Is life a natural state of matter?

General philosophy discussions. If you are not sure where to place your thread, please post it here. Share favorite quotes, discuss philosophers, and other topics.

Re: Is life a natural state of matter?

Postby hyksos on May 2nd, 2016, 3:52 pm 

such that the twisted ladder like structure of RNA and DNA, that unzips down the middle - and attracts chemical matches from the environment in order to reproduce itself, is implied by the chemistry.

Are you asserting that a molecular chain making a copy of itself through template reproduction will NOT lower the entropy of the immediate environment?
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014


Re: Is life a natural state of matter?

Postby uninfinite on May 2nd, 2016, 5:20 pm 

hyksos » May 2nd, 2016, 8:52 pm wrote:
such that the twisted ladder like structure of RNA and DNA, that unzips down the middle - and attracts chemical matches from the environment in order to reproduce itself, is implied by the chemistry.

Are you asserting that a molecular chain making a copy of itself through template reproduction will NOT lower the entropy of the immediate environment?



I wasn't. I didn't say anything about entropy - but yes, I would have to agree with that; because in fact the entropy of the environment will be increased - albeit by some miniscule amount, possibly in the form of a miniscule amount of waste heat radiated into the environment, or if these bonds are endothermic reactions, the absorption of a little heat from the environment. Given that the temperatures of the environment in which this occurred likely varied from the near absolute zero of space, up to the 4 - 6,000 degrees centigrade of molten lava - a wide range of chemical reactions, including state changes, would have opportunity to occur - without violating the second law of thermodynamics.
uninfinite
Member
 
Posts: 217
Joined: 16 Apr 2016
Blog: View Blog (1)


Re: Is life a natural state of matter?

Postby hyksos on May 2nd, 2016, 5:57 pm 

Given that the temperatures of the environment in which this occurred likely varied from the near absolute zero of space, up to the 4 - 6,000 degrees centigrade of molten lava - a wide range of chemical reactions,

Yeah. I was gonna say that a natural lightning strike would create way more than enough entropy to account for whatever the molecules were about to do.
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014


Re: Is life a natural state of matter?

Postby uninfinite on May 3rd, 2016, 9:37 am 

hyksos » May 2nd, 2016, 10:57 pm wrote:
Given that the temperatures of the environment in which this occurred likely varied from the near absolute zero of space, up to the 4 - 6,000 degrees centigrade of molten lava - a wide range of chemical reactions,

Yeah. I was gonna say that a natural lightning strike would create way more than enough entropy to account for whatever the molecules were about to do.



So now you agree? After writing above:

Matter + electric fields certainly does not lead to life. In fact, matter alone by itself is completely insufficient for life to emerge on a planet.


I think this is what Ecoglite was saying in the other thread. No-one knows where you are coming from one minuet to the next. I can only suppose the disconnect is between your understanding of these question, and your attitude. If you don't know something, just ask for an explanation, and no-one will think any less of you for it. In time, you'll decide what you really believe, carve yourself out a patch, and then you come across as a complete jerk defending it - like everyone else here, barring maybe Vivian.
uninfinite
Member
 
Posts: 217
Joined: 16 Apr 2016
Blog: View Blog (1)


Re: Is life a natural state of matter?

Postby vivian maxine on May 3rd, 2016, 10:38 am 

Right, uninfinite. That's because you all are defending different opinions while I want to hear all sides. You are each firm in your belief that you are right and you leave your readers with a chance to see which theory makes the more sense - if either does. From there a reader might be able to come to a decision also. Or, maybe just to enjoy the exchange. Did you ever join a debating class where you are judged on not are you right or wrong but do you present your position well? Something like that.

I haven't been idle, though. The two of you have each sent me to Wiki more often than I can say. Thank you for that.

Now my opinion? Neither of you comes off as a "complete jerk". You just have different ways of putting down your ideas. Carry On and Keep Calm. :-)
vivian maxine
Resident Member
 
Posts: 2745
Joined: 01 Aug 2014


Re: Is life a natural state of matter?

Postby uninfinite on May 3rd, 2016, 2:14 pm 

vivian maxine » May 3rd, 2016, 3:38 pm wrote:Right, uninfinite. That's because you all are defending different opinions while I want to hear all sides. You are each firm in your belief that you are right and you leave your readers with a chance to see which theory makes the more sense - if either does. From there a reader might be able to come to a decision also. Or, maybe just to enjoy the exchange. Did you ever join a debating class where you are judged on not are you right or wrong but do you present your position well? Something like that.

I haven't been idle, though. The two of you have each sent me to Wiki more often than I can say. Thank you for that.

Now my opinion? Neither of you comes off as a "complete jerk". You just have different ways of putting down your ideas. Carry On and Keep Calm. :-)



With the greatest of respect to all my fellow posters, I doubt here is where you'll find questions going back to Plato's time, finally answered definitively. The debates can be illuminating, and I enjoy showing off my knowledge - but things like nature/nurture, subject/object, the existence or not of God, the nature and purpose of life - and so on, can be held as passionate views, but cannot be proven outright. On any of these issues I suspect, people adopt positions consistent with their overall worldview - and consequently, are very invested - let's say - in a debate on that position, but I think complete jerk works just as well in most cases! Except you Vivian. You are a flower growing on a battlefield, a ray of sunshine through the clouds, the center of sanity around which we whirl in our mad anguish!

