Thoughts on the Existence of the Universe

[u196533]

Statistical physics of self-replication
It saw the relation, but not the direct relevance.  Did I miss something? (It did kinda make my eyes cross.)

[Hakurei Reimu]

I understand that within a system some elements can release energy and increase energy while others can do the reverse.  That’s how energetic molecules such as ATP are created.  In a Goldilock’s environment, it is certainly possible for molecules to “ratchet up” their energy and lose entropy.

It doesn't have to be a "Goldilocks environment". This sort of thing is quite common.

You also talk about entropy as if its a property of the substance itself instead of being a state function of the system. This is a huge conceptual error in regarding entropy, and it makes all the difference between your naive understanding of entropy and a proper understanding of entropy.

Let's say that there's a mixture of ADP and phosphate ions in equal proprotions, and we divide the space this mixture exists in into a number of partitions. What can we say about the distribution of ATP in this mixture? Well, there's no ATP in the mixture, so you can say something quite definite about the distribution: there is but one possible state the system can be in (regarding only the ATP) â€" all partitions are empty of ATP. But as soon as you introduce an ATP molecule into the system (by combining an ADP and phosphate ion together), you get a huge explosion in the possible states of the system â€" because you have now added a new chemical species to the available states; there is now a molecule of ATP to be in one partition. In practical terms, this easily offests any reduction in entropy of the system due to the absorption of energy in the ADP + PO4 -> ATP reaction.

As we add more ATP, the number of possibilities grow, and each additional ATP molecule will continue to correspond to more entropy in the system than the ADP+PO4 contributed. Up to a point. After that point, converting an ADP to ATP no longer contributes more entropy to the system. It is this point that is the true equilibrium state of the system.

In short, the entropy of adding a single molecule of a chemical species depends on the system, and will even change as you add more molecules (by whatever means). The "entropy of a single chemical" is thermodynamic nonsense. Chemicals do not have an entropy. Only systems can have entropy.

And notice what I didn't do here: state how long this process will take. This is because you cannot derive from entropic principles the rate at which these reactions will occur. It could take miliseconds, or thousands of years, depending on the system in question.

However over time, as they move further from equilibrium they become unstable (like nucleic acids).  They will breakdown and release their energy as soon activation energy is reached.

And what makes you think that the "equilibrium state" for nucleic acids is single bases? You have no basis for this assumption whatsoever. While there is always the possibility for breakup of a nucleotide chain, there is also the possibility of two chains combining when they meet up (the energy coming from their thermal motion). Therefore it is not enough to say, "They will breakdown and release their energy as soon activation energy is reached," because that assumes that the reverse process will never happen. But they do, even randomly with no enzymes to catalyze them. Thus the question becomes "which process is faster," which you cannot derive from first principles.

For a concrete example, individual molecules of acids in solution exist in equilibrium with their conjugate bases and single protons. In fact, it is vital to the behavior of acids that they constantly disassociate and then recombine when in solution. This is what pH measures: the concentration (in negative powers of 10) of disassociated protons (actually, hydronium ions) in solution. For weak acids, it's not much â€" the number of intact acid molecules far outnumber the disassociated conjugate base molecules and hydronium ions, because that is the energetically favored state â€" but they are present. They are present because it is that concentration of ions that is the true thermodynamic equilibrium.

It is not conceivable for a process to continue to increase the energy and decrease the energy of a molecule for millions of years in an uncontrolled environment.

Again, you talk of the entropy of a molecule instead of a system. See the first section. Entropy does not apply to single molecules.

At some point in the process of abiogensis, self-preservation had to have developed in those molecules if that occurred.   

This "self-preservation" is nothing more than "the molecules' rate of formation outpaces their rate of destruction."

No, living organisms don't defy the "basic drives" (laws) of chemistry and thermodynamics.
I said defy, not violate.

If they don't violate the laws of thermodynamics, then the laws don't care. You are making a distinction without a difference. "Defy" doesn't mean a damn thing here. It's simply contrary to your flawed understanding of entropy, as if that meant anything at all.

There is nothing that prevents living things from seeking energy to maintain our low entropy.  Living things are able to defy the drive toward equilibrium (lower energy and higher entropy) via self-preservation.

Again, using the word "defy" as if it means a damn thing when it doesn't. As long as the system (the living organism and its surroundings) is increasing entropy overall, the second law of thermodynamics doesn't give a fuck what's going on in detail. Decreasing the entropy of a system is absolutely forbidden, and when a living organism runs afoul of this, it dies. How is any of this "defying" the laws of thermodynamics? It's not. What the living organism does is completely within the bounds of thermodynamics.

I am talking about pre-biotic molecules, and I don’t think self-preservation can be explained in simple chemicals.

Again, "self-preservation" in the context of chemicals means nothing more than "the chemicals' rate of formation outpaces their rate of destruction."

