Cells and entropy

[wellwisher]

This is very similar to electrons filling atomic orbitals. If we started with a stripped oxygen atom, and introduce electrons, the first electrons will fill the lowest energy state or 1S orbital and then work their way to higher and higher energy up to 2P.

In the case of life, the easiest adaption is done first (inner eco-orbitals) and then the higher energy eco-orbitals (harder) will fill in next. The advantage is natural selection maintains higher genetic entropy.

Entropy needs energy to increase, so filling in higher and higher energy eco-orbitals allows the background energy to remain higher so it can support higher genetic entropy (more diversity).

Relative to atoms, the diversity of chemistry is based on the outer most electrons. These electrons exist at the highest relative energy, compared to the very stable inner electrons. The outer electrons offer the most energy for entropy, allowing extreme diversify in chemistry. Inner electrons don't form much in the way of diversify since energy is too low to support much in the way of entropy.

Life is interesting since it forms the most diversity within chemistry. This has to do with even higher energy levels. Trees for example, form wood full of electron energy in reduced materials. This would minimize energy if it was CO2 and H2O. But as CO2 and H2O, the energy is too low for the entropy needed for adaptive radial diversity. We need to increase the energy of the electrons back to reduced materials so there is more potential energy for the entropy of radial diversity.

This is why cells, if you burnt their structures in a calorimeter, will give off a lot of energy. They need that potential energy for higher energy internal eco-orbitals. But since the energy of the universe needs to move in the direction of lower energy, there is a push lower energy and entropy; efficiency.

 

[wellwisher]

Life, by growing, increases its amount of stored energy value. The tree adds more and more wood as it grows. We can burn the tree as a function of growth to show this increasing energy value. Humans will add muscle and fat as we grow, which both have caloric value; energy value. Inanimate systems in the universe, based on energy and force typically move from higher to lower energy. Life builds up energy value as it grows, causing it to go in the opposite direction of inanimate matter.

As an analogy, say we had water in a storage tank, connected by a pipe to the lake below. The universal potentials will naturally go from higher to lower energy, or the water will flow from the tank toward the lower level lake due to gravity. Life does the opposite. As life grows, it would be like water being pumping up into the tank, from the lake, causing the tank level to rise; gaining potential energy.

Since life acts within the universe (not in isolation) both the effects occur at the same time, as life interacts and grows within the universe. In the above analogy, life is pumping water uphill into the tank. At the same time, the universe is trying to let the water flow out of the tank toward lower energy. When we reach maximum growth size there is a balance of the two. The tank reaches steady state.

The cells build and store energy, while also grinding down food materials to lowest energy; water and CO2. The energy extracted from digestion is used to synthesize materials and push the cell up the energy hill. Instead of a tank, picture life as a water fountain that is pumping water. The universe is like gravity which pulls it back to earth. The fountain appears animated due to this dual action.

Beside energy the fountain of life also makes use of entropy. Life acting within the universe is also a fountain of increasing and decreasing entropy. For example, the DNA will increase entropy via mutations. This is the universal push up the entropy fountain. Natural selection, common to life, weeds out all this genetic entropy and choses only a fraction; best. This loss of genetic entropy is connected to life pulling the entropy down the fountain.

The average modern cell is about 85% efficient. This means the ratio of theoretical entropy (universe acting) is about 15%. The 85% efficiency is used for work cycles to gain energy and lower entropy. Within the 15% universal share there is a push toward increasing complexity such as at the DNA.

If plotted the cell as a function of energy and entropy, we would get something similar to a graph where X (energy) and Y (entropy) goes from plus to minus values. What you do next, is place aspect of the cell within this grid based on their local energy and entropy balances. There are four quadrants the cell. For example, the mitochondria are in the quadrant of negative energy and positive entropy.

We have one cell, composed on many parts, doing what appears to be four separate things at one time, but all coordinated. The complexity and balance of this is what we call the life force.

 

[HectorDecimal]

We have one cell, composed on many parts, doing what appears to be four separate things at one time, but all coordinated. The complexity and balance of this is what we call the life force.

