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What constitutes Life?


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Do you have support for those claims HB? (particularly the long term vs. short term memory entropy claim)

 

Memory creates a physical state within the brain that records things. Short term memory does not last as long as long term memory. Regardless of the mechanism for this difference, the lose of structural integrity of short term memory, faster than long term memory implies it defines higher entropy (as a function of time). Short term breaks down easier and increases entropy quickly.

 

I would like to change direction and look at energy as a function of life and nature. Nature seeks lowest energy, while life is able to increase its energy value. By energy value, I am talking in terms of calorimetric value. We can burn a tree because the tree has stored energy within wood. The energy that plants create is used by animals, with their own cells growing and dividing, with each generation accumulating reduced C and N. This is increasing their calorimetric energy value.

 

I would like look at ATP.

 

ATP is the main energy transfer molecule within the cell. If we conceptually cut the ATP molecule into two, triphosphate (TP) and adenosine (A) and burned both halves in a calorimeter, the bulk of the released energy will be in the adenosine. Yet within the cell, the energy available for work is within the triphosphate end. It is a very slick design which makes evolving life possible.

 

The triphosphate end is an electron acceptor, while the A end is an electron donor. The energy that life accumulates is contained within electron donors, such as all the reduced materials which which can be burned. They feed electrons to O2 and give off energy in the process. Because the usable energy of ATP, within the cell, is based on an electron acceptor, ATP is actually connected to the nature side of the energy balance. In a loose sense, the potential in ATP and O2 are similar, since both are electron acceptors. ATP is sort of the mini-me of O2.

 

Life is accumulating energy value within its many reduce materials, including enzymes. We can burn them or metabolized them. ATP is loosely analogous to sparks that come from the nature side the metabolic combustion, which is causing electrons to drop in energy toward O2. Like O2, the goal of ATP is also natural, and is to lower the energy value of reduce materials. But its ability is limited to a dangling -OH group. Once we attach the terminal phosphate, the enzyme will lose electron density to the P and release energy. Also with the phosphate attached, pound for pound, the enzyme has lost caloric energy value. Luckily, the phosphate is usually released, increasing energy again.

 

If look at an enzyme, with the ATP spark trying to burn it, the energy release, is about that of hydrogen bonding. This is not quite enough to damage its covalent bonds. This provides energy that can increase the entropy within the enzyme, since entropy increase needs to absorb energy. Nature has the enzyme exactly where she wants is, lower energy and higher entropy. But life seeks higher energy and lower entropy, reversing the process again and again, using the various steps for catalytic activity.

 

What is slick about ATP, being on nature's side, as life gains energy value and lowers entropy, the potential to the ATP keeps on rising. ATP then tries to burn enzymes at higher and higher rates. Enzymes play an important role for life, because they are designed to absorb the burn, caused by the spark, recycle, and use the energy-entropy shifts to gain even more energy value for the cell, etc.

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No, Rade, life is never self initiated:)

If we look at an enzyme is a very general way, its specificity is often represented using a lock and key analogy. The key is a specific molecule or part of a molecule, that attaches in a very specific way. This unlocks the enzyme, causing some enzymatic affect. Modern enzymes are analogous to modern laser etched lock and keys sets, with the enzymatic effect at low entropy.

 

Let us go the other way, and look at a hypothetical enzyme with higher entropy of activity, more like an old fashion skeleton key and a crude lock. Since life is moving toward lower entropy, this crude lock and key set would analogous to something in the past with respect to evolution.

 

Instead of the laser cut key being a very specific molecule or part of a molecule in a very specific orientation, the skeleton key is not so fussy and can be any close molecule in roughly the correct position. Once the lock opens, instead of a very specific reaction at a very specific bond, even in 3-D stereo space, because the key fits loosely in the lock, our crude key has wiggle room, also allowing the possibility of different bonds being affected by the enzyme. If we plotted the input and the output from this high entropy enzyme, each could be defined by a probability function. As we lower entropy of the enzymatic activity, the probability function gets narrower leading to modern laser cut lock and keys.

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The monomers of RNA and DNA are nucleotides. These are composed of any one of the hydrogen bonding bases, a five carbon sugar and a tri-phosphate. Although the calorimetric energy lies within the sugar and bases, the energy used to make the DNA is connected to the triphosphate which is an electron acceptor. Like ATP, all the monomers of RNA and DNA are analogous to other mini- me's of O2, or the natural side of the potential.

 

What this suggests are the enzyme complexes, which assist the formation of RNA and DNA, are the actual target of the nucleotides. Like any high energy enzyme, nucleotides, like ATP, are used to try to lower their energy. The natural side of the potential uses all these mini-me's to lower the energy of the complex, with the enzyme complex designed to be sturdy, turning the energy-entropy shift around to form RNA and DNA.

 

These enzyme complexes for making RNA and DNA are not exactly laser cut lock and key sets with only one key, like many enzymes, since they are capable of using four different nucleotide keys. The only rough constraint is connected to proper base pairing which define the lowest entropy. But being an older lock set, the design allows wiggle room in the lock allowing those genetic defects which help increase the natural genetic entropy used for evolution. This suggest these lock and key sets evolved early, when skeleton lock and keys was the rule among enzymes.

 

An interesting conceptual extrapolation is what would happen if these enzyme complexes lowered entropy so there is only one key. Instead of one complex, this would imply four complexes needed to make RNA or DNA, with each set made with with laser precision, causing the DNA to copied almost perfectly.

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I remember a definition of life, given by Ilya Prigogine, as a "dissipative system far from equilibrium"... I never saw it discussed so I cant decide how relevant it is for the discussion... Perhaps you can clarify a little for us not exposed to much chemistry :)

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