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Author Topic: Nether caps - chlorophyll of the caverns  (Read 16784 times)

psychologicalshock

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Re: Nether caps - chlorophyll of the caverns
« Reply #45 on: April 01, 2012, 04:21:59 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".

Funny how that works isn't it? A whole generation of books have made this mistake and probably generations before them as well, but it's in the word : Endothermic.
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Xnidus

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Re: Nether caps - chlorophyll of the caverns
« Reply #46 on: April 01, 2012, 04:22:54 pm »

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.

Ok, I like this.
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psychologicalshock

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Re: Nether caps - chlorophyll of the caverns
« Reply #47 on: April 01, 2012, 04:38:39 pm »

Speaking of Endergonic and Endothermic -
An Endergonic reaction CAN be Endothermic. This implies our Enthalpy  is going up but we have a negative Entropy overpowering it at the temperature we're at, so if we lowered the temperature the reaction would become exergonic and endothermic.

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Kofthefens

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Re: Nether caps - chlorophyll of the caverns
« Reply #48 on: April 01, 2012, 05:47:52 pm »

Hmm... This thread has science that is far more advanced than I know about. PTW
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Re: Nether caps - chlorophyll of the caverns
« Reply #49 on: April 02, 2012, 02:47:09 pm »

What does anyone else think?

I think spiders.

Naryar

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Re: Nether caps - chlorophyll of the caverns
« Reply #50 on: April 02, 2012, 03:28:44 pm »

Hate thermodynamics. I know I should put myself to it one day though.

Anyways, I just realized that you can make nether cap axles that will not melt in magma !

wierd

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Re: Nether caps - chlorophyll of the caverns
« Reply #51 on: April 02, 2012, 03:40:18 pm »

There was a recent paper released showing that LEDs can emit more photonic energy than they receive as electricity, if they are held just slightly above the tipping point for the LED's operation in terms of voltage and current.

Turns out that the thermal noise in the junction provides the extra energy, resulting in the junction geting colder, emitting the heat energy as light, despite the obvious thermodynamic violation.

The situation requires a highly ordered structure to pull off though.

Many organic compounds can function as semiconductor materials, and a complex process to bump a valence electron to do chemical work instead of emitting a photon using a similar system seems possible, if improbable. (Then again, the crazy complex "dance" of quantum physics that enables chlorophyll to work is also crazy to imagine being a random convergence too, if it wasn't there staring you in the face.)

Granted, I don't see an organism getting 100% of its bioavailable energy that way. It would help offset the energy production problem of the cavern system though.

complimentary article
« Last Edit: April 02, 2012, 03:54:54 pm by wierd »
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Ramirez

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Re: Nether caps - chlorophyll of the caverns
« Reply #52 on: April 02, 2012, 04:16:56 pm »

I think one of the main problems people seem to have with thermodynamics is that chemists tend to simply use the term "heat" to mean energy. They almost completely disconnect the term "heat" from "temperature".

Anyway, back on topic. One of the principles of entropy is that within an isolated system entropy can only increase (or remain the same), but never decrease. As decreasing temperatures decreases entropy, this entropy would have to be shifted elsewhere (an example is how refrigerators work, they decrease their contents entropy but instead increase the temperature and entropy of their surroundings in the process, both through their heatsinks at the back and the fuels burnt to produce their electricity). This means that for the mushrooms of the nether cap to chill themselves indefinately, they would have to generate vast amounts of heat somewhere (which could be in the bulk fungus which saturates the underground soil and mud).

However the nether cap retains its properties even when cut down, so therefore there are only really three ways I can think of to explain its properties: one is practically infinite heat capacity (so no amount of energy would be able to change its temperature) while the other is a vast reservoir of chemicals inside itself that have appropriate processes (either physical or chemical) that would maintain it's temperature. The third option is magic.
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RedWick

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Re: Nether caps - chlorophyll of the caverns
« Reply #53 on: April 02, 2012, 04:23:53 pm »

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slothen

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Re: Nether caps - chlorophyll of the caverns
« Reply #54 on: April 02, 2012, 04:31:50 pm »

wrong kind of science
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NonconsensualSurgery

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Re: Nether caps - chlorophyll of the caverns
« Reply #55 on: April 02, 2012, 04:38:08 pm »


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


Many microbes do eat rocks but they do so very, very slowly. The ones that are comfortable in a sealed environment can take thousands of years to divide. If you leave a fingerprint in a deep (far from bats) cave, microbes will still be fighting over the massive influx of nutrients left behind in the oils long after you're dead and gone. The only place you find enough energy to power nightmarish interesting ecosystems from hell is in caverns that are treated to a constant shower of bat guano and sick, dying, easily preyed-upon bats.

