Cells and entropy

The foundation for this discussion begins with understanding biological thermodynamics. Here are is a presentation and study guide, in case you're interested:

https://docs.google.com/viewer?url=http%3A%2F%2Fcasegroup.rutgers.edu%2Flnotes%2FThermodynamics_lecture.pdf

https://docs.google.com/viewer?url=http%3A%2F%2Fcatdir.loc.gov%2Fcatdir%2Fsamples%2Fcam031%2F00031272.pdf

 

Log in or Sign up to hide all adverts.

The links aren't working for me. Could be my work firewall.

 

Log in or Sign up to hide all adverts.

Big thanks, links work for me.

 

Log in or Sign up to hide all adverts.

If a living organism dies and therefore all its structures and molecules, decompose, and atoms are oxidized, so they return to simpler states, this is the direction of increasing entropy and lowering energy. This will happen spontaneously over time since it is driven by the spontaneous direction of energy and entropy.

If we played this in time-lapse photography, backwards, such as with a video recording, going from dust and simple gases, back into the living organism, what we get is the opposite, or the direction of lowering entropy and increasing structural energy.

This reversal could not happen spontaneously, since by gaining energy and lowering entropy it would move in the wrong directions in terms of the spontaneous direction of energy and entropy.

If we go back to life, but before death, to avoid death it needs to find a way to prevent the spontaneous direction of energy and entropy. Or it needs to lower entropy and increase energy as fast as the spontaneous direction for energy and entropy occurs. This is done with biological work cycles.

 

Yes. it is very impressive how evolution working by selection has constructed over millions of years the complex life forms that can do this (without the slightest knowledge of entropy or even entropy being in anyway their unknown guide).

 

This digression was useful, because the concept of entropy can become very nebulous since it has many meanings and situations, often leading to confusion. It can be defined as the inefficiency within works cycles, in terms of statistical or quantum mechanics, in terms of free energy, in terms of complexity, in terms of loss within data and information transfer, in terms of randomness, etc. There are even more definitions than this.

As a way to simplify this confusing concept of entropy, so it is like a compact Swiss army knife instead of a truck load of supplies, I like to think in terms of the concept, degrees of freedom. This term should not to be confused with the same term used to describe the rotational, vibrational and translational energy levels of gases, although these states are only a few of the many degrees of freedom defined by entropy.

In a more general sense, the concept of degrees of freedom define all the changes of state from a given status quo. This is very open and can include all the above, at the same time. This allows one to compare whether entropy decreases or increases, from any given status quo, based on how the degrees of freedom change. If we start with a gas under given conditions of standard pressure and temperature, if we lower the volume (also remove the generated heat back to constant pressure and temperature) there is a loss of freedom therefore entropy goes down. Randomness also decreases, within this loss in the freedom.

In the case of evolution, as life becomes more complex, there are more degrees of freedom for life’s expression, so complexity increases entropy. If we transmit information to the moon and there is loss, this adds a secondary noise stream (more freedom) to the information, so entropy increases. If we compress a raw picture image into a JPEG, there is data loss from the status quo, or the degrees of freedom have falling and entropy decreased. The JPEG is less complex, than the raw image, thereby saving storage space. The same analysis, or degrees of freedom, can be applied to the cell as a whole or in part.

The second law, about entropy, states that the entropy of the universe needs to increase. This law is based on the net total. It does not mean it is not possible to decrease entropy, on the local scale. This can occur, as long as there is an increase in entropy elsewhere. For example, although a JPEG lowers entropy compared to the raw image, in the bigger picture this causes entropy to increase elsewhere. If you blow up the JPEG image, it starts to break down detail faster than the raw image, causing mental confusion or entropy in the mind. One may asks is that a bird or bug; more fuzzy degrees of freedom.

When we apply entropy or degrees of freedom to the cell, there can be zones of lowering entropy. However, this needs to be balanced by zones of higher entropy. Even if a cell’s net lowers its structural entropy, due to the order within its structures (less freedom than randomness and chaos) there needs to be higher entropy somewhere to balance this out. This is useful because one can focus on one aspect of the cell and infer connected aspects based on cause and effect. The loss of entropy defined by the JPEG is what is causing the enlargement confusion within the mind, with this confusion being a secondary or spin off effect from the JPEG cause. We did not invent JPEG because of enlargement confusion. If resulted from it.

When looking at a cell, I like to begin the entropy balance at the cell membrane where cationic pumping is occurring. This is because of the high amount of cellular energy being devoted to this. This is tops in the cell. This energy is used to drive enzymatic work cycles which are designed to lower the cationic entropy (segregation means less freedom to mingle). This is our JPEG analogy. Now we need to find the related increases within the cellular entropy (confusion; more degrees of freedom), which will result and which are needed to balance this out. This is cause and effect.