No, sorry, no debate team where I'm from. I understand the concept; though I'm much happier defending a position I believe in, than one that's assigned, and which I may not necessarily agree with. A useful skill I'm sure - which is why the political class are taught debate at their posh schools; so they can turn on a sixpence and defend a view that privately, they may find abhorent and wrong. Ha ha!
uninfinite
Member
 
Posts: 217
Joined: 16 Apr 2016
Blog: View Blog (1)


Re: Is life a natural state of matter?

Postby hyksos on May 6th, 2016, 4:23 pm 

uninfinite » May 3rd, 2016, 5:37 pm wrote:
hyksos » May 2nd, 2016, 10:57 pm wrote:
Given that the temperatures of the environment in which this occurred likely varied from the near absolute zero of space, up to the 4 - 6,000 degrees centigrade of molten lava - a wide range of chemical reactions,

Yeah. I was gonna say that a natural lightning strike would create way more than enough entropy to account for whatever the molecules were about to do.



So now you agree? After writing above:

Matter + electric fields certainly does not lead to life. In fact, matter alone by itself is completely insufficient for life to emerge on a planet.


I think this is what Ecoglite was saying in the other thread. No-one knows where you are coming from one minuet to the next. I can only suppose the disconnect is between your understanding of these question, and your attitude.


Electric fields exist everywhere. They are in rocks and dust and they bind atoms and create chemical reactions. So electric fields are pervasively everywhere, provided charge is not neutralized. Electric fields are not just an isolated phenomenon found in lightning strikes. There's where I am "coming from".
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014


Re: Is life a natural state of matter?

Postby hyksos on May 6th, 2016, 4:38 pm 

I wasn't. I didn't say anything about entropy - but yes, I would have to agree with that; because in fact the entropy of the environment will be increased - albeit by some miniscule amount, possibly in the form of a miniscule amount of waste heat radiated into the environment, or if these bonds are endothermic reactions, the absorption of a little heat from the environment

There is a vast confusion on your part here. (barring everything else we might say about the actual physical interactions) the entropy of the environment outside the living organism must go up. Why? "because of endothermic this's and that's"? No. Because duplicating a copy will lower entropy, and anywhere entropy is lowered in one part of the universe must be offset by entropy increasing somewhere else in the universe.

So matter how the organism, machine, living thing, system, (call-it-what-you-like) lowers entropy by duplicating itself, it must, by hook-or-crook, raise the entropy somewhere else.

waste heat radiated into the environment, or if these bonds are endothermic reactions, the absorption of a little heat from the environment. Given that the temperatures of the environment in which this occurred likely varied from the near absolute zero of space, up to the 4 - 6,000 degrees centigrade of molten lava - a wide range of chemical reactions, including state changes, would have opportunity to occur - without violating the second law of thermodynamics.


No no. You see this argument has nothing to do with the specifics of endothermic reactions nor of temperatures. You are further vastly confused by the fact that you believe I am referring to a single incident that "accidentally made life". I'm not. I am instead referring to principles that would undergird any lifeform, whether alive today, or alive eons ago as protocells. I am speaking in terms of over-arching physical principles of 'aliveness' , not of specific events.

I mean, if we are going to allowed to call each other "jerks" in this thread -- then I will just say what needs said. All things being equal. You have pigeonholed me as a woodoo peddler who (you believe in your own head) is adopting a creationist stance like somehow life could not have formed by natural processes. You have inserted yourself into this thread to "challenge the creationist" by referring to lightning strikes forming amino acids from water vapor. And to sprinkle your attacks on the strawman with socializing with vivian (or flirting or whatever it is you think you are doing.).
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014


Re: Is life a natural state of matter?

Postby TheVat on May 6th, 2016, 4:59 pm 

I think this is what Ecoglite was saying in the other thread. No-one knows where you are coming from one minuet to the next.


I was thinking more like a tango.
User avatar
TheVat
Forum Administrator
 
Posts: 7631
Joined: 21 Jan 2014
Location: Black Hills


Re: Is life a natural state of matter?

Postby uninfinite on May 6th, 2016, 10:22 pm 

I wasn't. I didn't say anything about entropy - but yes, I would have to agree with that; because in fact the entropy of the environment will be increased - albeit by some miniscule amount, possibly in the form of a miniscule amount of waste heat radiated into the environment, or if these bonds are endothermic reactions, the absorption of a little heat from the environment


There is a vast confusion on your part here.


Funny. From where I'm sitting it's you who seem confused. Funnier still, everyone else here is telling you you're wrong, or off-target, and they're not telling me the same thing. Why is that?

