Is life a matter of evolving chemistry?

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mjs
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is life a matter of constantly evolving chemistry?
 

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  • #2
Ygggdrasil
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Can you explain your question in more detail? I'm not quite sure what you're asking? Life is constantly evolving, and life is based on chemistry.
 
  • #3
mjs
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What is the difference between chemistry and biology (If any?)
 
  • #4
Hornbein
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What is the difference between chemistry and biology (If any?)

Biology is about living things. Chemistry is about both living and non-living things. Chemistry of living things only is ...<drum roll>... biochemistry.

So, what's the difference between biochemistry and biology? It is a matter of scale. The study of big structures like organs and bones is biology. The study of atoms, molecules, and cells is biochemistry. Tissues are sort of in between.

Atoms don't evolve, nor do basic molecules like water. More complicated molecules like DNA improved over time, so they evolved, as did cells, tissues, and organisms. I don't know that there is any room for DNA to improve any more, but it is hard to be sure about that.
 
  • #5
Ygggdrasil
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What is the difference between chemistry and biology (If any?)

I agree completely with @Hornbein's answer. Biology obeys all of the rules of physics and chemistry, so in theory, biology is just applied chemistry. However, biological systems are very complicated, with a huge diversity of molecules interacting in a very small, confined space. Although we've worked out the rules of chemistry for certain, much simpler systems, we don't have enough experience with systems exhibiting as much complexity as biological systems to be able to model them from physical and chemical principles alone (though efforts are being made to computantionally model simple organisms like bacteria).

What's the dividing line between a non-living bag of chemicals and a living bag of chemicals? These questions are questions that scientists who study abiogenesis (i.e. the origin of life) wish to address. This is very much still an active area of research where we don't understand the complete picture, but here are some previous PF discussions on the topic:
https://www.physicsforums.com/threads/what-gives-dna-replicating-ability.846493/#post-5310125
https://www.physicsforums.com/threads/a-question-about-natural-selection.743420/#post-4690960
 
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  • #6
mjs
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So you mean that biology maybe is very complicated chemistry that was selected?
And what about thermodynamics then?
 
  • #7
rootone
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Biology is the study of living things in general, biochemistry is a specialisation within the general field of biology which focuses very specifically on what is happening at the molecular level.
It turns out that biochemistry is almost exclusively about the chemistry of Carbon.
Carbon atoms have unique ways of bonding both with other carbon atoms, and to other commonplace atoms and substances such as water and nitrogen.
(A small amount of less commonplace elements such as calcium and phospherous play a part too).
The result is that there are millions of possible chemical reactions involving millions of possible carbon based molecules.
Some of these reactions have been harnessed by lifeforms for example as a way of gathering energy from sunlight.
No doubt that DNA and it's simpler cousin RNA are the crowning masterpeices of natural biochemistry though,
These long chains (sometimes rings) of carbon based molecules are responsible for reproduction.
They also encode information which leads to the building of proteins, and these proteins perform many tasks, for example they provide much of the building blocks from which the actual physical parts of a plant or animal are assembled.
 
  • #8
Feeble Wonk
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You're really asking a question regarding a classification of interaction, and scales of causative relationships. Yes... Biology breaks down (in a reductionist fashion) to chemistry. But chemistry similarly breaks down to physics. So, ultimately, biology is an application of physics.

But the relationships described in biology are an upper level of "emergent" behavior in complex systems. You'll have to look into the concepts of emergence to understand the differentiation. That will raise questions regarding the nature of causation in biological systems that some find both intriguing and perplexing. So, the effort might be worthwhile for you.
 
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  • #9
mjs
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Chemistry can indeed break down into physics. However there are difficulties into breaking down biology into (selected) complex organic chemistry, because there is a problem mainly with respect to thermodynamics and creation of order… But can we overcome this uncompatibility one day if really biology is a part of chemistry??
 
  • #10
jackmell
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is life a matter of constantly evolving chemistry?