 

Sorry, I lost track of this thread....

Son of a gun. You're right, I failed to notice I was defaulting to google docs as my PDF viewer. Here are the actual URLs:

Here is the link to the tutorial article-

http://www.phys.unsw.edu.au/~jw/CellularThermodynamics.pdf

and here is the link to the other tutorial in slide format-

casegroup.rutgers.edu/lnotes/Thermodynamics_lecture.pdf

Either or both of these would help debug this dialogue.

 

Here is a quote from the second link:

This quote applies to a spontaneous process, but not a process that will not occur spontaneously. For example, sodium and potassium ions would not spontaneously segregate on two separated sides of a membrane. However, if this state was induced by enzymatic work, these cations would spontaneously try to desegregate and equilibrate on both sides of the membrane. That is the direction of higher entropy. Segregation is not spontaneous and reflects lowering entropy.

Energy will spontaneously flow from higher to lower energy. However, going from ionic equilibrium on both sides of the membrane into cationic segregation is the direction of lower to higher energy. This cannot occur spontaneously, but requires work. In both cases, enzyme work cycles are responsible.

When dealing with entropy and energy, the main thing you need to remember is entropy can only increase if there is energy. This is usually provided by energy going from higher to lower potential. By definition, at absolute zero, since there is no heat energy, entropy is defined as zero. As we add energy and the temperature rises the entropy increase is reflected in new degrees of freedom.

My goal with energy and entropy is not quantitative, Rather my goal is qualitative. I am only interested in either up or down. This up-down direction allows a Swiss Army knife simplification that would not be kosher if the goal was quantitative. With up or down and a little logic we can make some interesting connections. This is a good way to test some basic assumptions of life.

An interesting, but very important entropy consideration, that is on the entropy swiss army knife is connected to randomness. Randomness is another aspect of entropy (degrees of freedom), which like all forms of entropy requires energy. To give an example, say we started with a perfect diamond, which any girl would love to have. You can wait and watch, but nothing random will spontaneously happen to the internal structure of the diamond. The reason is the C-C bonds are strong and the amount of energy needed to change the status quo is much higher than found at ambient conditions. Random will lack the energy. We may need to heat to 2000C to start getting enough energy for a tiny amount of random to begin.

Say we start with water vapor or steam. The entropy and the randomness can be modeled with statistical mechanics. If we take away heat, we will take away some of the energy that is needed for entropy and randomness. If remove energy all the way to ice, then the only randomness that might be left will be built into the ice (defects). But all dynamic randomness will be gone. It lacks the energy to be random in a dynamic sense. We can tweak randomness.

 

You're assuming enzymes appear out of thin air. They don't, they are manufactured, by using energy. This is why it is important to always remember what we mean by a closed system. You have to account for ALL the energy, and once you have done that, you have a proper boundary for measuring entropy. Look at slide 5:

When enzymes appear out of thin air, the total energy is not conserved and you violate the First Law. This makes your entropy analysis invalid. Anyone can leave out part of a system and claim its entropy increases. I can leave out the gas in my tank and bring the exact same argument that my engine violates the 2nd Law.

And here's another pitfall. You have to be careful not to leave out the transformations between chemical, mechanical, thermal, electric and all the other ways in which energy can be converted. You also have to remember that all of your predictions will tend to be theoretical, because you are forgetting how many ways that things don't happen ideally. So right off the bat you're losing all the energy contributions from the phenomena you ignored.

Only you made it that way by bringing enzymes in, as if they are free. They're not; they cost energy to make and use.

Be careful, they are just lysing chemical bonds. Before jumping to conclusions, you should at least go to some representative enzymatic reaction, and account for the energy changes you believe are free.

And that's why you need a proper diagram of the system you are putting a boundary across, to be sure you haven't left any gains or losses out of the TOTAL that must be conserved under the 1st Law. Because, if you have positive entropy it means you haven't drawn the boundary properly. How many times are we going to go back over this? :wallbang:

At some boundary which you avoid. Otherwise you can violate the 1st Law and of course as equally violate the 2nd Law.

Except of course energy has many forms. A dead battery at room temperature, that is charged and allowed to cool down, stores energy, without heat. It's merely in the form of accumulated charge. Similarly, fuel stores chemical energy. Any there are numerous other forms and countless examples. So be careful restricting everything to heat, although it is an important consideration.

This statement is one of your core fallacies. You can't qualify the 1st or 2nd Law without first quantifying the total energy, summing it to zero, and then, when you are finished, you will see that the entropy increases. And you have to account for ALL sources and sinks, or your entropy number is bogus - pure invention, nothing more.