This is likely true. Ironically it relates to one of my current projects.

The blood vessels in the human body, or all vascular system driven animate life for that manner, are composed of millions of directional and check valves. These valves keep the blood flowing in one direction void of any reverse surges. We know electrical impulses are part of the animation process, still the topic question is answered by another question: Are chemical bonds formed and maintained by the strong or weak electromagnetic forces?

 

[AlphaNumeric]

Beside energy the fountain of life also makes use of entropy. Life acting within the universe is also a fountain of increasing and decreasing entropy. For example, the DNA will increase entropy via mutations. This is the universal push up the entropy fountain. Natural selection, common to life, weeds out all this genetic entropy and choses only a fraction; best. This loss of genetic entropy is connected to life pulling the entropy down the fountain.

Evolution is not about weeding out highly entropy genetic patterns. A mutation can be beneficial or not independent of the complexity of its gene encoding. It might be entropically favourable to replace some of my junk DNA with the genes for gills but it would serve me no evolutionary advantage at the moment. What if gills have a lower entropy in terms of DNA coding than lungs? Does that mean it'd be an evolutionary advantage for humans to have gills rather than lungs? Of course not, it doesn't help us survive in our niche.

Besides, while entropy is a rough and ready measure of complexity and has its place in thermodynamics, it has serious short falls when it comes to being a good complexity measure. For example, it is permutation invariant. If someone took your DNA and rearranged it, without adding or removing a single letter, your DNA's entropy wouldn't change but clearly it would have massive effects on you. The simplest mutation is to just swap two letters in DNA coding, but it has no effect on entropy.

 

[wellwisher]

Are chemical bonds formed and maintained by the strong or weak electromagnetic forces?

Life's enzymatic animation is based on the weaker secondary bonding forces, the most of important of which is hydrogen bonding. The hydrogen bonding in liquid water, although a weaker secondary bonding force, can nevertheless add up to break the stronger covalent bonding to form the pH effect. Sort of a bunch of ants carry off a beetle.

Life does a similar thing, using secondary bonding to coordinate a enzyme to break or form stronger covalent bonds within other molecules.

There is an EM trick to this, which is special to hydrogen bonding. Hydrogen bonding can form cooperative hydrogen bonding with a group of hydrogen bonding moieties. Cooperative hydrogen bonding allows the team to be stronger than the sum of the parts. Any member of the cooperative is like mini-hercules, until the first bond of the cooperative breaks. Then it is everyone man for himself. This increase of entropy absorbs energy and helps to tug reactions up the activation energy hill.

 

[wellwisher]

The second law of thermodynamics states that in general the total entropy of any system will not decrease other than by increasing the entropy of some other system. Hence, in a system isolated from its environment, the entropy of that system will tend not to decrease. It follows that heat will not flow from a colder body to a hotter body without the application of work (the imposition of order) to the colder body.

One mistake made with biological entropy is to ignore work cycles when it comes to life and enzymes. Entropy is maximized when work is not being applied but will decrease if there are work cycles present.

For example, say I had a gallon of gas and all the air needed to burn it to H2O and CO2. I burn it as a flame, releasing all the energy, maximizing entropy. We will call this the theoretical maximum entropy.

In the next scenario, I burn a similar gallon of gas, in an engine that is 85% efficient. The engine performs a work cycle. In this case, the entropy will still increase, but at only 15% of its theoretical maximum. The 85% efficiency uses the energy, earmarked for entropy, in another way.

For example, our engine and work cycle is being used run a heat pump that will take heat/energy from the outside cold air and pump that energy into a warm house. I can use work to move energy from cold to hot causing 85% of the theoretical entropy to move in the wrong direction. This is engineering 101.

Enzymes are like little nano-machines that can perform work. Reactions that would not occur on their own, at a given set of conditions; would be the wrong direction for reaction entropy, can be made to occur at high reaction rates by enzymes. It like the heat pump using work to move heat from cold to hot. We can use enzymes to build high energy molecules which prefer to move to lower energy.