It is demonstrably false that you will decay as soon as your energy input is cut off, as indicated by the fact that you can preserve food (or people) in a fridge or by drying them out, and will keep for a very long time (thousands of years) provided you keep them cold or dry.
Soon after we die, the cellular machinery decomposes.  The unstable molecules such as ATP breakdown, enzymes normally used as catalysts breakdown other molecules etc.  Bacteria certainly completes decomposition, but once you cut of the energy supply, cells breakdown.

While there is some breakdown, it is not as much as you think. Because ATP drives basically all celular machinery, it gets depleted because the biochemistry doesn't know better. And enzymes will continue to break down their ligases as long as there are some available. However, eventually the enzymes run out of their ligases, and the ATP depletes and everything stops, and sans bacteria most of your biomolecules will remain more or less intact for much, much longer than the decay of a corpse out in the open would take. The bacteria (and other scavengers) which you state "completes decomposition" â€"as if they were latecomers to the partyâ€" are actually the heavy lifters in decomposition in the real world. The evidence of this are the mummies of the world, both natural and artificial. They can survive thousands of years in the proper conditions. Some specimens can even be eaten. And when their preservation is compromised, natural decay takes over and specimens that survived thousands of years intact deteriorate on the order of years to decades, as has happened in some cases to Egyptian mummies.

Statistical physics of self-replication
It saw the relation, but not the direct relevance.  Did I miss something? (It did kinda make my eyes cross.)

And you laughably say that you are "familiar with the thermodynamic dissipation theory"! This basically says it all.

[Baruch]

This ...

"This "self-preservation" is nothing more than "the molecules' rate of formation outpaces their rate of destruction.""

In complicated chemical situations this can happen, it can also happen that the rate of destruction is greater.  Disequilibria is a teeter-totter.

Vitalism isn't scientific ... it can't be.  But one does have to ignore the elephant in the room ... that reductionism is no panacea, however useful it might be.

[u196533]

One of the reasons for our disagreement is that you are using the Boltzman statistical definition of entropy, which is a dimensionless value, using micro states.  There are some who contest the validity of that approach so I use the classic definition of heat disbursement, Q/T measured in Joules/degree. The classic definition is mathematically derived and therefore unequivocal.  I don’t have an issue with the Boltman view, but I can understand that is can be more easily misapplied and described as disorder. 

The "entropy of a single chemical" is thermodynamic nonsense. Chemicals do not have an entropy. Only systems can have entropy.
This is simply not true.  One of the advantages of using the classical definition of entropy (beside the fact that it is irrefutable), is that it can be empirically measured.  A quick google search uncovered these tables.  If you read the articles you’ll see the author describing how different folds and structures raise or lower the entropy associated with the molecule.
http://home.uchicago.edu/~jvieregg/pubs/EAC_review.pdf

(It didn't paste well and I'm not sure how to paste an image here.)
Table 2 Nearest-neighbor parameters for base pairing of RNA duplexes, including free energy change at 37 °
C. Sequences are presented as 5-XY-3
for the top row paired to 3
ZW-5
on the bottom. For comparison, the free energy penalty for forming a hairpin, internal, or bulge loop at 37 °
C is 4â€"6 kcal molâˆ'1 minus the free energy of forming the closing base pair. Data from Xia et al.(22)
Sequence GC GG CG GA GU CA CU UA AU AACG CC GC CU CA GU GA AU UA UU

H° (kcal molâˆ'1) âˆ'14.9 âˆ'13.4 âˆ'10.6 âˆ'12.4 âˆ'11.4 âˆ'10.4 âˆ'10.5 âˆ'7.7 âˆ'9.4 âˆ'6.8

S° (cal (mol·K)âˆ'1) âˆ'36.9 âˆ'32.7 âˆ'26.7 âˆ'32.5 âˆ'29.5 âˆ'26.9 âˆ'27.1 âˆ'20.5 âˆ'26.7 âˆ'19.0

G°37 (kcal molâˆ'1) âˆ'3.42 âˆ'3.26 âˆ'2.36 âˆ'2.35 âˆ'2.24 âˆ'2.11 âˆ'2.08 âˆ'1.33 âˆ'1.10 âˆ'0.93


http://csb.stanford.edu/levitt/Levitt_CIBA72_Folding_Nucleic_Acids.pdf
See table on page 7 for another table of entropy associated with DNA strands.


And you laughably say that you are "familiar with the thermodynamic dissipation theory"!   This basically says it all.
You clearly did not read the article.  The dispersal theory basically states that matter will self-organize in order to disburse energy.  The basic takeaway from this article for me was: "In other words, basic thermodynamic constraints derived from exact considerations in statistical physics tell us that a self-replicator's maximum potential fitness is set by how effectively it exploits sources of energy in its environment to catalyze its own reproduction. Thus, the empirical, biological fact that reproductive fitness is intimately linked to efficient metabolism now has a clear and simple basis in physics.”   The author proved that an empirical observation was based in physics.  I didn’t see a direct relevance to our current discussion.