It's a good way to violate the 1st Law on your way to violating the 2nd Law, which appears to be your goal. This is why this kind of thinking is called pseudo science. It appears (to naive lay people - in church, for example) to be true. But it's not true. It's false. Pseudo means false. Pseudo science means false science. All you have proved is that you can convince anyone (especially those seeking the same confirmation) of anything.

Brownian motion is increased by added energy. The probability distribution does not change, only the rate of random collisions changes. They are not the same. This is another problem with trying to be qualitative. You need to nail down what you mean by randomness in a reaction, before you can try to treat it as a producer or consumer of energy. Besides, you have failed to be qualitative as soon as you ignored the TOTAL sources and sinks in the system you think you are analyzing.

Geez.

If that were true, a diamond would be at absolute zero, so no, the atoms are shaking. They have kinetic energy, and you can prove this simply be raising and lowering it by heating or cooling the diamond.

We haven't even begin to speak about bond energy, which fundamental is you pretend to apply the 1st and 2nd Law to a chmeical reaction.
I notice we left biological thermodynamics in the dust, back at slide 1 or 2. Here you want to give a qualitative but not quantitative explanation for a crystal lattice, which is going to lead to a false conclusion, because you are doing this to avoide the 1st and 2nd Laws of thermodynamics. Pseudoscience.

Nope. Au contraire. Motion and energy are intimately related. Randomness speaks to the probability of something you define, such as the odds that particle A collides with particle B. All you're doing here is raking probability theory over the same coals you raked thermodynamics over. Just as your failure to use a proper boundary in thermo, her you are not bounding what you mean by a process. You need to define what processes are taking place. Otherwise, you yourself are the randomness, nothing more.

Random doesn't have an "amount" because it's an adjective, not a noun. just as you can have three socks or green socks, but not three green, you can have random or particles or massive particles, but you can't have massive random. This again speaks to your errors in qualitative not quantitative, although here you are in reverse, trying to assign quantity to "random", which is a quality. Pseudoscience.

But you can't do that qualitatively. Besides, you aren't even attempting to qualify what kind of process you're talking about.

No, the collisions will continue to occur randomly. You have only reduced the number of undefined time-dependent processes per second. So what?

What? That's crazy. The final position of each molecule in the crystal is what's randomized. Here you go again zoning out with

. You are jumping to conclusions by skipping the science.

Hopefully you now understand why this statement is false.

Meaning: I can tweak anything, because I reject science, even though I pretend to apply it, as an actor in a movie imitating the words of a scientist, but only according to a script, and without "doing any work" as you might say. (It's very anti-entropic).

So far all you have proved is that you know how to generate pseudoscience.

So? :shrug:

Let's talk about cell entropy, at some elementary level. I'll come back later and see if I can "tweak" your brain!

Please Register or Log in to view the hidden image!

 

One other, perhaps relevant, point: a cell in equilibrium with its environment is dead.

Life seems to be a process that allows cells to maintain a non-equilibrium with the same environment. This appears to be because cells can store energy (even if it costs energy, which if course, it does).

It seems reasonable to assume that life has evolved processes which store energy at a minimal cost.

 

The connection between energy, entropy and randomness is important to life, since by regulating local and bulk energy, life can regulate and direct entropy and randomness. To better explain this, consider a typical chemical reaction. Before the reaction can proceed, the reactants need to climb an activation energy hill as shown below:

Please Register or Log in to view the hidden image!

Because of the activation energy hill, there are energy restriction placed on the spontaneous expression of entropy and randomness into products. For example, wood burns. However, you will never see trees spontaneously combust in a random way. This is because entropy and random lacks the energy needed to climb the activation energy hill.

Say we took a match to ignite the wood. This causes the molecules within the local wood to climb the activation energy hill. Since burning wood is exothermic the resultant reaction gives off more energy than was required to climb the activation energy hill. This can provide the needed energy for spontaneous movement into increasing entropy and randomness causing the fire to spread and burn.

There is a local restriction to this entropy and randomness. Trees far away will not suddenly spontaneously burst into flames in a random way. The reason is the activation energy is localized near the flame, restricting randomness only to there.

Let us change the scenario and make the wood wet by adding water. The wet wood won’t burn quite as well using the match. The entropy and randomness at the burn is limited, compared to the above, because the water is absorbing the energy needed for additional activation energy, thereby removing the energy needed for the chain reaction combustion related entropy/random. There will be an increase in entropy/random in the water, but this is not self amplifying. In the above scenarios water was used to regulate the organic entropy and randomness compared to the dehydrated scenario. Life takes advantage of this.

Let us now look at an enzymatic reaction(image above). Enzymes act as catalysts, allowing chemical reactions to proceed, which may not proceed spontaneously. Under normal conditions there is not enough energy for entropy/random to spontaneously climb the activation energy hill. If we add the enzyme this becomes sort of possible.

