place we can increase and direct entropy from another place. We can take advantage of chemical potentials like pressure to direct an entropy increase.

 

"...Originally Posted by wellwisher
The energy is going into entropy."

It certainly is. Likewise his:
"chemical potentials like pressure" is gibberish too.

He doe not even understand what he has read! Mixes it all up - spouts nonsense. I waiting for "gravity is energy" "temperature is entropy", etc.

Worse, I troubled to explain at the level a six grader could understand what are "degrees of freedom" with examples but it went over his head. - He only speaks gibberish and has no knowledge of the subject. - He can not even define entropy for a gas, much less for cell.

The sum total of his knowledge is that energy can reduce entropy (which he does not know what that is, as he cannot define it, etc.) locally but it will increase elsewhere.

 

Wellwisher, for someone who claims to be a chemical engineer, I find it very puzzling that you don't seem to have a grasp on the concept of entropy.

 

I tried your experiment with a a canister of helium, but it didn't work the way you said it would. I cracked open the valve and the escaping gas heated up! Where did the energy come from? Is this an explanation for abiogenesis?

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Wellwisher is totally ignorant of thermodynamics. Spouting many false statements about facts that have been known for more than 200 years:

When gas rapidly expands (very little heat transfer with the environment, as was the case when you let He escape from a high pressure tank) the temperature change can be negative or positive depending upon the temperature of the gas before expansion. This is because the Joule/Thompson coefficient is function of temperature given by this curve:

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Note that at room temperature (T = ~300 degrees K) this coefficient is negative for only H2, He and Neon (not shown on the graph) so they heat with rapid expansion at room temperature. An "ideal gas" has no temperature change if expansions is into vacuum. If the expansion is restrained, for example by piston, then it will cool. Work is being done on the piston and this energy comes from the internal energy of the gas, dropping its temperature.

I.e. as you experimentally observed for He, these three gases will heat when pressure is rapidly reduced (I.e. when it undergoes a throttling process expansion) at room temperature. If you had a tank of N2 which was warmer than 621 K (348 °C) then the N2 when released would heat up, not cool.

From: http://en.wikipedia.org/wiki/Joule–Thomson_effect

SUMMARY: Wellwisher is totally ignorant and spouting nonsense which he thinks supports his false conclusions

 

That is an obvious smoke screen by those who who are trying to defend against impending obsolence. It is just the most used play out of the atheist religion handbook, which doesn't fool anyone but fools.

In engineering, entropy is connected to irretrevable heat that is lost during work cycles. This lost energy is conserved, but goes into various forms of entropy. It is pointless to make a list of entropy situations since there are many many ways for entropy to be expressed. One only has to consider the variety of materials within machines offering endless combinations to lose work efficiency. My guess is a narrow list is the reason evolution did not see this coming. You need to open the mind and think, not memorize.

The segregation of cations at the cell membrane lowers the entropy of these two cations; the cations lose that extra degree of freedom they had in the uniform solution, such as banging off the other cation. If we stopped adding energy to the cation pumps, the cations would attempt to diffuse back into a uniform solution, so they can maximize their entropy, just like the rest of nature.

This most energy intensive process within life (ion pumps) is designed to go against the normal direction of cationic entropy, thereby making use of the induced entropy potential to help direct the rebound that will attempt to increase the entropy again. All the cell needs to due is direct the natural push to gain more degrees of freedom, into useful tasks, like murations.

The choice of these two cations, sodium and potassium, for inducing the lowered entropy at the cell boundary, was not a random choice, but based on the unique impact each cation has on water. This was already part of the design for life, even before life, since you can't substitute other cations and get the same level of impact. No matter how much trial and error there may or may not have been, these cations were the best choice way in advance. Some people call that natural design.

Sodium cations are kosmotropic which means they create order within water relative to pure water. Potassium cations are chaotropic which means these creates disorder (chaos) in water relative to pure water. The water would prefer balance its aqueous entropy, on both sides of the membrane, rather than become segregrated into high and low aqueous entropy. There is a double entropy push; cationic concentration gradient and the balance of the aqueous order. This doubles the options for directing entropy.