Suppose we had only to work with that. First, consider the four basic properties of life:
(1) Containment,
(2) Replicate,
(3) Metabolize,
(4) Evolve.

Then as we know life, constantly evolving chemistry in an ocean would not be considered life as it's not contained (in a cell). The same holds for replication and metabolism. So no, life is not a matter of constantly evolving chemistry. Rather life is a "contained" chemical system capable of metabolism, replication, and evolution.
 
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  • #11
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However there are difficulties into breaking down biology into (selected) complex organic chemistry, because there is a problem mainly with respect to thermodynamics and creation of order
There is no such problem.
Every biological process increases total entropy. Usually in the form of produced heat from either chemical energy or sunlight, sometimes with more exotic energy sources (like radioactivity).

It is an interesting question how systems evolved that use low-entropy energy sources and high-entropy energy drains efficient enough to create some order, but this is a purely biological question, not a problem of thermodynamics.
 
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  • #12
Ygggdrasil
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Chemistry can indeed break down into physics. However there are difficulties into breaking down biology into (selected) complex organic chemistry, because there is a problem mainly with respect to thermodynamics and creation of order… But can we overcome this uncompatibility one day if really biology is a part of chemistry??
As mfb noted, biological systems locally create order but they increase the overall entropy of the universe because they are dissipating energy (e.g. using sunlight or burning food molecules). Along these lines, there are attempts to understand the theory of how the laws of thermodynamics would drive the evolution of life. Here's a news piece describing work by Jeremy England on the subject:
http://www.businessinsider.com/physicist-has-a-groundbreaking-idea-about-why-life-exists-2016-1?amp

Along with the corresponding discussion thread on PF:
https://www.physicsforums.com/threads/novel-idea-on-the-origin-of-life.851106/
 
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  • #13
jackmell
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As mfb noted, biological systems locally create order but they increase the overall entropy of the universe because they are dissipating energy (e.g. using sunlight or burning food molecules). Along these lines, there are attempts to understand the theory of how the laws of thermodynamics would drive the evolution of life. Here's a news piece describing work by Jeremy England on the subject:
http://www.businessinsider.com/physicist-has-a-groundbreaking-idea-about-why-life-exists-2016-1?amp

Along with the corresponding discussion thread on PF:
https://www.physicsforums.com/threads/novel-idea-on-the-origin-of-life.851106/

Is it still not possibly the underlying non-linear dynamics principally responsible for the emergence and evolution of life? I do recall Ygggdrasi, one particular thread here where you proposed if a suitable set of non-linear differential equation were set up appropriately, dynamics we ascribe to living systems could (or might) emerge. I am of that school: if you write the equations of mathematical physics on scraps of paper and throw them onto the kitchen floor, they won't get up and dance. But if the scraps of paper behaved in a sufficiently non-linear manner, I believe something resembling the properties we identify as "living" would emerge. :) Consider the work of Stuart Kaufmann and Camazine in "At Home in the Universe" and "Self-Organization in Biological Systems." Kauffman proposes that it was the dynamics of the primeval Earth that gave rise to life, and Camazine submits (non-linear) mathematical models to represent organization in biology. And therefore, in an effort to remain on topic, to answer the question posed by the thread author, some have suggested that life is not just a matter of evolving chemistry, but rather more fundamentally, of sufficiently-complex non-linear dynamics. Consider also the Brusselator: https://en.wikipedia.org/wiki/Brusselator. Interesting how a simple set of coupled non-linear PDEs, just by virtue of the intrinsic non-linear dynamics encoded in their couplings, can evolve spirals and dots from an initial random state: order emerges from chaos by virtue of dynamics.
 
