Is life a matter of evolving chemistry?

[mjs]

.Earth in total? Which is still not an isolated system...

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?

 

[Feeble Wonk]

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…

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.

Yes, and you can compare this to a random arrangement of the same atoms in the same space, for example.

Though again, throughout the entire thermal environment of the cell (or entire thermal environment of life in general), the entropy will increase overall.
But the implication seems to have been that since life appears to create a LOCALIZED decrease in entropy, biology is somehow different from, and supersedes, the underlying chemistry and/or physics. This is not the case. Again, the only thing that would demonstrate that would be if fundamental "top-down" causation is achieved through biological/neurological function.

 

[mfb]

No! A system that only includes the sum of living cells. It is not an isolated system, but can it have entropy anyway?

You can assign an entropy to it, yes.

Is this entropy increasing or decreasing over time?

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?

If increasing, isn't this a sign that biology is indeed very close to chemistry?

No. It is a sign that the biomass is increasing.

 

[Feeble Wonk]

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?

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.
Returning once again to the initial question posed by the OP... Is biology just evolving chemistry? It still comes down to a question of that causation. Regardless of how complex, chaotic and unpredictable the underlying reductionistic physical process is, if bottom-up causation is the determining mechanism, then the answer must be YES. Biology is just evolving chemistry, which in turn is evolving physics. For biology, and life in general, to be considered something fundamentally and phenomenologically different than that, top-down causality must be demonstrated as an emergent quality of biology/consciousness.

 

[ogg]

Isn't the OP a troll? Perhaps not. Why s/he is so concerned with the way we choose to categorize our science escapes me. Why some of us got caught in the error that there is some objective reason that, for instance, the movement of a Ca+2 ion through a cell membrane is "biology" (or "biochemistry" ) and not "chemistry" seems to show that either some haven't thought very much about it, or that they are trying a bit too hard to be helpful. History. History is the study of the "untouchable" past (I just made that up, I hope its good enough, I doubt it's bullet proof). Biology is predicated on the history of life (although there is some synthetic biochemistry, I admit). Biology is predicated on temperatures/environments at around 0°C and pressures (and radiation fields and gravitational fields) at around Earth Surface "normal". 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. It is also an error, imho, to separate the "Laws of Thermodynamics" from the subjects of Physics, Chemistry or even Biology. But elementary Thermo deals with systems close to equilibrium, and life is not that. The answers you'll find in Non-equilibrium (far from equilibrium) Thermo will be quite unsatisfactory, imho. How do you "close" a system to neutrinos, electromagnetic radiation, gravity or the vacuum enegy? So, we know it is delusional to claim we've tested thermo in such systems, and yet we do it...Out of time and I've not touched the chemical systems paradigm. 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).) It is not off topic to note that a scientific subject must be able to award diplomas in less than 20-25 years of schooling. Our disciplines are more about our own limitations and mortality than any extrinsic logic.

 

[Feeble Wonk]

Isn't the OP a troll?

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.

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.

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.

Chemistry, Biology and (as far as we know) Physics do not "evolve". Living systems do...

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.

 

[Bob10]

The chemical of life is DNA. The DNA molecule has no chemical bonding between CGAT molecules. It is precisely this random sequence that assembles the proteins that performs almost all the biologic functions in life. There is of course a hydrogen bond across the strand but no bond between the linear arrangement on one strand. 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 that does not depend on the laws of chemistry.

 

[mfb]

Everything in the DNA depends on the laws of chemistry.

There is of course a hydrogen bond across the strand but no bond between the linear arrangement on one strand.

It is called a "strand" because there are bonds between its elements (via deoxyribose and a phosphate group).

 

[Bob10]

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).

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]

There is no bond between the bases one the single strand that is being translated.

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.

For instance if the sequence was ATGGTACG there is no chemical attraction between AT TA GG for example.

They are all bound together in a string.
The opposite strand that forms - TACCATGC - binds to this strand, and only this specific sequence can bind to it. There is the sensitivity.

 

[aroc91]

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.

Incorrect. There doesn't need to be a covalent bond for DNA to match up with the opposite strand or the various RNAs.

For instance if the sequence was ATGGTACG there is no chemical attraction between AT TA GG for example.

Anything but TACCATGC wouldn't fit correctly opposite to ATGGTACG.

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.

Chemistry covers non-covalent interactions.

 

[mjs]

The differentiation between the disciplines is simply a question of semantics and logistical categorization.
.

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..

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).)

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).

 

[Ygggdrasil]

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.

I would agree with you here. There are no chemical or physical principles that (directly) explain why the human genome has the particular sequence that it does. In fact, you can synthesize DNA strands (even genomes) to have almost any arbitrary sequence you want. Of course, arbitrary DNA sequences are not guaranteed to have any function, and a large portion of biology is dedicated to understanding the connection between DNA sequence and biological function (this is the goal of the field of genetics).