(barring everything else we might say about the actual physical interactions) the entropy of the environment outside the living organism must go up. Why? "because of endothermic this's and that's"? No. Because duplicating a copy will lower entropy, and anywhere entropy is lowered in one part of the universe must be offset by entropy increasing somewhere else in the universe.


That's correct, only that's not what you said earlier. You said:

Are you asserting that a molecular chain making a copy of itself through template reproduction will NOT lower the entropy of the immediate environment?


So, what's that? Were you just careless? Or do you not understand how the second law of thermodynamics and entropy are related to informational organization? The point about exothermic and endothermic chemical reactions is a valid point, because the second law states that energy flows from a hotter to a cooler environment, always. For an exothermic chemical reaction to form greater complexity, the environment must allow for the disposal of waste heat.

So no matter how the organism, machine, living thing, system, (call-it-what-you-like) lowers entropy by duplicating itself, it must, by hook-or-crook, raise the entropy somewhere else.


Now you have it.

waste heat radiated into the environment, or if these bonds are endothermic reactions, the absorption of a little heat from the environment. Given that the temperatures of the environment in which this occurred likely varied from the near absolute zero of space, up to the 4 - 6,000 degrees centigrade of molten lava - a wide range of chemical reactions, including state changes, would have opportunity to occur - without violating the second law of thermodynamics.


No no. You see this argument has nothing to do with the specifics of endothermic reactions nor of temperatures. You are further vastly confused by the fact that you believe I am referring to a single incident that "accidentally made life". I'm not. I am instead referring to principles that would undergird any lifeform, whether alive today, or alive eons ago as protocells. I am speaking in terms of over-arching physical principles of 'aliveness' , not of specific events.


How are the two seperable? What it seems to me you're doing is provocative jazz - based on a vague understanding of a few key concepts. You are gnawing at the bone - because it tastes of ham, while the ham sits there untouched because you don't know what it is.

I mean, if we are going to allowed to call each other "jerks" in this thread -- then I will just say what needs said. All things being equal. You have pigeonholed me as a woodoo peddler who (you believe in your own head) is adopting a creationist stance like somehow life could not have formed by natural processes. You have inserted yourself into this thread to "challenge the creationist" by referring to lightning strikes forming amino acids from water vapor.


Call me what you like. I am addressing the question. Also, I'm trying to figure out where you're coming from. If you're not a creationist as such, sure does seem like you're trying to leave a door open to creationism, or some like minded idea.

And to sprinkle your attacks on the strawman with socializing with vivian (or flirting or whatever it is you think you are doing.).


Oh, flirting with Vivian, definitely. But I'm not attacking you, or your many straw friends.
uninfinite
Member
 
Posts: 217
Joined: 16 Apr 2016
Blog: View Blog (1)


Re: Is life a natural state of matter?

Postby hyksos on May 7th, 2016, 12:26 am 

If you're not a creationist as such, sure does seem like you're trying to leave a door open to creationism, or some like minded idea.

I'm not peddling creationism. I'm trying to build a life form in a lab from raw material.

Also, it would be nice to know how prevalent life is in the galaxy. Gonna need some principled theories.
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014


Re: Is life a natural state of matter?

Postby uninfinite on May 7th, 2016, 3:05 am 

If you're not a creationist as such, sure does seem like you're trying to leave a door open to creationism, or some like minded idea.


I'm not peddling creationism. I'm trying to build a life form in a lab from raw material.


Leaving half eaten food under your bed until it's ready to crawl away doesn't count as trying to build a life-form.

Also, it would be nice to know how prevalent life is in the galaxy. Gonna need some principled theories.


The assumption you can move easily between theories on how life began and how prevalent life is in the galaxy is entirely unscientific.
uninfinite
Member
 
Posts: 217
Joined: 16 Apr 2016
Blog: View Blog (1)


Re: Is life a natural state of matter?

Postby neuro on May 7th, 2016, 7:56 am 

hyksos » May 6th, 2016, 9:38 pm wrote:There is a vast confusion on your part here. (barring everything else we might say about the actual physical interactions) the entropy of the environment outside the living organism must go up. Why? "because of endothermic this's and that's"? No. Because duplicating a copy will lower entropy, and anywhere entropy is lowered in one part of the universe must be offset by entropy increasing somewhere else in the universe.


hyksos,
I would strongly suggest that you progressively move toward a less arrogant position.

You keep telling other people - either explicitly or implicitly - they do not know what they are talking about.

You had better be careful because some moderator will sooner or later warn you - by the way, I may warn you myself, exactly now - but, what is more important, because you may be wrong yourself, at times...

For example, you state that duplicating a copy lowers entropy.
This is a presumptuous statement on your part!
Are you so sure about this?

The Gibbs free energy of a double strand nucleic acid is not higher than that of the two separate strands, and it is lower than that of the isolated bases that constitute it.

You do need energy to combine the bases because you need to overcome the energy barrier to produce covalent bonds.

And the final system does appear to be more ordered.

But it actually is not. Free energy has been lost. The entropy has increased. And that is simply due to the fact that the atoms that constitute the nucleic acids are "better at ease" in this condition. (if you wish, they were kept in an improbable - "forced", and therefore ordered - condition before).