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  • #14
Ygggdrasil
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Is it still not possibly the underlying non-linear dynamics principally responsible for the emergence and evolution of life? I do recall Ygggdrasi, one particular thread here where you proposed if a suitable set of non-linear differential equation were set up appropriately, dynamics we ascribe to living systems could (or might) emerge. I am of that school: if you write the equations of mathematical physics on scraps of paper and throw them onto the kitchen floor, they won't get up and dance. But if the scraps of paper behaved in a sufficiently non-linear manner, I believe something resembling the properties we identify as "living" would emerge. :) Consider the work of Stuart Kaufmann and Camazine in "At Home in the Universe" and "Self-Organization in Biological Systems." Kauffman proposes that it was the dynamics of the primeval Earth that gave rise to life, and Camazine submits (non-linear) mathematical models to represent organization in biology. And therefore, in an effort to remain on topic, to answer the question posed by the thread author, some have suggested that life is not just a matter of evolving chemistry, but rather more fundamentally, of sufficiently-complex non-linear dynamics. Consider also the Brusselator: https://en.wikipedia.org/wiki/Brusselator. Interesting how a simple set of coupled non-linear PDEs, just by virtue of the intrinsic non-linear dynamics encoded in their couplings, can evolve spirals and dots from an initial random state: order emerges from chaos by virtue of dynamics.

Yes, I would agree with this (the post you reference is here). Thinking of life as a large set of non-linear system of differential equations is not at odds with what England has proposed.
 
  • #15
mjs
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Questions:

a)How easy it is for these theoretical interpretations to be experimentally tested?

b)Entropic changes of life as a whole or at a local level are a-priori theoretical assumptions or are they backed by experimental evidence?
 
  • #16
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a)How easy it is for these theoretical interpretations to be experimentally tested?
Which theoretical interpretations do you mean?
b)Entropic changes of life as a whole or at a local level are a-priori theoretical assumptions or are they backed by experimental evidence?
Backed by millions of experiments. Trillions of experiments if you include "I made sports, now I am sweating".
In addition, the interactions of the components of life are studied in great detail. If a living object would violate thermodynamics, it would need some component that does so, and no such violation was observed ever. The fact that entropy is not reduced is more a mathematical statement than a physical one - and in mathematics you can prove things: you can prove that entropy cannot be reduced in a systematic way, no matter how the system looks like.
 
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  • #17
jackmell
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Questions:

a)How easy it is for these theoretical interpretations to be experimentally tested?

In the book, "Self-Organization in Biological Systems," Camazine and others construct among other many examples, a coupled set of three non-linear PDEs modeling the dynamics of termites during the construction of the marvelous clay cathedrals that they construct using three variables: termites, mud, and pheromone:

##\begin{align*}
\frac{\partial H}{\partial t}&=\epsilon M-k_2 M+D\nabla^2 H\\
\frac{\partial L}{\partial t}&=\phi-k_1 L+\mu \nabla^2 L-\gamma \nabla\left(L\nabla H\right) \\
\frac{\partial M}{\partial t}&=k_1 L-\epsilon M
\end{align*}
##
with ##H## being pheromone, ##M## mud, and ##L##, termites.

Aren't they beautiful! And one should keep in mind that the particular forms of the equations were not just "conveniently" constructed but rather formulated on the best reasonable analysis of how these three variables ACTUALLY interacted based on experimental data. But equally beautiful, out of a random initial state, "mounds" albeit simplified versions, emerge (the ##L\nabla H## is the non-linearity and since the equations are coupled, the entire system is non-linear). So that in the context of the thread topic, we see here some modicum of experimental evidence suggesting life is perhaps a little more than just chemistry but rather non-linear dynamics of complex systems.
 
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  • #18
mjs
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Which theoretical interpretations do you mean?Backed by millions of experiments. Trillions of experiments if you include "I made sports, now I am sweating".
In addition, the interactions of the components of life are studied in great detail. If a living object would violate thermodynamics, it would need some component that does so, and no such violation was observed ever. The fact that entropy is not reduced is more a mathematical statement than a physical one - and in mathematics you can prove things: you can prove that entropy cannot be reduced in a systematic way, no matter how the system looks like.

I am skeptical with assumptions like “oh, life sustains order, because for instance, a cell is much more ordered than its components, so life is about sustaining order and avoiding chaos” or things like that. I think that this is maybe not the whole picture, because we forget that a cell never exists in isolation. It’s a result of the other life that already exists.

