mjs
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is life a matter of constantly evolving chemistry?
mjs said:What is the difference between chemistry and biology (If any?)
mjs said:What is the difference between chemistry and biology (If any?)
mjs said:is life a matter of constantly evolving chemistry?
There is no such problem.mjs said: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
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:mjs said: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??
Ygggdrasil said: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/
jackmell said: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.
Which theoretical interpretations do you mean?mjs said:a)How easy it is for these theoretical interpretations to be experimentally tested?
Backed by millions of experiments. Trillions of experiments if you include "I made sports, now I am sweating".mjs said: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?
mjs said:Questions:
a)How easy it is for these theoretical interpretations to be experimentally tested?
mfb said: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.
AgentSmith said: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.
Feeble Wonk said: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.
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.1161427By 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.
Ygggdrasil said:"...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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Monsterboy said: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 ?
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).Feeble Wonk said: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.
mfb said: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).
Dr. Courtney said: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.
That is not a well-defined thing. Entropy is a property of systems, and comparing the entropy of completely different systems is meaningless.mjs said:so the entropy of life as a unique entity
mjs said: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.
mfb said: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?mfb said:That is not a well-defined thing. Entropy is a property of systems, and comparing the entropy of completely different systems is meaningless.
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.mjs said:A cell as a system has intrinsic entropy, right?
Earth in total? Which is still not an isolated system...mjs said: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
No! A system that only includes the sum of living cells. It is not an isolated system, but can it have entropy anyway? Is this entropy increasing or decreasing over time? If increasing, isn't this a sign that biology is indeed very close to chemistry?mfb said:.Earth in total? Which is still not an isolated system...
Did you mean to say that the larger system has "some intrinsic ENTROPY too..."? If so, then the answer is definitely yes. And yes, the entropy of a living cell is definitely lower than "a random arrangement of the same atoms in the same space" as mfb said.mjs said: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…
Though again, throughout the entire thermal environment of the cell (or entire thermal environment of life in general), the entropy will increase overall.mfb said:Yes, and you can compare this to a random arrangement of the same atoms in the same space, for example.
You can assign an entropy to it, yes.mjs said:No! A system that only includes the sum of living cells. It is not an isolated system, but can it have entropy anyway?
To a very good approximation, the entropy is proportional to the total biomass, details of the structure do not matter much. Is the total biomass increasing? I don't know, but is that really what you want to figure out?mjs said:Is this entropy increasing or decreasing over time?
No. It is a sign that the biomass is increasing.mjs said:If increasing, isn't this a sign that biology is indeed very close to chemistry?
You're getting pretty deep into the concept of entropy here, and there are some complicating issues. You've designated a "system that ONLY includes the sum of living cells", but then suggested that it's not an isolated system... which it must be by definition. But, I'd argue that your general logic seems to be on the right track. At least in the sense that when assessing the "entropy of life as a whole", you've got to look at the universal extent of the system... all incoming information contributing to the formation and processes of life, and all outgoing information (including infrared radiation). Entropy for the entire thermal system will increase over time, demonstrating the causal arrow of time.mjs said:No! A system that only includes the sum of living cells. It is not an isolated system, but can it have entropy anyway? Is this entropy increasing or decreasing over time? If increasing, isn't this a sign that biology is indeed very close to chemistry?
Quite possibly. If so, I'm definitely guilty of biting. I guess I took him/her at face value in a "Is that really all there is to it?" kind of way. I was trying to offer a potential escape from the suggested existential angst without sliding down the philosophical rabbit hole.ogg said:Isn't the OP a troll?
You're absolutely right, of course. The differentiation between the disciplines is simply a question of semantics and logistical categorization. It's only relevant from a bigger picture, philosophical perspective that is not appropriate for this forum.ogg said:So, as said: Biology is Chemistry (and Physics - unless organisms don't require the application of mechanical force) APPLIED to a very particular set of conditions.