 

You have obviously read about ion pumps maintaining non-equal ionic concentrations for the inside and outside of cell. If there were no energy driven selective transport process simple diffusion would eventually make all ionic concentrations of the two sides the same; but as you don’t understand what entropy is, you are already stating non-sense here. I.e. “cationic entropy” is nonsense as entropy is not a property of ions (of either charge) It is system property. Then a few words later, in the same sentence, more nonsense as you speak of “induced entropy potential” – Entropy is not a potential either. The next sentence:

only has one clear example of your ignorance and nonsense – cell don’t “gain more degrees of freedom” for useful (or useless) tasks. “degrees of freedom” is a well define concept that I explained to you in post 296, even with example, not just some words you can fling out at random in an effort to impress equally ignorant people. As written your sentence is yet another example of your gibberish. Perhaps you too have mild dyslexia and intended the three words I have made bold in the sentence to be: “are due to its”? Then the sentence would not be gibberish; it would only be a nonsensical statement, not both nonsense and gibberish.

You can use the phrase “degrees of freedom” in a political context, etc. but don’t use it again in a thermodynamic context until you understand the very well defined concept it is referring to.

Here you are trying to rationalize your religious like belief – that a choice was made by some greater intelligence, etc. You could equally well say the “choice of ~20% oxygen 80% atmosphere for Earth and a distance from the sun with water in all three states was the best “choice way in advance” and evidence of “natural design.” It is not a choice by some designer and in fact until green plants evolved, the Earth, for most of its history had reducing, not oxidizing atmosphere. Before that evolution only anaerobic life existed on Earth some of which can still be found in the guts of cows etc. I.e. life evolved to fill the possible niches, and they changed after green plants produced O2 for the air.

The first part of that is true but irrelevant to the ion pumps. I don't know about the second part but tend to think it false as around ANY positive ion the permanently polarized water molecules do from clusters with the ion in the center and the O atom of H2O closer to the + ion than the two Hs (essentially protons that are repelled by the + ion). So water with ions in it is more ordered than pure water when not near boiling temperatures. The reason why this has nothing to do with the “ion pumps” is that none of these stastically clusters do pass thru the selective channel in the cell membrane wall – only the ions do as is well illustrated here:

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The energy for over powering the tendency of diffusion to make all concentrations the same come from chemical reaction acting on ATP converting it to a lower energy molecule ADP. There is an enzyme involved and in the process the three Na+ ions (the red spheres in the drawing) with its action, the shape of the ion channel changes releasing 3 Na+ to the cell exterior. That removal of positive charge from the interior leaves it negative wrt to the exterior and the new configuration of the channel now permits two K+ to pass thru the channel. – Nothing to do with the statistical formation of H2O cluster around ions in water as you suggest with more nonsense. Typically this net transport of one + charge to the exterior can continue until it achieves ~ -70mV interior, then the "sodium pump" is not strong enough to pump more Na+ to the outside against the electrostatic attraction of the negative interior.

So much nonsense here I hardly know where to start. (1)Water does not have preferences or dislikes. (2) there is no such thing as “aqueous entropy” (nor is there “liquid entropy” nor is there “gaseous entropy” or “hydrogen entropy” – You need to learn what entropy is and what it is not before inventing and slinging crazy terms with the word “entropy” in them. (3) the water is not “segregated” – what you are trying to express, I think, is that: “the normal equal concentrations that diffusion would make on both sides of the membrane is disturbed by and ACTIVE, energy driven process the cells have evolved. (4) Entropy does not "push" it is not force. (5) How does the "balance of the aqueous order" provide the other part of the "push"? - in fact what the hell does "balance of the aqueous order" mean? - That seems like more gibberish, so I can't call it example of nonsense (6) .

 

To show why "degrees of freedom" relates to how many mode of energy storage there are, and is a very well defined concept, here is the molar heat capacity of some gases:

Data at 15°C and 1 atmosphere.
Gas Constant Volume Heat Capacity cV(J/K)

Ar 12.5
He 12.5 note these two monatomic gases only have 3 degrees of freedom so less energy is required to rise their temperature 1 degree.
CO 20.7
H2 20.4
HCl 21.4
N2 20.6
NO 20.9
O2 21.1
Cl2 24.8 These 7 diatomic gases have 6 degrees of freedom, (3 of translation plus the stretch mode and two rotational ones) so can absorb more energy in the six modes before temperture rises one degree.
CO2 28.2
CS2 40.9
H2S 25.4
N2O 28.5
SO2 31.3 These five triatomic molecules have at least two "flex modes" or 8 degrees of freedom so it takes even more energy to rise them one degree. From the value 40.9 for CS2, I am nearly sure the three atoms form a triangle and it then has 9 degrees of freedom. (The rotational moment of inertia is not zero for any of the three possible rotations.)

