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Author Topic: Nether caps - chlorophyll of the caverns  (Read 16796 times)

psychologicalshock

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Re: Nether caps - chlorophyll of the caverns
« Reply #30 on: April 01, 2012, 02:48:55 pm »

As for plants producing heat, yes they do, but that is mostly from respiration, where they turn the sugars they made from photosynthesis into useful energy, in the form of ATP, and not so useful energy, in the form of heat.  Using the ATP releases yet more heat.  I never claimed that plants convert heat into sugar, they take light, use the energy from it impacting a chlorophyll (which is in the form of an electron being elevated to a higher energy level, not heat energy), and then using that energized electron to drive the process.  Not all of the energy harvested from the photon is used, some is released as heat.  Endothermic does not necessarily mean "gets colder", it more often means that as the system absorbs energy from the environment, it does not heat up as much as it would if the endothermic reaction were not taking place.  I don't think we really disagree about what endothermic means, I think we're arguing past each other.
I disagree  calling the whole process endothermic, because I don't see the point at which plants take in heat, I only see heat coming out. I don't see how endothermic can not mean "getting colder" it means heat is absorbed from the environment so yeah it will start feeling colder, what else can happen if heat is absorbed? Heat is a process of exchanging collision energy, endothermic/exothermic simply tells us who gets a net positive change in it  - our system or the surroundings. Systems can have both endothermic and exothermic processes but that depends on what you're considering, but when we say system we consider the net change, for a plant its definitely work in -> partial work out + partial heat out , i.e. exothermic.
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Sadrice

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Re: Nether caps - chlorophyll of the caverns
« Reply #31 on: April 01, 2012, 02:55:36 pm »

A system that takes in enough heat energy to raise it's temperature by 10 degrees, but in fact, only raises 5 degrees is endothermic.  Heat energy was trapped by the reaction, usually by being turned into bond energy, but the process wasn't quite efficient enough to get it all, so there's still an increase in temperature.

Photosynthesis is generally considered endothermic (the first page is mostly yahoo answers and wiki.anwers, neither of which are reliable, but there are good sites sprinkled in there).
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psychologicalshock

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Re: Nether caps - chlorophyll of the caverns
« Reply #32 on: April 01, 2012, 03:02:15 pm »

I looked it up myself when we began the conversation and was ALMOST convinced by the plethora of results, but then I thought about it myself and it became apparent that there is no way that photosynthesis can be endothermic. It seems that this is a mistake that is very, very widely made in the biology community because people interpret endothermic reactions as an input of any kind of energy whereas physical chemists and physicists make a very strong distinction between work and heat.

So we just discovered one of the most common mistakes that biologists make.
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psychologicalshock

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Re: Nether caps - chlorophyll of the caverns
« Reply #33 on: April 01, 2012, 03:06:36 pm »

Here's an answer on the page you cited which follows the right line of thinking:

http://www.bio.net/bionet/mm/btk-mca/1993-December/000133.html
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Xnidus

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Re: Nether caps - chlorophyll of the caverns
« Reply #34 on: April 01, 2012, 03:13:00 pm »

It's possible the fungus isn't doing this itself, and has a symbiotic relationship with some sort of autotrophic microorganism.  That's a historically very popular life strategy for fungi, and lichenized fungi are thought by some to have evolved at least 5 separate times (3 in ascomycota, 2 in basidiomycota), though other researchers believe that it's actually the ancestral strategy that was lost in the groups that don't have it, and may have only evolved once or twice.

Yeah, is the same that I say before:

Other option is that all the plant-like organisms of the caverns, are a symbiotic fungus-lithoautotrophic bacteria association. This bacterias used the minerals compounds of the soil and the gases of atmosphere to produce organic products; the fungus create a structure that support and protect the bacterial community, perhaps, synthesizing some toxins against the cavern grazers and other bacterial communities (the fungus have a very complex metabolism that create great toxins, see Amanita; and substances that stop the bacterial grow or directly kill this, see Antibiotics like penicilin). And this symbiotic association support all the cavern ecosistem.

A system that takes in enough heat energy to raise it's temperature by 10 degrees, but in fact, only raises 5 degrees is endothermic.  Heat energy was trapped by the reaction, usually by being turned into bond energy, but the process wasn't quite efficient enough to get it all, so there's still an increase in temperature.

Photosynthesis is generally considered endothermic (the first page is mostly yahoo answers and wiki.anwers, neither of which are reliable, but there are good sites sprinkled in there).