Sane people do not voluntarily go to such places, and the insane require a special kind of insanity that lets them cope with being chest-deep in a fluffy mixture of moving, wriggling insects and bat guano that's trying to work its way past the gas mask to get at what they smell underneath without simply giving in and letting the horde of creatures take the nutrients off their bones.

http://www.yourdiscovery.com/video/dirty-jobs-bat-biologist/

Personally, the idea that nether-caps and others perform a magical kind of photosynthesis that can't happen in the light makes more sense to me than any of the alternatives. Nether-caps obviously contain Maxwell's demons in place of chloroplasts.
« Last Edit: April 02, 2012, 04:43:14 pm by NonconsensualSurgery »
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Deon

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Re: Nether caps - chlorophyll of the caverns
« Reply #56 on: April 02, 2012, 05:43:55 pm »

Magic.
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wierd

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Re: Nether caps - chlorophyll of the caverns
« Reply #57 on: April 02, 2012, 06:26:57 pm »


*EDIT*

Damn, this is a really long post! I apologise for its lack of brevity! Hopefully this will explain how it could theoretically be possible to have something like nethercaps actually do the things they do.

*/EDIT*



Boiled down:
Thermodynamic laws.

1) in a closed system, the change in  internal energy is equal to the amount of heat, minus the work donne.

2) in a closed system, entropy can only increase or stay the same, but never decrease.

3) the entropy of a perfect crystal at absolute zero is exactly 0.


Assertions:

The cavern system is not closed. Energy is continually added to the system via a semi-steady influx of heat, light, and chemical energies from volcanic processes. Excess thermal waste bleeds out of the system through passive diffusion through the surrounding rock. Nearby volcanism injects hydrogen sulfide (SH2),sulfur dioxide (SO2), and carbon dioxide (CO2) gasses, which permeate heat fractured rocks along depositional layers and faults. A slow but steady stream of these gasses enters the ecosystem from the floor of cavern layer 3. In addition, there is a surplus heat gradient of cavern layer 3, vs cavern layer 2. Heat flows from layer 3 to layer 2, in the attempt at reaching equilibrium. This disequlibrium can drive thermal processes to perform work. (See carnot heat engines, such as sterling engines. See also the "overunity" LED pointed to earlier.)

Observations:

Nether caps lower surrounding temperatures, creating a thermal gradient.  The law of energy states that energy is never destroyed. This means the thermal energy is converted to some other form for the thermal gradient to exist. Since the nether cap does not emit energy of any known form, the energy must be stored in some fashion, such as in chemical bonds. This implies an endothermic metabolic process.  In order to create a thermal gradient, energy must be expended to perform this sequestration. This energy cannot logically come from heat, because it is being used to move heat, unless a gradient of some sort is already existing that can be exploited. (In this case, however, the induced gradient cannot be greater than the natural one powering it.)

Nether caps grow in cavern layer 3, which has the highest concentration of chemical energy from the volcanic vent. The chemical energy from the volcanic vent supplies the energy needed to create a strong thermal gradient with which to do useful work.  This implies the consumption of several chemical reactants for energy, to create a reaction gradient favorable to the synthesis of the high energy compound. This reaction must be exothermic.

This means:

1) nether caps respire osmotically, absorb SO2, CO2, and H2O, and synthesize H2SO4 as a primary source of chemical energy.  Reaction of H2SO4 with metallic ions in the bedrock can provide a low level ion pump, which can drive other reactions.

2) nether caps use this energy from the chemotrophic metabolism of sulfur and water along with the low grade electrical potential of the sulfuric acid waste product interacting with the mineral substrate to fascilitate the synthesis of more complex molecules for long term energy storage. This synthesis reaction makes use of the absorbed CO2, is endothermic, and uses a methodology similar to the prevoisly cited "over unity" LED. More chemical energy is stored than is produced by the chemical respiration of the sulfur cycle, by passive absorption of thermal energy.

3) the stored chemical energy of the long term energy-rich storage compound is released to further promote heat energy "consumption" via a secondary exothermic respiration reaction.

4) the energy released by exothermic reactions is less than the thermal energy absorbed, by exploitation of the energy state thresholds of the enzymic catalysts used. (In the case of the LED, a low level electrical current just barely enough to bridge the bandgap of the semiconductor produces more photons than the source input should normally allow. The difference in photon output comes from the random fluctuations in the baseline of the junction caused by thermal noise. The thermal noise is just enough to push the valence electrons across the band gap, releasing the energy as a photon. The temperature of the junction drops proportionally to the energy of the photon emitted. The nethercap, however, uses a semiconducting enzyme near the cellular membrane that makes use of the ionic potential between the internal H2SO4 concentration, and the metallic ions outside, to prime itself as the current source. Passive thermal absorption by the enzyme is then converted into useful work by adding additional electrons to its substrate. Rather than emit the energy as photons, it emits the energy by pushing a higher energy valence electron out of place, catalyzing a higher energy reaction than it would otherwise be able to do. This is similar to what chlorophyll does when it absorbs photons to push electrons into higher energy states to form sugars.) Metabolism of the stored energy molecule is used to increase enzyme density, concentrate absorbed fuel gasses, and improve internal cellular efficiency. This increases the rate of thermal conversion, favoring sequestration of energy rich compounds.