If a cell is 85% efficient then 85% of the energy goes to work. This work can heat from cold to hot or reverse spontaneous reactions, so they go in the wrong direction compared to no work being applied. There will still be 15% entropy that can be used for increasing complexity.

Natural selection only selects a fraction of all possible genes. If the earth was infinite in size and all life ever born had room to live, grow and procreate this would give the theory maximum entropy. Natural selection will skinny this theoretical maximum entropy down to a tiny fraction. This natural work cycle, called natural selection reduces entropy to a tiny fraction.

The difference between an engineering POV and the biological consensus is I normalize entropy to the theoretical maximum. This allows me to see the loss of entropy due to work cycles. The biology consensus, does not normalize but only sees the incremental increase of entropy. If you ignore normalization there is no need to consider order or work. You fixate on just the random 15% which is not as random as currently assumed.

For example, say we have a machine that does a work cycle. The 15% theoretical maximum entropy, which still remains, is due to gear fraction. That work cycle is defining how entropy is being expressed. Entropy will not randomly appear as gases diffusing away. There is an order even in the entropy. If we stopped the work cycle, the 15% entropy also stops.

An analogy is the diffusion of a gas into an open space will absorb energy and increase entropy. I can put baffles in the same room and let the gas out. Now the entropy moves around the baffles. There is now predictable order in the apparent randomness of the entropy.

 

[origin]

One mistake made with biological entropy is to ignore work cycles when it comes to life and enzymes.

The biggest mistake though, is to not be able to realize that the earth is not a closed system and to go arm waving into the land of pseudo-science.

 

[wellwisher]

The wild card that biology overlooks are work cycles. Heat in the universe will spontaneously go from hot to cold.

However if we apply a work cycle this can go the other way. For example, if you went to your refrigerator/freezer, feel the heat coming out the back or bottom of the unit. We are taking heat from the cold freezer to make it even colder. The inside of the freezing, by losing all its heat to the warmer outside, also takes heat away from the entropy that was in the thawed food, as it begins to freeze into solid order.

If we unplug the refrigerator, then the natural flow of entropy would return. Now heat moves, like expect, from hot to cold, since there is no work cycle reversing this.

I assume enzymes operate work cycles thereby allowing a high level of cellular efficiency. Biology assumes only random because there are no work cycles therefore heat can only flow from hot to cold and refrigerators cannot exist nor can food freeze in the summer.

 

[origin]

The wild card that biology overlooks are work cycles. Heat in the universe will spontaneously go from hot to cold.

That is correct.

However if we apply a work cycle this can go the other way. For example, if you went to your refrigerator/freezer, feel the heat coming out the back or bottom of the unit.

Nope, you are wrong. Heat is still going from hot to cold. Do you know how a regrigeration cycle works.

We are taking heat from the cold freezer to make it even colder. The inside of the freezing, by losing all its heat to the warmer outside, also takes heat away from the entropy that was in the thawed food, as it begins to freeze into solid order.

"Takes heat away from the entropy" that is pretty funny. I wonder if you are ever going to figure out what this mysterious entropy is.

If we unplug the refrigerator, then the natural flow of entropy would return. Now heat moves, like expect, from hot to cold, since there is no work cycle reversing this.

It was never reversed - the heat always moved from hot to cold - you are really quite amazing. You speak with such authroity and confidence even when you are completely wrong.

I assume enzymes operate work cycles thereby allowing a high level of cellular efficiency. Biology assumes only random because there are no work cycles therefore heat can only flow from hot to cold and refrigerators cannot exist nor can food freeze in the summer.

So you have proven you do not understand refrigerations cycle, entropy and biology - it's a goddamn trifecta of confusion! Bravo!

 

[billvon]

See that's the whole point. None of this can be simplified into a Grand Unified Theory of Everything, as wellwisher wants to to be.

I agree. As I mentioned earlier, his favorite tool is a hammer and therefore everything looks like a nail to him.

We all do this at some point in our learning. When I first learned about gravitation and the Bohr model of the atom I thought "this is so cool! This one concept - gravitation - explains everything! It explains the orbits of the planets around massive stars and the orbits of the electrons around the massive nucleus. Once you understand gravitation you understand everything!"