Just to give you some food for thought, your arrogant claim would imply that an oxygen molecule is more ordered (and therefore lower entropy = higher free energy) than two oxygen atoms.

I am not interested in correcting your ideas.
I - like most people here - am simply interested in being able to discuss without being arrogantly taught.
User avatar
neuro
Forum Moderator
 
Posts: 2616
Joined: 25 Jun 2010
Location: italy


Re: Is life a natural state of matter?

Postby neuro on May 7th, 2016, 8:05 am 

By the way, the above is one of the reasons why nucleic acids - that can be replicated but do not need net input of energy from the outside to preserve or be replicated - may also be a good example of autocatalysis but do not look much like life (at least to me).
User avatar
neuro
Forum Moderator
 
Posts: 2616
Joined: 25 Jun 2010
Location: italy


Re: Is life a natural state of matter?

Postby TheVat on May 7th, 2016, 10:31 am 

"Leaving half eaten food under your bed until it's ready to crawl away doesn't count as trying to build a life-form. "

Good one.

The verb "build" needs clarification. For me, it conjures careful molecular assembly following a blueprint, rather than just setting up an ideal abiogenetic stew and letting it simmer.
User avatar
TheVat
Forum Administrator
 
Posts: 7631
Joined: 21 Jan 2014
Location: Black Hills


Re: Is life a natural state of matter?

Postby uninfinite on May 7th, 2016, 3:55 pm 

Brainvat,

I was under the impression that this had already been achieved - fairly recently. Googled it. Craig Ventner - playing God, sparking further illusions that such a life-form might escape and take over the world because it has no natural predators. (I once saw a goat eat a tin can.)
uninfinite
Member
 
Posts: 217
Joined: 16 Apr 2016
Blog: View Blog (1)


Re: Is life a natural state of matter?

Postby hyksos on May 7th, 2016, 6:13 pm 

For example, you state that duplicating a copy lowers entropy.
This is a presumptuous statement on your part!
Are you so sure about this?

This is not presumptuous at all. (That will be explained in a minute after we get through this next part).

There is also a miscommunication here. What I am contending, precisely -- is that the mere act of replication will lower entropy. But no physical system can simply lower entropy, full stop. That would violate physics. So therefore we conclude that the entropy in the universe outside the replicating system must have gone up. I don't know if you follow that, but that is precisely what I have been saying and I have never deviated from that claim.

The specifics of how exactly the outside world offsets the lowering of entropy does not matter. (I'll talk about that below). So go slow and take what I'm saying very literally. The pure, isolated fact of a system making a copy will lower entropy. Period. No other references to the outside environment, no reference to waste heat, no references to nuclear reactions on the sun, nothing. Just take that sentence in complete isolation. Okay? I hope you follow this.

Now.

That sentence in isolation would violate physics. Therefore, by a method of logic called reductio-ad-absurdum, we say to ourselves, "No that can't be right. No physical system can just lower entropy willy-nilly". From that we then conclude that the entire organism-environment-universe system must have created more entropy elsewhere in order to offset the loss . Okay? Do you follow that?

The laws of physics do allow an isolated pocket of the universe to reduce entropy, and that happens all the time in the freezing of rocks, in the formation of tornadoes, in organisms and cells and all sorts of other places. However! We understand today that no physical system can create more order unless it creates more disorder somewhere else, to offset the loss.

Okay this is getting too wordy. This is the logic of the argument laid out in a bullet point list.

  1. Making a copy will lower entropy.
  2. The total entropy of the universe must go up. This is the "global entropy" denote E_g
  3. Therefore, if any device, machine, or organism replicates itself, it will lower the local entropy, denote E_l.
  4. Since E_g can never go down, any instance of E_l must create additional entropy somewhere else to offset its loss.

A closed physical system that has reached its maximum entropy can no longer form any order. To do that, you must pump more energy into it from the outside.

This concludes the part of this reply that addresses the miscommunication. Now I will turn to the topic of why building a copy lowers (local) entropy.

( I need to draw diagrams. So this post will be submitted first. Just be patient and I will get around to the new post, complete with diagrams. No reason to ban anyone, ladies and gentleman)
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014


Re: Is life a natural state of matter?

Postby hyksos on May 7th, 2016, 8:19 pm 

In this post I will demonstrating why TEMPLATE REPRODUCTION by nucleotide bases will lower the entropy in an isolated region, and as consequence, raise the entropy in the environment outside that region.

Entropy is the size of the informational description of a physical system. It is the amount of microstates that a system could occupy and still exhibit the same macroscopic behavior. Take the pixels on an LCD television. The amount of possible microstates that correspond to noise is far larger than the amount of configurations that could correspond to a single frame from Game of Thrones. This is an exaggerated example. The probability that random pixels will accidentally form a photo of Khaleesi is vanishingly small.

entropyhilo.png


The laws of physics as we understand them today do not allow a system to spontaneously form order , unless an until some more disorder is created somewhere else to offset the loss. In other words, the total entropy of the universe must either always go up or it must remain constant. The only reason it is possible that your television can play an episode of Game of Thrones is because the energy in a power plant generated the electricity for your TV. During that generation process, the power plant created enormous waste heat. That rise in entropy is enough to offset any order seen in the pixels of your TV during the episode.