The photosynthesis endothermic in the sense that need external energy, this energy is the light. But the plant have the same temperature than the environment and use high amounts of water for not overheat at cause of this reaction. In some environments use protections against the cold ("hairs" for example) or heat (not photosynthesize).

But the nether caps represent a really big problem if we really said that this creature had a surface more cold than the surrounding environment. Without crazy ideas, the most easy solution is that the nether cap had a surface that the dwarfs can sense easily (a clean and beautiful surface). And the environmental temperature is really cold. For this, when one dwarf touch this material, the termic sensation (not the real temperature) seems cold, or more cold than other cave entities.
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Sadrice

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Re: Nether caps - chlorophyll of the caverns
« Reply #35 on: April 01, 2012, 03:18:21 pm »

That would be reasonable, except I have been totally unable to find any website that claims it is exothermic, and if it is a misconception, it is so universal that it would get on someone's nerves enough that they would rant about it on the internet somewhere.

Perhaps endergonic would be a more appropriate term.  It's a very similar, though not exactly synonymous term, and my organic chem professor often uses *thermic when *gonic would probably be more appropriate, but then, he's not a physical chemist.

EDIT: interesting link, he's the only one I've seen yet that thinks that, I'll pester my general chem teacher about it tomorrow, as he's a physical chemist.  Photosynthesis seems to be clearly endergonic, but it might manage to be exothermic despite that. 

As for the nether cap just seeming cold, the raws specifically state that it is cold.  Perhaps the raws simply describe the dwarves perception?
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psychologicalshock

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Re: Nether caps - chlorophyll of the caverns
« Reply #36 on: April 01, 2012, 03:19:14 pm »



The photosynthesis endothermic in the sense that need external energy, this energy is the light.
Again, this is the wrong type of thinking. Light is not a form of heat. It's in the name guys : endothermic means "heat inside".


That would be reasonable, except I have been totally unable to find any website that claims it is exothermic, and if it is a misconception, it is so universal that it would get on someone's nerves enough that they would rant about it on the internet somewhere.

Perhaps endergonic would be a more appropriate term.  It's a very similar, though not exactly synonymous term, and my organic chem professor often uses *thermic when *gonic would probably be more appropriate, but then, he's not a physical chemist.

EDIT: interesting link, he's the only one I've seen yet that thinks that, I'll pester my general chem teacher about it tomorrow, as he's a physical chemist.  Photosynthesis seems to be clearly endergonic, but it might manage to be exothermic despite that. 

As for the nether cap just seeming cold, the raws specifically state that it is cold.  Perhaps the raws simply describe the dwarves perception?
Caloric theory was  universally accepted, but that didn't mean it was right.

I am a phys chem graduate student, of course that doesn't mean I can't be wrong on the subject but I have taken a pretty in depth class on Statistical Thermodynamics.
« Last Edit: April 01, 2012, 03:23:10 pm by psychologicalshock »
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Sadrice

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Re: Nether caps - chlorophyll of the caverns
« Reply #37 on: April 01, 2012, 03:22:36 pm »

Here is the reply to the message you linked to.

I'm perfectly willing to assume you know more about thermochemistry than I do, it was never my strong point, which is probably why I used endothermic when I was thinking more about endergonic.
« Last Edit: April 01, 2012, 03:37:35 pm by Sadrice »
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psychologicalshock

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Re: Nether caps - chlorophyll of the caverns
« Reply #38 on: April 01, 2012, 03:38:49 pm »

Here is the reply to the message you linked to.
I don't agree with him - heat is a form of energy transfer that does not involve radiation where the energy leaves as vibrational energy in the lattice ,whereas light radiation is a form of energy with a direction and thus is regarded as work.

The deeper explanation for it would  relate it to wave function interaction  where heat and work are just conceptualizations  I mean after all how many molecules need to move in the same direction before something becomes "work" ? So perhaps the distinction between heat and work is somewhat blurry  , but in the macroscopic world it  makes perfect sense.
« Last Edit: April 01, 2012, 03:41:50 pm by psychologicalshock »
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psychologicalshock

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Re: Nether caps - chlorophyll of the caverns
« Reply #39 on: April 01, 2012, 03:51:13 pm »


EDIT: found a lovely (though extremely simplified) reaction coordinate diagram of photosynthesis.  Notice that the line finishes at a higher point that it starts.
Spoiler (click to show/hide)

Cool picture.

The photo part appears to be producing acid and oxygen, then the acid is used for the synthesis part.

So one would assume you'd need a similar reaction in a cave, to produce acid you need some alternative form of energy.
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Xnidus

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Re: Nether caps - chlorophyll of the caverns
« Reply #40 on: April 01, 2012, 03:58:27 pm »



The photosynthesis endothermic in the sense that need external energy, this energy is the light.
Again, this is the wrong type of thinking. Light is not a form of heat. It's in the name guys : endothermic means "heat inside".