Chemical and physical principles can play some role, however. For example, one aspect of this problem is protein structure/function prediction: Given a protein-coding DNA sequence, can you predict the structure and function of the protein encoded by that gene. In principle, one should be able to use physical and chemical modeling to predict how a protein should fold and from that information be able to deduce its function, but we don't yet have good enough modeling tools to do this (there are decent structure/function prediction tools, but the best structure prediction methods rely a lot on comparing unknown sequences to databases of proteins with known structure and function as a starting point and do not rely solely on physical and chemical modeling).

 

[Feeble Wonk]

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...

For the sake of discussion, I would concede your larger point here. You can't explain the totality of biological activity on the basis of INDIVIDUAL chemical reactions. That's why I have stressed the necessity of considering the entire system resulting in that activity... not just the organic compounds themselves, but the wholistic sequence of physical events that have lead up to their production. As ogg said earlier, "Biology is predicated on the history of life". I would take that another step further and suggest that biology is predicated on the history of physical existence.
So, I would agree with you Bob. The incredible information content in the molecular structure of DNA can not be reduced to a specific chemical reaction. Rather, it is information storage of the cumulative sequence of reactions over countless millennia, resulting from the comprehensive history of physical events both locally and systemically. Again, I fully concede that that evolutionary process, including the vast variety of systemic feedback mechanisms, is incalculably complex, unimaginably chaotic and utterly unpredictable. And yet, all of it is driven by the underlying physics through bottom-up causation, unless fundamental top-down causation is achieved as an emergent phenomenon.
While I absolutely admit that this argument is purely rhetorical, I would suggest that this implies (in the absence of the aforementioned top-down causation) that biology IS a systemic application of physics.

 

[Feeble Wonk]

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..

I'm not sure what you see as the practical and theoretical implications of this issue. Can you clarify that for me?

 

[mjs]

I'm not sure what you see as the practical and theoretical implications of this issue. Can you clarify that for me?

I don’t know exactly, but I quess every knowledge is important. However, a general idea on how this knowledge can be exploited is:

1)With respect to medicine, if biology is chemistry, then this leaves the option to someday (although maybe not in the near future) know the full map of chemical reactions of each organism, and know exactly how a chemical pathway goes wrong in a disease and then go treat everything as a chemical automaton…

Additionaly, maybe we can develop strategies on how to preserve this system as much as possible, with all the implications with respect to aging…I mean, viewing the system holistically, as a complex system that it is, and not just trying to find the magic gene that can make us immortal, which is the case in todays research!

2)With respect to the origin of life, It shifts/simplifies the question into:

How self-sustainable complex organic chemical systems can be created? Leave the rest to Darwinism…

 

[mfb]

1)With respect to medicine, if biology is chemistry, then this leaves the option to someday (although maybe not in the near future) know the full map of chemical reactions of each organism, and know exactly how a chemical pathway goes wrong in a disease and then go treat everything as a chemical automaton…

That is exactly what is done. We are far away from knowing all chemical reactions, but identifying those critical for diseases is done frequently.

2)With respect to the origin of life, It shifts/simplifies the question into:

How self-sustainable complex organic chemical systems can be created? Leave the rest to Darwinism…

That shift has been done long ago.

 

[Feeble Wonk]

I don’t know exactly, but I quess every knowledge is important. However, a general idea on how this knowledge can be exploited is:

1)With respect to medicine, if biology is chemistry, then this leaves the option to someday (although maybe not in the near future) know the full map of chemical reactions of each organism, and know exactly how a chemical pathway goes wrong in a disease and then go treat everything as a chemical automaton…

...

2)With respect to the origin of life, It shifts/simplifies the question into:
How self-sustainable complex organic chemical systems can be created? Leave the rest to Darwinism…

So, your curiosity has nothing to do with the implied determinacy of life being relegated to being a big chemical reaction?

If the points you've listed are your primary concerns, IMHO, you're making much to do about nothing, for the same reasons mfb noted above.

 

[mjs]

.That shift has been done long ago.

I didn't know that was the mainstream viewpoint! In that case i don't understand why so many efforts to come up with a theory with respect to the origin of life, since the answer is simple, since everytime organic complexity will naturally do its job, throught the survival and selection of the most sustainable emerging systems...

That is exactly what is done. We are far away from knowing all chemical reactions, but identifying those critical for diseases is done frequently.

I agree, but there is still the implication that due to complexity, sometimes blocking a particular pathway may be like closing a particular hole in a sieve..
Anyway, as i see, in general we are saying pretty much similar things anyway!

 

[mfb]

Well, the question is: "how did the first self-sustainable replicating organic chemical system form, and how did it look like?"
And, of course, "in which way did it change over time to give the structures we observe today?"

 

[Drakkith]

In that case i don't understand why so many efforts to come up with a theory with respect to the origin of life, since the answer is simple, since everytime organic complexity will naturally do its job, throught the survival and selection of the most sustainable emerging systems...

The devil's in the details! How did it happen here on Earth? Which chemicals formed first? How do those lead to life? Etc.