That was, of course, a very simplistic way of looking at things. But when you're 13, even incorrect models can teach you _something_ about physics. It wasn't until age 17 that I learned about valence shells and the implications that quantum mechanics has for atomic structure. And honestly the Bohr model is so simple and elegant that I can see someone wanting to hang on to a simple model that seems to explain everything.

As you note, entropy of a cell can be studied. But to connect this to evolution as wellwisher thinks it connects? No way.

Well, on the plus side, it's great that he's thinking about it.

 

[origin]

Well, on the plus side, it's great that he's thinking about it.

That was very generous of you!

 

[wellwisher]

“
We are taking heat from the cold freezer to make it even colder. The inside of the freezing, by losing all its heat to the warmer outside, also takes heat away from the entropy that was in the thawed food, as it begins to freeze into solid order.
”
"Takes heat away from the entropy" that is pretty funny. I wonder if you are ever going to figure out what this mysterious entropy is.

Obviously you don't understand engineering or physical chemistry. The smoke screen that you and others are setting up makes no sense. What are you so afraid of? Below is link to show you the math needed to calculate the loss of entropy when water freezes.

http://pruffle.mit.edu/3.00/Lecture_14_web/node4.html

I am patient and can dumb down until you can understand.

 

[origin]

Obviously you don't understand engineering or physical chemistry. The smoke screen that you and others are setting up makes no sense. What are you so afraid of? Below is link to show you the math needed to calculate the loss of entropy when water freezes.

http://pruffle.mit.edu/3.00/Lecture_14_web/node4.html

I am patient and can dumb down until you can understand.

I don't believe you can dumb down any more than you have. Your belief that a refrigerator cause heat to flow from cold to hot is proof enough

No one ever said there is no entropy change with phase changes. Where did that come from?

You said that a freezer 'takes heat away from entropy', which makes no sense, and shows you don't have a grasp on what entropy is.

 

[wellwisher]

No one ever said there is no entropy change with phase changes. Where did that come from?

I said the freezer will lower the entropy of thawed food as the food freezes. The water in the food is turning to ice and entropy is lowering.

You said that a freezer 'takes heat away from entropy', which makes no sense, and shows you don't have a grasp on what entropy is.

Entropy needs energy to increase. This is why it is often connected to irretrievable heat. Based on energy conservation, if the entropy decreases the energy, that had been within the lost entropy, is released.

If I freeze water, I take energy away from the water. This energy comes partially from entropy decrease. The conservation of energy is why work cycles can lower entropy.

Work cycles can lower the theoretical entropy but removing the energy that would go into entropy.

 

[origin]

I said the freezer will lower the entropy of thawed food as the food freezes. The water in the food is turning to ice and entropy is lowering.

No one disputed that as far as I know.

Entropy needs energy to increase.

That is like saying temperature needs heat. Or saying Potential Energy needs energy. I mean WTF?

This is why it is often connected to irretrievable heat.

Entropy is not connected with irretrievable heat, entropy IS irretrievable heat (energy).

Based on energy conservation, if the entropy decreases the energy, that had been within the lost entropy, is released.

Entropy does not decrease the energy - entropy IS the energy that is lost.

If I freeze water, I take energy away from the water. This energy comes partially from entropy decrease.

No, the entropy IS the energy that is removed.

The conservation of energy is why work cycles can lower entropy.

Nope

Look at it this way; we have a name for the energy that is lost in the form of irretrevable energy, the name of this energy is entropy.

Have you figured out yet how that refrigeration cycle works?

 

[wellwisher]

Entropy does not decrease the energy - entropy IS the energy that is lost.

Entropy being energy, is analogous to saying matter is energy. I suppose we could do it that way but that causes us to lose clarity. We normally separate matter and energy into two distant things. Biology is not normally based on just energy considerations even if E=MC2. It is easier to treat matter and entropy as separate, but connected to energy.

Maybe an easier way to see entropy is to start with matter in a solid state. We will add energy to the matter. This cause changes in states and properties of the matter as a function of the energy added. These energy changes within atoms and the entire system have a connection to the system entropy.