I suppose that's true with respect to the biological/ecological "Darwinian" type of evolution. I was thinking more in terms of the physical evolution of the unitary quantum wave function. This is obviously where the philosophical issues involving various interpretations of quantum mechanics come into play, but again are not appropriate for this forum.ogg said:Chemistry, Biology and (as far as we know) Physics do not "evolve". Living systems do...
It is called a "strand" because there are bonds between its elements (via deoxyribose and a phosphate group).Bob10 said:There is of course a hydrogen bond across the strand but no bond between the linear arrangement on one strand.
there are bonds between its elements (via deoxyribose and a phosphate group).[/QUOTE] I agree with this. But correct me if I'm wrong, There is no bond between the bases one the single strand that is being translated. The bases AGCT could be substituted with any other base. For instance if the sequence was ATGGTACG there is no chemical attraction between AT TA GG for example. But it is precisely this sequence that determines the structure and therefore functionality of a protein or RNA. Maybe I'm wrong but in order to explain life you have to explain how these sequences of bases organized to produce thousands of proteins hundreds of amino acids long plus the regulatory RNA that goes with it. It can't be chemistry because there is no bond between the bases to allow DNA to chemically organize. The bond between deoxyribose and the phosphate has no bearing on which base attaches. Thanks for your reply.mfb said:Everything in the DNA depends on the laws of chemistry.It is called a "strand" because there are bonds between its elements (via deoxyribose and a phosphate group).
Not a direct one, but that comes from our arbitrary naming of DNA parts. Group the base with the sugar and the phosphate group to something called "DNA component", and you have direct bonds between the DNA components.Bob10 said:There is no bond between the bases one the single strand that is being translated.
They are all bound together in a string.Bob10 said:For instance if the sequence was ATGGTACG there is no chemical attraction between AT TA GG for example.
Bob10 said:But correct me if I'm wrong, There is no bond between the bases one the single strand that is being translated. The bases AGCT could be substituted with any other base.
Bob10 said:For instance if the sequence was ATGGTACG there is no chemical attraction between AT TA GG for example.
Bob10 said:It can't be chemistry because there is no bond between the bases to allow DNA to chemically organize. The bond between deoxyribose and the phosphate has no bearing on which base attaches. Thanks for your reply.
I don't agree. I think there are many practical and theoretical implications behind this categorization (e.g. biological experiments, medicine, theories about the origin of life, etc). Think about it..Feeble Wonk said:The differentiation between the disciplines is simply a question of semantics and logistical categorization.
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Its not that simple. Darwinism is a concept with wider implications. The general idea is that in any complex interacting non equillibrium system, in the long term only the more sustainable systems will prevail and thus, be selected in a way and exist in the final mixture. Literally Darwinism applies in almost all complex non-equillibrium systems (e.g. struggle between gut bacteria, cancer cell heterogeneity and growth, complex organic chemical reactions, even Wall Street, Bussiness Companies, etc).ogg said:Chemistry, Biology and (as far as we know) Physics do not "evolve". Living systems do (in the limit of small (or no) changes to their environment (small perturbations from "homeostasis" and "stable" poplulations).)
Bob10 said:I agree with this. But correct me if I'm wrong, There is no bond between the bases one the single strand that is being translated. The bases AGCT could be substituted with any other base. For instance if the sequence was ATGGTACG there is no chemical attraction between AT TA GG for example. But it is precisely this sequence that determines the structure and therefore functionality of a protein or RNA. Maybe I'm wrong but in order to explain life you have to explain how these sequences of bases organized to produce thousands of proteins hundreds of amino acids long plus the regulatory RNA that goes with it. It can't be chemistry because there is no bond between the bases to allow DNA to chemically organize. The bond between deoxyribose and the phosphate has no bearing on which base attaches. Thanks for your reply.
Bob10 said:Therefore I propose that chemistry is the software that runs the program but there is more to the story. In order to explain life one needs to explain the massive amount of information in the DNA molecule...
I'm not sure what you see as the practical and theoretical implications of this issue. Can you clarify that for me?mjs said:I don't agree. I think there are many practical and theoretical implications behind this categorization (e.g. biological experiments, medicine, theories about the origin of life, etc). Think about it..