This is because you cannot derive from entropic principles the rate at which these reactions will occur.
Actually the Gibbs free energy equation can be used to determine the relative rates of reaction. The lower the value, the faster the reaction will proceed.

One source for the statement that nucleic acids are unstable:
http://nar.oxfordjournals.org/content/early/2014/07/09/nar.gku499.full
Nucleic acids are not stable in aqueous solutions at ambient temperatures for long periods (several days to 1 month) (21) because of degradation by contaminating nucleases (22) and because of inherent chemical instability.

The other article provided (Thermodynamic dissipation theory for the origin of life) provides a theory that starts from DNA on the ocean surface.  (If you can describe how the DNA got there, you’d convert me.)
Some excerpts from it:
“For example, the second difficulty mentioned by Orgel (2004), the polymerization of polynucleotide from mononucleotides is an endergonic reaction (positive free energy change) which will not proceed spontaneously”

“At temperatures above 90 ◦C (at one atmosphere and pH 7), almost all of double strand RNA or DNA is denatured into flexible single strands (Haggis, 1974).”

“A central problem with all theories on the origin of life has been the difficulty in demonstrating efficient abiogenic reaction pathways for producing high yields of the primary molecules of life (Orgel, 2004). High yields are important since the half-lives of these molecules are relatively short at high temperature, on the order of hours for ribose, and years or days for nucleic acid bases (t1/2 for A and G ≈ 1 yr; U ≈ 12 yr; C ≈ 19 days at 100 ◦C; Levy and Miller, 1998). Many of these molecules require chemical reactions which are “uphill”, corresponding to overall positive changes in the Gibb’s free energy, while others have large activation barriers that require special enzymes in order to proceed”

Back to the basic premise:  Life exists in a low state of entropy far from equilibrium, and the path from replicator molecule to life is thermodynamically uphill.  You haven’t said anything to contest that.
There is still no attempt at explaining self-preservation in primitive life.

[trdsf]

Since this problem is sidestepped and ignored, I can't imagine it ever being explained.

And this is explicitly the ID/creationist fallacy.  Just because you can't imagine it being explained, no human being now or ever existing possibly can?

I'm sorry, I do not accept that you personally are the cleverest, most intelligent, most insightful researcher that can conceivably exist.

[widdershins]

I learned recently that, although the universe is about 14 1/2 billion years old, the Cosmic Background Radiation is about 46 billion light years away in every direction, so, that made me think about the existence of the universe.  I also learned that, although nothing can go faster than the speed of light, the furthest galaxies from us are traveling away at faster than the speed of light, WITHOUT breaking this barrier.  That also made me think about the existence of the universe.

In case you don't know, both of those things are the result of space expanding faster than the speed of light, not any physical material traveling at faster than the speed of light.

[trdsf]

I learned recently that, although the universe is about 14 1/2 billion years old, the Cosmic Background Radiation is about 46 billion light years away in every direction, so, that made me think about the existence of the universe.  I also learned that, although nothing can go faster than the speed of light, the furthest galaxies from us are traveling away at faster than the speed of light, WITHOUT breaking this barrier.  That also made me think about the existence of the universe.

In case you don't know, both of those things are the result of space expanding faster than the speed of light, not any physical material traveling at faster than the speed of light.

Yeah, that's a hard one to get one's brain around, the concept of the 'comoving distance'.  I think it's the idea of where things would be, if you were able to step back from the universe and see all points at the same cosmological age -- as opposed to what we see when we look out, and see objects at a different (younger) cosmological age than we are.

The expansion of space, of course, is not limited to the speed of light, even under general relativity, because that's not a physical object.  It's the geometry in which events occur.

[Hakurei Reimu]

Kinda late to say anything, but:

One of the reasons for our disagreement is that you are using the Boltzman statistical definition of entropy, which is a dimensionless value, using micro states.

Wrong.

S = k log W

See that 'k' term? That's Boltzmann's constant. It has dimensions of energy/temperature. Specifically, 1.38065 × 10^âˆ'23 Joules/Kelvin. You derive the classical definition from Boltzmann's statistical defintion through statistical mechanics. There is a one-to-one correspondance between Boltzmann's defintion and the classical one.

Basically, this happens whenever one tries to use google as a substitute for a real education. You miss the solid foundation upon which all the theory you're trying to use is based upon. When I say that "the entropy of a single chemical is thermodynamic nonsense," everyone with a solid foundation in a subject will agree. Thing is, in the real world all of these chemicals exist inside of systems, so you can say how the entropy of that system changes when you diddle with the chemicals. All of Mr. U's errors come from this very simple fact.

[reasonist]

https://www.youtube.com/watch?v=JiyrRbYNm0Q