This entropy equation, with its zero-sum-or-increase law, applies to all physical systems. So if a small region of physical stuff lowers its entropy, it must have raised the entropy of the environment outside of it. This is not theoretical science. This law is deeply interwoven with foundational notions of conservation of energy and momentum. Any person who denies this law is pitting themselves against the foundations of science.


statetransitiontoorder.png

As far as we know, life on earth is not magic. It is subject to the same laws of physics as everything else. All organisms will replicate genes in their nucleus using template reproduction. This replication process is happening right now all over your body as your cells grow and divide, In the following diagram, the sequence CTAGCTATTT finds itself in a soup of amino acids sloshing around. The sequence is marked with dots. Over the next few minutes, the sequence will be replicated by an enzyme (not shown) that unzips the new sequence from the original. The final configuration shows the results of several rounds of template replication.

templatereplication.png

In the isolated region in its final configuration the entropy was lower than it was in the initial soup. So the outside environment must have had its entropy go up, one way or another. This is illustrated here by blue dots.

As was mentioned above, this is not a special property of living systems. This is a LAW OF PHYSICS. So any system, living or not, mechanical artifact or product of nature, -- If that thing makes a copy of itself, or replicates a sequence of some kind or another, it must also raise the entropy of the outside environment.

Thinking along these lines has led a number of thinkers to adopt a certain position on abiogenesis. Their central claim is that on the ancient prebiotic earth, stable metabolism must have preceded genetics. We don't yet know if that is true or not, but the arguments for it are compelling.
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014


Re: Is life a natural state of matter?

Postby hyksos on May 7th, 2016, 8:31 pm 

I was under the impression that this had already been achieved - fairly recently. Googled it. Craig Ventner

Craig Venter took an existing organism and transplanted a genome into it which was constructed by a machine. It is great research, but not yet an engineered organism.
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014


Re: Is life a natural state of matter?

Postby uninfinite on May 7th, 2016, 8:53 pm 

hyksos » May 8th, 2016, 1:31 am wrote:
I was under the impression that this had already been achieved - fairly recently. Googled it. Craig Ventner

Craig Venter took an existing organism and transplanted a genome into it which was constructed by a machine. It is great research, but not yet an engineered organism.



hyskos, Those are some very well prepared posts and deserve a decent reply - but it might take a while. so be patient and I'll edit this.
uninfinite
Member
 
Posts: 217
Joined: 16 Apr 2016
Blog: View Blog (1)


Re: Is life a natural state of matter?

Postby neuro on May 8th, 2016, 6:10 am 

hyksos,
this is my last attempt at communicating with you.

Please stop teaching us logics pretending you are talking physics.

You seem very fond of the second principle of thermodynamics, and very convinced that other people cannot UNDERSTAND what you are saying.

I'm very fond of the second principle of thermodynamics myself, but happen to have a different attitude.
I try and understand, instead of spitting sentences.

There was no miscommunication between us.
You say: in order for a system to reduce internal entropy (a strand of RNA + bases turning into a two copies of the RNA strand) the entropy of the larger system must increase.
I say: bases getting into a strand of RNA do not lower the entropy of the system: it is an esergonic reaction.
It is not of any utility for anybody that you explain to me your point between the entropy of a system and that of the surrounding universe.
If you wish to show I'm wrong, then back up your assumption that a double strand DNA is a lower entropy (higher free energy) system than a single strand + bases.

I agree that it seems curious: the system appears to be more ordered.
However, it is not.
It is not, because the components of the system (atoms and subatomic particles) are more strained (limited number of possible states) in the single bases than they are when the bases are connected in the double strand DNA.
this paragraph was edited by adding a comma before "because", upon suggestion by Positor

Your argument would imply that a crystal (ordered) is a low entropy system and you need energy from the outside to generate it. You may realize how wrong this view is.

This misunderstanding of yours also brings you to the idea that autocatalysis might be particularly relevant for life.

The point you keep to miss is that catalysis does not change the direction of any reaction. Catalysts simply lower the energy barrier for a reaction to occur. Then, the direction will solely be determined by the concentration of reactants and reagents (and in particular RT times the log of the ratio of the concentrations) and the deltaG (difference in free energy between reagents and products).

A reaction can be driven "against" its natural direction if you keep subtracting the products (here is something much more interesting for life). Otherwise, catalysts or not, it will proceed downhill.

Autocatalysis makes no difference.
Autocatalysis does not reduce entropy.
Autocatalysis does not require energy.
Unless you wish to drive it uphill.
Which is not the case in crystal formation.
And is not the case in RNA duplication.