Imagine you have a flask with water that is heated with fire. The molecules of water will start speeding randomly toward various directions. Virtually, what you are doing here with the cell argument is ignoring the fire and the majority of other water molecules and focusing only on 1 or 2 specific molecules. These molecules will be perceived as gaining speed without an obvious (or rational) reason,..


So the question is if entropy of life as a whole was ever directly or indirectly calculated (for instance indirectly through changes in heat production, or something like that?).

Or a man as he grows, starting from a baby and becoming an adult or an old man, does his entropy increase or decrease as he ages?
 
  • #19
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What does "entropy of life as a whole" even mean?
 
  • #20
Feeble Wonk
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There are many interesting ideas being discussed here. And yes, without question, functional causative relationships within complex dynamic systems (such as those frequently seen in biology/ecology) appear at times to decrease entropy in "localized" regions. However, unless you are prepared to argue that true "top-down" causation is achieved as an emergent phenomenon, then biology IS a complex manifestation of chemistry, which in turn, IS a complex manifestation of physics.
 
  • #21
AgentSmith
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Entropy can decrease locally if it increases globally. The increase in the entropy of the sun far exceeds the decrease caused by life on earth.
 
  • #22
Feeble Wonk
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Entropy can decrease locally if it increases globally. The increase in the entropy of the sun far exceeds the decrease caused by life on earth.

Exactly. That's why I said that life/biology/ecology "appears" to decrease entropy "locally"... while entropy is increased on a larger scale. That is essentially the basis of England's theory as well.
But, that doesn't directly address the OP's initial question, which was "Is life a matter of evolving chemistry?" My argument is that the answer to that issue comes down to a question of causation. If biological action can be reduced to the underlying chemistry, then the answer is yes. Though, that logic suggests that the chemistry is then further reduced to the underlying physics. In that sense, biological action/evolution is a deterministic process. Chaotic, yes. Unpredictable, yes. But still deterministic despite that.
IMHO, the only escape from that inevitability is if true, fundamental "top-down" causation emerges at the upper level of neurological development. It essentially comes down to a question of whether cognitive functions allow actual "free will". But that's a slippery slope of debate that slants toward the philosophical abyss.
 
  • #23
Ygggdrasil
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My argument is that the answer to that issue comes down to a question of causation. If biological action can be reduced to the underlying chemistry, then the answer is yes. Though, that logic suggests that the chemistry is then further reduced to the underlying physics. In that sense, biological action/evolution is a deterministic process. Chaotic, yes. Unpredictable, yes. But still deterministic despite that.

I don't think that reducing biology to chemistry and physics necessarily implies that biological systems are deterministic processes. Chemical reactions are inherently stochastic and only appear deterministic because of the law of large numbers. However, in biological systems, you are not dealing with large numbers (e.g. humans have only two copies of each gene), so this stochasticity can have important effects on biological systems. Here's a really beautiful paper from one of my colleagues describing how bacteria switch between two different phenotypic states based on the regulation of a specific set of genes. They are able to model the regulation of these genes in terms of the chemical reactions and molecular interactions involved (plus validate their model through experiments), and they show that a stochastic event is responsible for causing the bacteria to switch between the phenotypes. Thus, even though they can explain how the system work from chemical and physical principles, their theory and experiment demonstrate that the system is stochastic, not deterministic.