 

[Ronie Bayron]

What is the difference between chemistry and biology (If any?)

Chemicals don't think, they mingle naturally. Biology to some extent, includes chemistry, physics and interactions (social) -which is complicated, since, just like humans, they can decide to critical conditions just like response to dilemma and can value things (example elephants).

 

[Feeble Wonk]

Chemicals don't think, they mingle naturally. Biology to some extent, includes chemistry, physics and interactions (social) -which is complicated, since, just like humans, they can decide to critical conditions just like dilemma and can value things.

So, you are suggesting top-down causation?

 

[Ronie Bayron]

So, you are suggesting top-down causation?

I am sorry, Feeble wonk, I admit, I lack the comprehension to some of your "terms". I am not quite familiar with the terminolgy, probably, I won't be able to debate credibly on the issue.

But I meant what I said.

 

[Feeble Wonk]

I am sorry, Feeble wonk, I admit, I lack the comprehension to some of your "terms". I am not quite familiar with the terminolgy, probably, I won't be able to debate credibly on the issue.

But I meant what I said.

I only ask because it gets back to a point I had made previously. You appear to be saying that biology is different than chemistry and physics in that biological entities behave socially, according to (consciously mediated) values. This sort of behavior definitely qualifies as an upper level of emergent systemic activity. Absolutely.
However, the next question is whether the neuronal activity that results in that "consciously" mediated behavior is simply driven by physical/biochemical processes in response to the physical stimuli initiating the process. In short, is this a physically deterministic process?
If so, then I would still argue that (regardless of the incredible systemic feedback complexity) it is still just a manifestation of the underlying physics.

 

[mfb]

It is just physics by definition of "physics": the study of all matter and other observable stuff in the universe.

 

[Feeble Wonk]

It is just physics by definition of "physics": the study of all matter and other observable stuff in the universe.

Yes. That is certainly true "by definition". And, in general terms, that goes back to my previous position that any differentiation between physics, chemistry and biology is simply a matter of logistical categorization of the systems being referred to... as long as physical determinism (bottom-up causality) is upheld.

 

[mfb]

There is no need for determinism. Physical rules can be expressed as probabilities.
There is also no need for "bottom-up" in any way.

 

[Feeble Wonk]

This is where the discussion tumbles over the cliff into philosophy, so I'll have to drop it here. But I'll leave it with a question. If Ronie is right, and an emergent property of biological/cognitive activity actually moderates behavior in ways that are not physically determined, but rather are consciously determined, would you still consider that to be a fundamentally "physical" process?

 

[Ronie Bayron]

I only ask because it gets back to a point I had made previously. You appear to be saying that biology is different than chemistry and physics in that biological entities behave socially, according to (consciously mediated) values. This sort of behavior definitely qualifies as an upper level of emergent systemic activity. Absolutely.
However, the next question is whether the neuronal activity that results in that "consciously" mediated behavior is simply driven by physical/biochemical processes in response to the physical stimuli initiating the process. In short, is this a physically deterministic process?
If so, then I would still argue that (regardless of the incredible systemic feedback complexity) it is still just a manifestation of the underlying physics.

You sound like the guy from MIT who studied AI. Though, behavior might be influenced by physical/biochemical process and responses, interestingly, say for example, when you are intoxicated with alcohol, you are always confronted with 2 set of options, (Yes or No) in everything. And, you can have your unique choices either you pick Yes or No and the freedom to choose whatever to pick. Chemical processes do not have yes or no stimuli, they mingle or not, as they are naturally designed, they have no thoughts and no feelings, either values anything.
Anyhow, if you are Josh T., I want you to know that I am a big fan of yours

 

[Feeble Wonk]

...can have your unique choices either you pick Yes or No and the freedom to choose whatever to pick. Chemical processes do not have yes or no stimuli...

Actually Ronie, physics is replete with "either/or" phenomenon. And in regard to your "freedom to choose"... that is the central question. Do you REALLY have that freedom?

...if you are Josh T., I want you to know that I am a big fan of yours

I'm shockingly flattered that you might think so, but no. Not even remotely close.

 

[Ronie Bayron]

Actually Ronie, physics is replete with "either/or" phenomenon. And in regard to your "freedom to choose"... that is the central question. Do you REALLY have that freedom?

Yes, I have

I'm shockingly flattered that you might think so, but no. Not even remotely close.

The way you write as though you are speaking his words.

 

[Feeble Wonk]

have

Ummm... Sorry. Not sure I'm following you here. Prime numbers assigned to tone, but what am I to infer from that?

 

[Feeble Wonk]

Yes, I...

Yes, you...?

 

[Ronie Bayron]

Ummm... Sorry. Not sure I'm following you here. Prime numbers assigned to tone, but what am I to infer from that?

Those are probabilities and unpredictability, since you said you don't have freedom. The image infers a definite geometry but infinite random freedom. So as, primes, they are random. Then, don't tell me, that we are fixated.