Please, try and understand the above before explaining me once more that entropy relates to order an probability - or better to RT·log(p) - i.e. the number of possible states: you mustn't stop at the bases, ACTG, you must go down to atoms and electrons, and in particular the possible states of electrons in appropriately coordinated molecules, which may be much more numerous (higher entropy) than the possible states in an apparently ordered larger molecule.

There is MORE disorder in a strand of RNA than in the apparently disordered single bases floating around.
There would be more disorder in two RNA strands that are randomly scrambled than in two mirroring RNA strands, but THIS is the autocatalytic function: making it EASIER for the bases to undergo the necessary transitions to a mirroring copy of RNA rather than building a new random RNA strand on their own.
The reaction proceeds from a higher free energy situation toward a lower free energy state (your second oval figure is WRONG). Not toward the lowest possible state (random RNAs: your first oval figure is correct), this is true, but simply because the activation energy happens to be lower along this particular path.

Hope you spend a few instants of your precious time in trying and understanding this, instead of teaching.
User avatar
neuro
Forum Moderator
 
Posts: 2616
Joined: 25 Jun 2010
Location: italy
TheVat liked this post


Re: Is life a natural state of matter?

Postby uninfinite on May 8th, 2016, 7:38 am 

hyskos, Your second post here is very different from your usual style, and this overcomes one of the main problems we were having, I think, following from your lack of clarity. For example, in the post above you say:

"There is also a miscommunication here. What I am contending, precisely -- is that the mere act of replication will lower entropy."

This is far from precise. As your second post shows - entropy lowered in one place must be offset by an increase in entropy in another place. What you were saying, precisely - was not specific. Perhaps you meant to say that the entropy of the molecule is decreased, but even this would not be the best way of expressing the idea. From wikipeadia we note:

''In thermodynamics, entropy is commonly associated with the amount of order, disorder, or chaos in a thermodynamic system. This stems from Rudolf Clausius' 1862 assertion that any thermodynamic process always "admits to being reduced to the alteration in some way or another of the arrangement of the constituent parts of the working body" and that internal work associated with these alterations is quantified energetically by a measure of "entropy" change.''

In your first post, you don't use the concept of order once - but it is more customary to speak in terms of an increase in order, rather than a lowering of entropy. While technically correct, it's a very clumsy description, and as you did not specify that you were talking about the molecule, the impression was that you were talking about the environment. Rather, in this context it's necessary to speak of order and entropy - as two sides of the same coin, where entropy is understood as the thermodynamic state of the overall system, tending toward the universal maximum. Thus, order is revealed as negentropic against the universal tendency.

This brings me to a problem with your second post - which is much more clearly written, and employs the concept of order. However, this 'isolated high entropy region' (2nd diagram) bothers me. As stated above, there is no isolation from entropy - it is a universal tendency. On a primitive earth, we would have massive variations in environmental temperature, effecting the chemistry and the thermodynamics of chemical reactions taking place - particularly given Boltzman distribution of atoms at varying temperatures, during state changes from gas, to liquid to solid.

This presents problems as you fail to account for any of these factors, while moving seamlessly onto diagram 3, whereupon, as if by magic - we have an RNA sequence floating around in an entropically isolated region amidst a soup of chemical bases. You say 'as far as we know, life on earth is not magic' - but your omission of the question of how this strand on RNA got there - to focus on the thermodynamics, smacks of a distraction technique - while driving at a pre-ordained conclusion. It seems to me, you cannot simply avoid the question of whether these reactions could have taken place within real world environmental conditions - if you are to describe abiogenesis as a process.
uninfinite
Member
 
Posts: 217
Joined: 16 Apr 2016
Blog: View Blog (1)


Re: Is life a natural state of matter?

Postby hyksos on May 8th, 2016, 1:37 pm 

I say: bases getting into a strand of RNA do not lower the entropy of the system: it is an esergonic reaction.

I'm presuming you meant to type eXergonic (esergonic?). Exergonic reaction will decrease the Gibb's free energy. Hell that's the definition of exergonic. That's exactly what we expect to have happen in a system that performs work in order to get the nucleotide bases into order. Gibbs can be used to perform work, but after the work is performed the energy is in a unusable state. That's completely consistent with everything I have said.

If you wish to show I'm wrong, then back up your assumption that a double strand DNA is a lower entropy (higher free energy) system than a single strand + bases.

That was not my assumption at all. You are not paying attention. The entire cellular matrix will allow letting molecular magnetic poles line up against the template. But then it must unzip the pair by using an enzyme (something called a replicase). Over many minutes and hours this WORK {Gibbs energy decreasing} will transform a high entropy soup into a low-entropy collection of identical strands. That work must be fed Gibbs energy from somewhere -- probably from the outside of the cell. This is totally consistent with every diagram I have posted.

I think what is happening here is that you are seeing trees, and I am talking about a forest. This is pretty common in internet communication where the participants will always try to steer the conversation towards their special topic of expertise, and then harp on minute details of their pet topic. In large multicellular organisms on earth, the formation of identical rows of cells in a tissue is a drastic reduction in entropy in the matter which composes those cells. If you succeed in dragging this conversation into tracing individual amounts of potential energy in hydrogen bounds among amino acid bases, then you are "harping" rather than having a discussion about the true topic of this thread.