Here's the abstract of the paper and a citation:
By monitoring fluorescently labeled lactose permease with single-molecule sensitivity, we investigated the molecular mechanism of how an Escherichia coli cell with the lac operon switches from one phenotype to another. At intermediate inducer concentrations, a population of genetically identical cells exhibits two phenotypes: induced cells with highly fluorescent membranes and uninduced cells with a small number of membrane-bound permeases. We found that this basal-level expression results from partial dissociation of the tetrameric lactose repressor from one of its operators on looped DNA. In contrast, infrequent events of complete dissociation of the repressor from DNA result in large bursts of permease expression that trigger induction of the lac operon. Hence, a stochastic single-molecule event determines a cell's phenotype.
Choi, Cai, Frieda & Xie. 2008. A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell. Science 322: 442. http://dx.doi.org/10.1126/science.1161427
freely available version
 
  • #24
Feeble Wonk
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"...even though they can explain how the system work from chemical and physical principles, their theory and experiment demonstrate that the system is stochastic, not deterministic.
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Actually, I might argue that the stochastic appearance is due to the large numbers of events being observed. Yet, for any given event, the submolecular activity that drives the process is a deterministic chemical reaction. I recognize that this is a LaPlacian argument, and is vulnerable to various stochastic interpretations of quantum mechanics. Regardless, it still leaves the resultant biological activity as being describable in terms of the underlying physics unless "top-down" causation is achieved.
 
  • #25
Monsterboy
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Can abiogenesis be solved using second law of thermodynamics ?
https://www.quantamagazine.org/20140122-a-new-physics-theory-of-life/
In the book "What is life?" written by Erwin Schrödinger ,it is explained that the physical laws are only statistical in nature hence the behavior of very few molecules cannot be predicated by the laws ,since abiogenesis is about finding the smallest set of self replicating molecules ,the laws are not applicable here ?
 
  • #26
Feeble Wonk
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Can abiogenesis be solved using second law of thermodynamics ?
https://www.quantamagazine.org/20140122-a-new-physics-theory-of-life/
In the book "What is life?" written by Erwin Schrödinger ,it is explained that the physical laws are only statistical in nature hence the behavior of very few molecules cannot be predicated by the laws ,since abiogenesis is about finding the smallest set of self replicating molecules ,the laws are not applicable here ?

Again, that depends on which interpretation of quantum mechanics one chooses. There certainly are stochastic interpretations, as well as overtly deterministic versions. There are interpretations that posit an ontological reality to the quantum wave function, and others that consider it merely a useful mathematical tool. However, regardless of which interpretation you choose, initial abiogenesis occurred with a specific chemical reaction driven by physical processes extant at that time. Dynamic biological systems have evolved since that time still being driven by those same physical processes which are describable by the underlying physics.
And yet, there are other interpretations of quantum physics that stipulate the need for "conscious" observation to produce "collapse" into a realized quantum state. These interpretations have admittedly fallen out of favor as the concept of environmentally induced collapse secondary to quantum decoherence has been developed, but there are still adherents to the idea even within the physics community. It would seem that that interpretation might offer a road to "top-down" causation, which would change the nature of the argument entirely. But, again, that discussion leads dangerously close to philosophy.
 
  • #27
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If biological action can be reduced to the underlying chemistry, then the answer is yes. Though, that logic suggests that the chemistry is then further reduced to the underlying physics.
That is possible by definition. If life would include features that violate the established laws of physics, then those laws would be wrong, and physicists would have to study what exactly leads to the violations in order to fix the laws. The same applies to chemistry as intermediate step, although some things are part of biology and physics, but not chemistry (e. g. optics in eyes).
 
  • #28
Feeble Wonk
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That is possible by definition. If life would include features that violate the established laws of physics, then those laws would be wrong, and physicists would have to study what exactly leads to the violations in order to fix the laws. The same applies to chemistry as intermediate step, although some things are part of biology and physics, but not chemistry (e. g. optics in eyes).

I suppose this is true, but I'm not aware of any features of life that do not obey the laws of physics. But, if any such features are found it would simply indicate that the laws of physics would need to be adjusted accordingly... as you said. In that case, the adjusted laws of physics would dictate biological activity. It eventually still comes down to a question of causation.
 
  • #29
Dr. Courtney
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In principle, biology is just applied chemistry, and chemistry is just applied physics. So why doesn't it all come down to solving the Schrodinger equation and other fundamental laws of physics?