This places bounds on the degree of induced thermal gradient that nethercaps can create, however. Outside of the "sweet spot" used by its enzyme, nethercap metabolism would be adversely effected. This means nethercaps would not be able to handle extreme temperatures. (They would want the environs to be a very precise temperature range. Outside of that range, they can't do their thermodynamic trickery.) This may further explain nethercap specificity to cavern layer 3. (Higher layers are too cold!) If nethercaps absorbed energy too quickly, they would suffer from being too cold. It is likely that the "coolness" of nethercaps is likely only a few degrees cooler than the bedrock they grow on.

Rate of energy sequestration would be directly tied to the rate of sulfur respiration, and the degree of electrical potential that could be induced between the cytoplasm and the mineral bedrock, with bounds set by the thermal reactivity range of the sequestering enzyme, and surface area used for the reaction.

In contrast to green plants, where complex synthesis happens in the leaves, the nethercap electro-thermalsynthetic reaction would take place in the "roots", where the electrical charge gradient is the highest.  Being a mushroom, this means the reaction occurs in the mycelium.

The fruiting bodies of mushrooms form as the result of two or more colonies of genetically heterogenous mycelium coming into contact with each other.  Mycelial fibers from both colonies act on each other through hormonal signals to rapidly grow, and produce a fruiting body. Within the fruiting body, gametes from each culture combine to create the spores that develop inside. Due to this, energy is concentrated in the fruiting body.

For this reason, I would personally expect nethercaps to make the ground cooler, but to be slightly exothermic in their fruiting bodies, like other fungi. The difference would be that nethercaps would be capable of actually adding energy to an ecosystem instead of consuming it.

That nethercap wood would be inducing a strong gradient at all defies rational explanation, given what little I know about chemistry and thermodynamic systems.


« Last Edit: April 02, 2012, 06:46:24 pm by wierd »
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psychologicalshock

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Re: Nether caps - chlorophyll of the caverns
« Reply #58 on: April 02, 2012, 07:11:59 pm »

There was a recent paper released showing that LEDs can emit more photonic energy than they receive as electricity, if they are held just slightly above the tipping point for the LED's operation in terms of voltage and current.

Turns out that the thermal noise in the junction provides the extra energy, resulting in the junction geting colder, emitting the heat energy as light, despite the obvious thermodynamic violation.

There is no violation. The first law states that internal energy must be conserved;  however, heat and work do not have to be conserved as they can convert into one another. The limitation is mechanical, not thermodynamic.

For example - car engines convert heat into work with pretty damn good efficiency, the fact that LEDs can convert vibrational motion into light doesn't violate thermodynamics.  Thermodynamics has one unwritten "rule" or rather tendency   : Thermodynamic laws have  NEVER been observed to be violated despite  many claims (the most common being life).



Quote

complimentary article

"At first glance this conversion of waste heat to useful photons could appear to violate fundamental laws of thermodynamics, but lead researcher Parthiban Santhanam of the Massachusetts Institute of Technology explains that the process is perfectly consistent with the second law of thermodynamics. "The most counterintuitive aspect of this result is that we don't typically think of light as being a form of heat. Usually we ignore the entropy and think of light as work," he explains. "If the photons didn't have entropy (i.e. if they were a form of work, rather than heat), this would break the second law. Instead, the entropy shows up in the outgoing photons, so the second law is satisfied.""


Interesting outlook, but from what I can see what is going on is that the band gap is small so thermal collisions are managing to excite electrons into the "free" state where they then flow to create light. From what I can tell he means to say that the light created is "entropic" by virtue of it being random in direction which is ok except light is very easy to redirect, unlike collisions so for practical purposes it's thought of as usable work. Taking photosynthesis for example the light falling on plant matter is all unidirectional.
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Kofthefens

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Re: Nether caps - chlorophyll of the caverns
« Reply #59 on: April 02, 2012, 07:51:53 pm »

Excess thermal waste bleeds out of the system through passive diffusion through the surrounding rock. Nearby volcanism injects hydrogen sulfide (SH2),sulfur dioxide (SO2), and carbon dioxide (CO2) gasses, which permeate heat fractured rocks along depositional layers and faults. A slow but steady stream of these gasses enters the ecosystem from the floor of cavern layer 3. In addition, there is a surplus heat gradient of cavern layer 3, vs cavern layer 2. Heat flows from layer 3 to layer 2

If I understand you correctly, that means that the excess heat could power other plants in the higher caverns.
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