When I say that the light is a form of heat? Or... Isn't the light a form of energy?
« Last Edit: April 01, 2012, 04:03:49 pm by Xnidus »
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psychologicalshock

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Re: Nether caps - chlorophyll of the caverns
« Reply #41 on: April 01, 2012, 04:02:33 pm »



The photosynthesis endothermic in the sense that need external energy, this energy is the light.
Again, this is the wrong type of thinking. Light is not a form of heat. It's in the name guys : endothermic means "heat inside".

When I say that the light is a form of heat?
You said that it needs external energy. That external energy is light, thus endothermic.
Endothermic means that the heat is the external energy.
Combine those 2 statements
Light=heat

The correct logic:
The reaction uses energy in the form of light
Light is work
Heat is the output (along with chemical work)
The reaction is exothermic.
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Sadrice

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Re: Nether caps - chlorophyll of the caverns
« Reply #42 on: April 01, 2012, 04:03:09 pm »

This article seems to agree with you, I'll have to try and get a copy from my school library.  If this really is such a common misconception, it seems odd that there's only like 3 people on the internet giving the right explanation.  The more I think about it, the less clear the arguments in either direction seem.  I'll have to do more reading on it later.

EDIT:  a common form of chemolithotroph oxidizes metal sulfides, usually pyrite, to sulfuric acid, leading to acid mine drainage. 

EDIT 2: you said that it is endothermic because it is taking in energy in the form of light.  Psychologicalshock is using a strict (but correct) definition of endothermic, in which the absorbed energy must be in the form of heat, light doesn't count unless it is absorbed to produce heat and then used, which is not what's happening here.  People who are a bit hazy on their thermochemistry use endothermic to mean "absorbs energy", regardless of the form of the energy. 

EDIT 3: It is endergonic, meaning that it absorbs free energy, regardless of form, and converts it into bond energy (right?).
« Last Edit: April 01, 2012, 04:05:42 pm by Sadrice »
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Xnidus

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Re: Nether caps - chlorophyll of the caverns
« Reply #43 on: April 01, 2012, 04:15:53 pm »



The photosynthesis endothermic in the sense that need external energy, this energy is the light.
Again, this is the wrong type of thinking. Light is not a form of heat. It's in the name guys : endothermic means "heat inside".

When I say that the light is a form of heat?
You said that it needs external energy. That external energy is light, thus endothermic.
Endothermic means that the heat is the external energy.
Combine those 2 statements
Light=heat

I'm disagree with this logic. And in actual books of biochemistry (like this, see pag. 249), use a different definitions of endothermic and exothermic; don't use the term "heat", use the term "energy".
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psychologicalshock

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Re: Nether caps - chlorophyll of the caverns
« Reply #44 on: April 01, 2012, 04:19:37 pm »

This article seems to agree with you, I'll have to try and get a copy from my school library.  If this really is such a common misconception, it seems odd that there's only like 3 people on the internet giving the right explanation.  The more I think about it, the less clear the arguments in either direction seem.  I'll have to do more reading on it later.
I thought it was pretty crazy too but it's not all that uncommon - some things are given an approximately correct interpretation and then no one bothers to question it for years on end, until someone does.

Quote
EDIT:  a common form of chemolithotroph oxidizes metal sulfides, usually pyrite, to sulfuric acid, leading to acid mine drainage. 
I have heard about that , sulfur-based energy. Incidentally my map has a lot of pyrite.


Quote
EDIT 2: you said that it is endothermic because it is taking in energy in the form of light.  Psychologicalshock is using a strict (but correct) definition of endothermic, in which the absorbed energy must be in the form of heat, light doesn't count unless it is absorbed to produce heat and then used, which is not what's happening here.  People who are a bit hazy on their thermochemistry use endothermic to mean "absorbs energy", regardless of the form of the energy. 

EDIT 3: It is endergonic, meaning that it absorbs free energy, regardless of form, and converts it into bond energy (right?).

That sounds right. Endergonic isn't a word I have seen used a lot but ergon = work , so that means work is being taken in for the reaction to proceed, this makes perfect sense because the photosynthetic reaction both has a rise in energy (because glucose is more energy rich than its building blocks) and also a lowering of entropy (glucose is a ring of carbons versus its starting components which was a bunch of CO2 molecules). So the only way this clearly unfavorable reaction (delta G > 0) can proceed is if you put work in.
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