In practice, we don't know how to actually solve the Schrodinger equation with available computing power for systems any more complicated than relatively simple molecules. Consequently, biology and chemistry take phenomenological approaches that hypothesize applicable natural laws other than the fundamental laws of physics.

This doesn't mean that each discipline does not have a subset of phenomena that can be explained by the laws of the more fundamental discipline. It means that chemistry and biology have many phenomena that are not adequately explained by the predictive power of physics and chemistry, respectively.
 
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  • #30
Feeble Wonk
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In principle, biology is just applied chemistry, and chemistry is just applied physics. So why doesn't it all come down to solving the Schrodinger equation and other fundamental laws of physics?

In practice, we don't know how to actually solve the Schrodinger equation with available computing power for systems any more complicated than relatively simple molecules. Consequently, biology and chemistry take phenomenological approaches that hypothesize applicable natural laws other than the fundamental laws of physics.

This doesn't mean that each discipline does not have a subset of phenomena that can be explained by the laws of the more fundamental discipline. It means that chemistry and biology have many phenomena that are not adequately explained by the predictive power of physics and chemistry, respectively.

Absolutely agreed. The operative word here is "predictive". As I conceded in post #22, biological systems are very complex, chaotic, and unpredictable. And yes, there are emergent properties/behaviors that could not be predicted from the known underlying physics, due to both ignorance and insufficient computing power. Yes, these properties and behaviors are well worth study in their own right. Absolutely.

Yet, unpredictability does not equate to indeterminate. The emergent biological activity is still a manifestation of the underlying physics, UNLESS top-down causation occurs.
 
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  • #31
mjs
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Complex chemistry, and especially organic chemistry with the myriads possible combinations of isoforms, if sustained for a long time, theoretically in the long term only those reactions that sustain themselves will prevail and will be in the final mixture. But what is life other that a sum of self-sustaining chemical systems??

However, things are not so easy, because in the first case there would usually be not so many local decreases of entropy in the long term.

Biology on the other hand, is based on the concept that in the beginning there was a primordial soup that became a system of ordered creatures…so the entropy of life as a unique entity decreased over time. Although I am not sure that experiments, if performed, would truly verify this, I think that this is the basic thing that lies in the core of what separates biology from chemistry.
 
  • #32
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so the entropy of life as a unique entity
That is not a well-defined thing. Entropy is a property of systems, and comparing the entropy of completely different systems is meaningless.
 
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  • #33
Feeble Wonk
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Biology on the other hand, is based on the concept that in the beginning there was a primordial soup that became a system of ordered creatures…so the entropy of life as a unique entity decreased over time. Although I am not sure that experiments, if performed, would truly verify this, I think that this is the basic thing that lies in the core of what separates biology from chemistry.

That is not a well-defined thing. Entropy is a property of systems, and comparing the entropy of completely different systems is meaningless.

The point to keep in mind here, I believe, is that the "entropy of life" is really just a subset of physical entropy. And, as we said before, entropy is only decreased in a localized region, while it is correspondingly increased overall when one considers the entire thermal system. And again, that changes nothing with regard to bottom-up causation.
 
  • #34
mjs
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That is not a well-defined thing. Entropy is a property of systems, and comparing the entropy of completely different systems is meaningless.
A cell as a system has intrinsic entropy, right? However, cells never emerge or exist in isolation. They are a part of a larger system that includes all other cells, plus anything living (altogether called “life as whole”). This larger system has some intrinsic energy too…It's like a flask of water. A single water molecule belongs in a larger system that includes all other water molecules in the flask. Why is it any different with living material since from the beginning they all started together?
 
  • #35
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A cell as a system has intrinsic entropy, right?
Yes, and you can compare this to a random arrangement of the same atoms in the same space, for example. Then the cell will have a lower entropy.
They are a part of a larger system that includes all other cells, plus anything living (altogether called “life as whole”). This larger system has some intrinsic energy too
Earth in total? Which is still not an isolated system...
The entropy of Earth is dominated by the temperature of its interior, so I would expect it to go down over time.
 

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