Entropy measures the changes from the status quo as we add each increment of energy. Say we take this all the way to a gas. The translation, rotation and vibration of atoms and their collisions all reflect entropy. Entropy is like the amount of freedom of expressions within the mass/energy, but it will require energy to achieve that full entropy freedom.

Have you figured out yet how that refrigeration cycle works?

As far as the refrigerator, it has a condenser and an evaporator. The evaporator expands the refrigerant which gets very cold. It gets cold because the lost heat goes into the entropy of the refrigerant expansion. This is actually a good way to see how entropy absorbs energy.

The compressor does the opposite, it gives off heat energy. The work cycle compresses the refrigerant and lowers the entropy of the refrigerant so its heat energy is released. What the expansion gained when it absorbed energy the compressor will release. Now the refrigerant entropy is low for another expansion where it can increase entropy and absorb energy again.

When I was talking about the fridge, I was only concerned with the inside of the freezer and the outside of the refrigerator. If we draw a black box, like we do with statistical models, the inside gets colder and outside hotter. The flow of heat in this black box is from the cold inside to warm outside.

 

[arfa brane]

Entropy being energy, is analogous to saying matter is energy.

No it isn't.

Thermodynamic entropy has units of energy per degree of temperature. Entropy doesn't even have the same units as energy. (Not even!)

Entropy describes, roughly, the freedom a particle has to move around randomly. As a gas expands its entropy increases because, roughly speaking, each particle has more freedom of movement.
A compressed gas has a lower entropy than an expanded gas because all the particles are restricted, their collective mean free path statistics are smaller than for an expanded gas.

If you consider what can be known about the particles, this corresponds to how much work they can (or can't) do. There is a close correspondence between what can be known about any particle and the run-length of an algorithm. In an informational sense, each particle is like a program whose "runtime" is like the volume a particle moves through (roughly speaking).

 

[wellwisher]

I didn't want to get bogged down splitting hairs. The Gibbs free energy equation is
G=H-TS. If we solve for S (entropy) the units of S is energy/mole/T. With mass and energy or E=MC2, mass is energy/t2/d2. These are sort of analogous in the loose sense there is a connection to energy.

 

[Trippy]

I didn't want to get bogged down splitting hairs. The Gibbs free energy equation is
G=H-TS. If we solve for S (entropy) the units of S is energy/mole/T.

BZZZT!

G=H-TS
$$S=\frac{H-G}{T}$$

Enthalpy is measured in Joules.
Gibbs free energy is measured in Joules.
Temperature is measured in Kelvins.

So we have:
$$S=\frac{Joules - Joules}{kelvin}$$
Which gives us the units for Entropy as J/K or Joules per Kelvin.
Which, as it happens is the SI units for Entropy.

I'm sure if I looked hard I could site an IUPAC definition if you think it would help convince you?

With mass and energy or E=MC2, mass is energy/t2/d2. These are sort of analogous in the loose sense there is a connection to energy.

Again, we have:
$$M=\frac{E}{C^2}$$
Which, on the face of it seems to indicate what you're suggesting.

HOWEVER.

Remember: $$K_e=\frac{1}{2}mv^2$$
m is kg, v is m/s which gives us as the units for energy $$kg.m^2.s^{-2}$$, which we give the symbol J (never forget, Joules are a derived unit).

Substituting that back into the previous equation, we find out that we started with:
$$\frac{J}{m^2.s^{-2}}$$
But once we realize the above we have:
$$\frac{kg.m^2.s^{-2}}{m^2.s^{-2}}$$
Which unfortunately for you is just kg.

 

[Gravage]

Does the entropy have anything with the organsim's death? If that's true how come there are species that can actually cheat death and resist death for thousands of years?
How come jellyfish Turritopsis nutricula seems to be biologically immortal?
If entropy really works in an organism, it would mean, that it would prevail, meaning there should be no organism biologically immortal, but yet some of the species manage to prevail thousands of years. It just doesn't make any sense to me.
I hope there is someone here who actually understands entropy in organism and how it works, I sure don't understand it fully.