All as I explained in post 296, but Wellwisher does not understand and still misuses the well defined term "degrees of freedom" in his posted nonsense.

 

According to evolution the genetic changes are random, with selective advantage deciding which of these changes will persist. In the case of bird color and mating, the bird's brain is chosing which colors will have selective advantage. The brain does not work in a random way, but is based on order.

This is not much different than the way humans do this. If we decided full figured or skinny women are the most desireable, through the advertising and herd migration, this becomes selective advantage. It is done in the brain, whose most fundamental potential, is connected to an ordering induction into lowered entropy via ion pumping. Random will be reduced to order ib line with other order.

 

If you look at modern cells, ATP energy is used to create potassium and sodium ion gradients across the cell membrane. In essense, the ATP energy, lowers the entropy of these two cations, via enzymes, by segregating them. This potential is then used for material transport, among other things.

The normal direction of entropy in the universe is for the entropy to increase, yet the cell membrane, through ATP energy and enzymes (more than any place in the cell) does the opposite, and decreases the entropy of these cations.

If you look at photosynthesis, water and CO2 are combined to form reduced materials such as cellulose. This is also an example of entropy lowering, with the energy required, coming from the sun. The disorder within CO2 gas and the disorder within liquid water are turned into molecular order; cellulose. The schema is the same as above, higher entropy moving toward fewer degrees of freedom, using energy. This too is a low entropy boundary condition.

Abiogenesis, I expect would have made use of a similar schema, where entropy is lowered into order by using energy. The current idea of a totally random set of steps is the problem, since it sort of implies a drunken god of chaos stumbling and falling, but somehow making life. That seems far fetched, which is why nobody has had any luck. Making life, which is highly ordered could not be done by a drunken god.

Creationism assumes order, with these two above entropy lowering inductions within modern cells, examples of energized boundary conditions for such an induction into order.

The way I would approach abiogenesis is to make use of the sun for energy, with the energy able to drive a simple mechanism that can lower entropy at a simple membrane boundary. The resonance structure of chlorophyl could be induced naturally, since it will move aliphatics into lower energy because of the resonance. Next, we need membrane material. This simple boundary is able to create an order induction inside its volume.

With an entropy lowering boundary, the genetic material needed for eoclution would have been expected to go from higher to lower entropy or RNA to DNA. The reason is RNA has higher entropy than DNA, is RNA can form both single or double helixes, while DNA can only form double helix (less freedom=lower entropy). This is consistent with an energy intensive ordered boundary approach to abiogenesis and evolution.

What I learn from creation is don't trust the drunken god of random, since he/she can not be depended on. Evolution is far ahead, while the drunken god, even with human holding him up, still can nnot get the ball of life rolling. You need a God that has a sense of direction based on an ordering approach such as entropy lowering boundaries.

One more addendum, natural proteins are left handed helixes instead of both left and right. This too impies loss of entropy, from two to one degree of freedom. This is expected not a mystery like in the land of the drunken god of random, who could not even prevent this since his magic is weak.

 

More tedious word salad.

 

It might be too difficut for you so, go slow.

 

Natural selection is a mental construct that helps us create a sense of order within the chaos. One assumption is that genetic change will occur and this is random. Of all the random changes occurring within a species, future order is created via natural selection. This means the original entropy within all the genetic variations, within the group, is lowered via natural selection; entropy lowers.

The question becomes where does this entropy lowering push come from?

 

I think it is important to think and question the cause and effect of selective advantage to make sure it adds up conceptually. This is better than living in a black box of tradition where questioning is frowned upon, less we blaspheme the sacred rites.

What we do know, from observation, is nature constantly changes. This means the parameters for selective advantage in nature also change with time. The dinosaurs had their day until the parameters changed and then different critters had the advantage. This suggests that the potential for selective advantage tries to become minimized in any given environment. Thick fur in a hot climate needs additional body feature to deal with the extra heat. Thin fur is a simple way to lower the energy requirement. Or selective advantage is the path of efficiency.