Your argument would imply that a crystal (ordered) is a low entropy system and you need energy from the outside to generate it. You may realize how wrong this view is.

Oh neuro. I realize how correct this is. The transition from liquid state to crystaline solid will correspond to a lowering of temperature through a phase transition. That means that heat must DEPART from the physical system to allow it to create the order seen in the crystaline structure. The departed heat from the crystalizing system will go into the environment, and raise the entropy of the environment. (And it may perform some work on the way out).

This is exactly what happens in reality.

These rock formations on the coast of Ireland are so perfect that it seems they were the careful work of a stone mason. That they formed by natural processes seems counter-intuitive. These hexagons formed from high temperature lava coming into quick contact with freezing ocean water temperatures while under intense pressure. The order seen in these rock columns can be traced to the free energy of the lava being forced to dissipate very quickly into the ocean.

Image

A more familiar example of this is ice in a freezer in your house. The refrigerator must perform work to move the heat energy out of the freezer. All the order seen in the ice crystals will be offset by an equal (or greater) amount of waste heat created by the refrigerator compressor. This is unintuitive, but it is completely true.

The point you keep to miss is that catalysis does not change the direction of any reaction. Catalysts simply lower the energy barrier for a reaction to occur. Then, the direction will solely be determined by the concentration of reactants and reagents

You can surely have grad students pour a catalyst into a beaker in a lab and induce a reaction. But that is not AUTO-catalysis. In autocatalysis, the products of the reaction are themselves catalysts that induce more reactions that further produce more of the catalyst. A self-reinforcing feedback is established.
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014
TheVat liked this post


Re: Is life a natural state of matter?

Postby hyksos on May 8th, 2016, 1:45 pm 

You say 'as far as we know, life on earth is not magic' - but your omission of the question of how this strand on RNA got there - to focus on the thermodynamics, smacks of a distraction technique - while driving at a pre-ordained conclusion.

It's not a distraction at all. We want these principles to apply equally well to life on earth today, as it would apply to protocells of the ancient earth. Remember, the topic of this thread is "Is life a natural state of matter?"

If anything is being omitted in this thread, it's that the OP segregated "electric fields" from "matter". I find that differentiation to be equal silly and confusing. All "Matter" always comes along with its charge. As it is said, electric flux lines always end on charges.
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014


Re: Is life a natural state of matter?

Postby uninfinite on May 8th, 2016, 2:30 pm 

hyksos » May 8th, 2016, 6:45 pm wrote:
You say 'as far as we know, life on earth is not magic' - but your omission of the question of how this strand on RNA got there - to focus on the thermodynamics, smacks of a distraction technique - while driving at a pre-ordained conclusion.


It's not a distraction at all. We want these principles to apply equally well to life on earth today, as it would apply to protocells of the ancient earth. Remember, the topic of this thread is "Is life a natural state of matter?"

If anything is being omitted in this thread, it's that the OP segregated "electric fields" from "matter". I find that differentiation to be equal silly and confusing. All "Matter" always comes along with its charge. As it is said, electric flux lines always end on charges.



I'm sorry, but I must disagree. In order to establish that life is a natural state of matter we must focus upon abiogenesis. The environmental conditions that apply in that scenario, on a primitive earth with temperature ranges from absolute zero to 6,000 degrees, bathed in solar radiation, with volcanic lightning and comet strikes - and so on, do not apply now. You have posted a picture of the Giant's Causeway - as if to show that apparently ordered, almost artefactual phenomena can arise from physical processes, but RNA is a far more complex object. In much the same way you explain that the rock formations in the Giant's Causeway are caused by 'the free energy of the lava being forced to dissipate very quickly into the ocean' you need to explain the occurrence of this strand of RNA.

This is a heavy burden, involving an understanding of the reactions, in various physical environmental conditions, of various chemicals, and the compounds made up from them. I do not envy you your task - but you adopted this burden voluntarily. Personally, I would have sufficient information at this point to form an opinion sufficient to my own reason - but you, it seems wish to close the debate. You realize, I suppose that - people will continue in ignorance of your conclusive proof, should you ever provide it, expressing the idea that DNA was created by an intelligent designer, or dispersed by panspermia, or created by aliens - or whatever idea suits their prejudices? And you will have to begin all over again - and again, and again, and again.
uninfinite
Member
 
Posts: 217
Joined: 16 Apr 2016
Blog: View Blog (1)


Re: Is life a natural state of matter?

Postby hyksos on May 8th, 2016, 3:02 pm 

Personally, I would have sufficient information at this point to form an opinion sufficient to my own reason - but you, it seems wish to close the debate. You realize, I suppose that - people will continue in ignorance of your conclusive proof, should you ever provide it, expressing the idea that DNA was created by an intelligent designer, or dispersed by panspermia, or created by aliens - or whatever idea suits their prejudices? And you will have to begin all over again - and again, and again, and again.