An enzyme works via a lock and key arrangement, which is very specific to reactant and products, and is able to lower the activation energy so difficult reactions can proceed even with low background energy conditions that preclude spontaneous reactions. The enzyme, by being very specific, offers a path available for entropy (a new degree of freedom) but this path is not available for randomness (very specific). Life can create this interesting dissection of entropy, removing the degrees of freedom which are defined by randomness. This conserves energy.

 

I see your point. It could also apply to the earth's biosphere in general, never reaching widespread equilibrium, a "living environment" in which the velocities, temperatures and pressures of fundamental chemicals like air and water are always in a state of flux.

 

But do you really think that an organism can truly be biologically immortal infinitely long life?
I think it can be extremely long lived for tens of thousands of years, but it will eventually die. Nothing can exist that long without a large price.

 

That's true 100%. I asked an bio-physicist several years ago, he explained me exactly this, but with more complex words.

 

I have one thing to say to entropy, and that is: determinism!

Everything has a set path to travel. No matter where or when it is, it will always take te path of least resistance. If it takes another path, it is artificial.

This means there is a path that we can gauge. If we were to know where it is, what paths lie before it, and how much energy it has put into it, then we should know where it is going, and how fast.

If you were to take a river, it will always fit into the grroves of prior rivers. This means that there is structure.

 

It could also be frozen or dehydrated. It can also be a seed. With dehydrated yeast, if you add water, the nonequilibirum state is restored and life reappears.

In the case of thawing frozen yeast, the frozen water had lowered its entropy when it froze into ice. If we melt the ice, heat/energy is absorbed and the entropy increases. This entropy increase in the water, helps the yeast come alive again.

 

"Regulate and direct" almost sounds like ... natural selection. Is it possible, after all these months (years?) that you are now beginning to converge at the doorstep of the illustrious Charles Darwin??

Remember this, you will need it later:

Yes- reactants, not entropy or randomness just reactants.

False. Look at the definitions:

Compare the definitions to what you are saying.

Trees only very rarely spontaneously combust for the same reason most things rarely spontaneously combust. It's fatal.

Bogus.

Does it matter if the wood is alive or dead...After all we were talking about living cells before you diverged into this...

And where did that energy come from? How do trees get their energy to build cells? Can you identify those sources? This is where you are missing the boat.

The randomness of the fuel makes it burn better? That's insane. What happened to the activation energy argument? Right now all that's spreading entropy and randomness is you. Grab a bucket, wellwisher, you're on fire.

Sweet mother of confusion...
:shrug:

It can happen. But this reasoning gets us nowhere.

If that were true, we could napalm the whole forest and it would be leafing out the next day.

Are you ever going to tell us what has been randomized (other than your ideas)?

Utterly bogus, beyond repair.

Meanwhile, back at the ranch:

Bogus

Bogus, except for your TRUE AND CORRECT statement that enzymes are very specific to reactant and products, which unfortunately, fizzles out when you drag in entropy and randomness as if they are reactants catalyzed by the bonding sites of enzymes.

The clouds break, the sun god appears, shining radiantly, and the First Law is preserved.

:shrug:

When do we get to talk about cell thermodynamics?

 

Evolution is discontinuous because the data evolution is based on is discontinuous due to data being only bits and pieces of the original data. We might be luck to find a T-rex or two, but might not gather the rest of the thousands of critters, within the same ecosystem, at the time.

As an analogy, say I made a circle of popcorn, with each piece touching the adjacent pieces. My theory is this is a continuous circle. With all the data, this theory can be supported. As I wait for people to verify this theory, with the data, days go by and birds start to eat the popcorn. The circle is now fragmented and discontinuous, and is not looking like a circle.

The original continuous circle can no longer be proven with this data, even if it was true. If you insisted on the circle, from that broken data, the truth will be called pseudo-science and your reputation brought to question. As such, if you wish to be taken seriously in the future, I will need to make something up, which better fits this data. I might say I made this figure, with a blind fold on, and it had no definitive pattern. This would fit the data and I could publish. It is easier to go with the consensus.

A better test of evolution would be to collect continuous time data, instead of depend on fragmented data. For example, bacteria are evolving due to the environmental pressures created by antibiotics. We could look at the data, in a more continuous way (one a day), to see if there are continuous but unstable intermediate states in the process of change.

 

Your analogy is flawed because every piece of popcorn is different than any other in an unrelated way. However, if you could show that popcorns that are adjacent to one another are more related in shape than popcorns that are separated, you could indeed show beyond a reasonable doubt that there was a progression going on.

 

I agree with you, but once pieces are missing you still cannot prove continuous even if the circle started that way. The data would still say discontinuous, since you don't have hard data in the missing zones.