If we set up a hierarchy of potentials, nature can change randomly and the DNA can change randomly. With all that entropy occurring, order via selective advantage wins the battle, with this order a function of overall efficiency in the chaos.

Consider the hypothetical situation where we have nature in random flux, the DNA in random flux and natural selection is also in flux, randomly changing its criteria. This does not coordinate with observation.

It would be like a herd of deer constantly changing the mating games and its rules, sort of like PC so everyone has the chance to be the winner. The result will be deevolutionary. Instead of this hypothetical, what we see is a push toward a sense of order, based on efficiency and minimizing potential with any environment, while also eliminating less optimized changes in the DNA that are inefficient. Life becomes better and better.

Where does this push come from; maximize efficiency in the light of two randomly changing potentials.

If you look at plant cells, photosynthesis fixes carbon. The CO2 starts with higher entropy or more degrees of freedom within space and time. The CO2 can float around the earth and even amplify global entropy via global warming.

Once the CO2 is fixed into the plant, the entropy of the CO2 and the earth lowers. Solar energy is being used to lower entropy by means of a natural chemical mechanism. It takes energy to lower entropy with the sun providing this energy.

Natural selection is also about lowering entropy in randomness of the DNA and the environment. My guess is the membrane boundary conditions of life, by using energy to lower entropy (solar or ATP), is the chemical foundation of selective advantage. The brain uses the same energy/entropy schema; used ATP energy to segregate cations, causing behavior to have the same goal in mind.

One question I posed to myself, would selective advantage also favor more regulatory control over the DNA. Human can control the random of the environment so our energy potential can be minimized if the environment changes?

To regulate the DNA in the mold of lowered entropy, would be like natural selection on the DNA, where the rules of selection favor behavior leading to predictable changes.

Certain aspects of the DNA change faster than others. Although this is in bulk it does display a degree of order and efficiency. The question is how far down the DNA does this plan extend; bulk or more specific?

There would be a selective advantage if cells could better control the random in the DNA so changes become more in line of what is needed and not needed changes have a buffer effect.

 

You should really get a better grasp on entropy. Or at least quit trying to apply it to everything.

 

To create something living we can follow the template of life. Here is an angle that came to me while I walkedthe beach this afternoon. If was based on thinking I used to do. If you look at the DNA to make RNA templates from the DNA templates we need energy. To go from RNA to protein, once again we need to add energy. As such, in terms of energy potential DNA is at lowest potential since we need to keeping adding energy to go to proteins.

Since the natural flow of energy potential, in this universe is higher to lower, in the cel this means from the protein grid to the DNA, since this is the direction of lowering energy. We can go the other way, from DNA to proteins but we need to add energy, with that energy building up energy capacitance within the higher potential of the protein grid.

Relative to the protein grid, even more energy is added to ion pump proteins to segregate and exchange cations. This is the top of the energy mountain. This sets the maximum potential with the DNA, which is at the bottom of the hill. This is a very useful arrangement.

When cells accumulate energy rich molecules, as a precursor to cell cycles, they climb another energy hill. This hill represents the energy peak. During cell cycles the cell goes the other way, toward lower potential. The transition into protein synthesis drives the DNA, RNA, protein cycle up its energy curve as the food materials lower potential (metabolized), with the net effects a energy movement down a global energy hill.

Duplication of the DNA, sort of stops the DNA, RNA, protein push up the energy hill sort of at DNA, RNA more or less, but not all the way to protein. It does not go all the way up the energy hill to protein at this point. But the double DNA is at higher potential that single DNA. Other things need to occur to get the DNA back down to lowest potential.

The object of this energy analysis is regardless of the bells and whistles in the details, the basic energy curves are the same for all cells. This suggests making life should try to copy the energy curves, since the bells and whistles are more for fine tuning that the barebones of life.

What is important about the DNA hard drive being at lowest potential is we can tweaks the DNA potential slightly, without changing the DNA other than by means of pertubatiins within in 3-D configuration. This allows us to get the dynmaic shape that optimizes potential of the protein grid.

The energy and entropy of the membrane is very important for defining the top of the energy hill, which impacts the DNA shape in the energy well.

Rather than build your life on random use the energy grid.