If any debate-closing is happening here, it is your doing. You are methodologically committed to ignoring any questions that could reveal underlying physical principles behind life.

You are philosophically and psychologically committed to the mantra that life began as one-off accident of a replicating genetic strand. So much so , that you refuse to even discuss principled science. Instead at all turns of the conversation you find and present your next excuse to exclude any such ideas, questions, connections, and additional avenues of research.
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014


Re: Is life a natural state of matter?

Postby uninfinite on May 8th, 2016, 3:20 pm 

hyksos » May 8th, 2016, 8:02 pm wrote:
Personally, I would have sufficient information at this point to form an opinion sufficient to my own reason - but you, it seems wish to close the debate. You realize, I suppose that - people will continue in ignorance of your conclusive proof, should you ever provide it, expressing the idea that DNA was created by an intelligent designer, or dispersed by panspermia, or created by aliens - or whatever idea suits their prejudices? And you will have to begin all over again - and again, and again, and again.

If any debate-closing is happening here, it is your doing. You are methodologically committed to ignoring any questions that could reveal underlying physical principles behind life.

You are philosophically and psychologically committed to the mantra that life began as one-off accident of a replicating genetic strand. So much so , that you refuse to even discuss principled science. Instead at all turns of the conversation you find and present your next excuse to exclude any such ideas, questions, connections, and additional avenues of research.



It may seem to you that way, but in fact I was suggesting - without stating that the complexity of the phenomena is beyond me ...and that probably, it's beyond you too. This is why you focus upon entropy as a mechanism, and throw in this strand of replicating RNA as if by magic, hoping we won't notice while we're focusing upon entropy - that you've avoided the pertinent issue. Describe the series of chemical reactions that take you from inanimate matter to self replicating strand of RNA - or recognize your view is an opinion.
uninfinite
Member
 
Posts: 217
Joined: 16 Apr 2016
Blog: View Blog (1)


Re: Is life a natural state of matter?

Postby hyksos on May 8th, 2016, 4:00 pm 

It seems like there needs to be a more clear consensus here regarding the relationship between on one hand,

(1.) What actually happened on the ancient earth during the transition to the first living organisms?

versus,

(2.) How could we, in theory, construct an artificial metabolism, and an artificial genetic code?

Maybe these are two entirely different issues. This seems to be the case in that (2.) could have answers such as peptide nucleic acid , PNA, instead of deoxyribonucleic acid, DNA. Regarding environmental factors, they play a huge, often central role in the (1), and no role at all in (2), because if we need zinc salt, we just purchase it for the lab.

On the ancient earth, regions just had to have zinc naturally occurring. The abundance of phosphorus on the pre-biotic earth is an outstanding mystery. It would have be resolved historically to make progress on (1).

"Phosphorus is the least abundant element cosmically relative to its presence in biology," said Matthew Pasek of the University of South Florida. This scarcity of phosphorus is even more acute on the Earth's surface, where much of the phosphorus is locked up in certain minerals that life has difficulty making use of.


Personally, I am not averse to discussion of abiogenesis on the grounds of pure chemistry. My only exposure to the topic was through a book by Horst Rauchfuss. The bulk of the book talked about the plausible pathways to DNA, and in particular its relationship to amino acids. But there were several chapters about how phosphorus had to be somehow extracted in the early earth to make abundant enough in "digestible" form for the new protocells and their chemistry.
User avatar
hyksos
Active Member
 
Posts: 1843
Joined: 28 Nov 2014


Re: Is life a natural state of matter?

Postby neuro on May 9th, 2016, 3:11 am 

hyksos,
you are without hope.
I'm not going to continue.
I am just suggesting you try and have your ideas more clear about heat coming in and out and free energy increasing and decreasing.

Your statement
hyksos » May 8th, 2016, 6:37 pm wrote:That means that heat must DEPART from the physical system to allow it to create the order seen in the crystaline structure.

simply is pure nonesense.

To "create the order" you need to INPUT energy (heat), not to have it DEPART from the structure.

I begin to be convinced there is no hope with you.
User avatar
neuro
Forum Moderator
 
Posts: 2616
Joined: 25 Jun 2010
Location: italy


Re: Is life a natural state of matter?

Postby Positor on May 9th, 2016, 7:58 am 

neuro,

May I ask two questions here?

1. Hyskos wrote "heat must depart from the physical system", but you wrote "...not to have it depart from the structure". Is there some misunderstanding here? The (crystalline) structure and the (whole) physical system are two different things.

2. If you agree that hyskos meant "heat must depart from the physical system as a whole", but are disputing that claim, can you please address the following point (particularly the first sentence) and explain why you think it is wrong?

hyksos » May 8th, 2016, 6:37 pm wrote:The transition from liquid state to crystaline solid will correspond to a lowering of temperature through a phase transition. That means that heat must DEPART from the physical system to allow it to create the order seen in the crystaline structure.
Positor
Active Member
 
Posts: 1156
Joined: 05 Feb 2010


PreviousNext

Return to Anything Philosophy

Who is online

Users browsing this forum: No registered users and 3 guests