User:Ujons/Entropy and life

Lead
Research concerning the relationship between the thermodynamic quantity entropy and both the origin and evolution of life began around the turn of the 20th century. In 1910, American historian Henry Adams printed and distributed to university libraries and history professors the small volume A Letter to American Teachers of History proposing a theory of history based on the second law of thermodynamics and on the principle of entropy.

The 1944 book What is Life? by Nobel-laureate physicist Erwin Schrödinger stimulated further research in the field. In his book, Schrödinger originally stated that life feeds on negative entropy, or negentropy as it is sometimes called, but in a later edition corrected himself in response to complaints and stated that the true source is free energy. More recent work has restricted the discussion to Gibbs free energy because biological processes on Earth normally occur at a constant temperature and pressure, such as in the atmosphere or at the bottom of the ocean, but not across both over short periods of time for individual organisms. The quantitative application of entropy balances and Gibbs energy considerations to individual cells has profound implications for growth and metabolism.

Ideas about the relationship between entropy and living organisms have inspired hypotheses and speculations in many contexts, including psychology, information theory, the origin of life, and the possibility of extraterrestrial life.

Entropy of individual cells
Entropy balancing

An entropy balance for an open system, or the change in entropy over time for a system at steady state, can be written as:

$$\frac{dS}{dT} = \frac{\dot{Q}}{T} + \sum_{B} S_{B}*d n_B + \delta S_{gen}$$

Assuming a steady state system, roughly stable pressure-temperature conditions, and exchange through cell surfaces only, this expression can be adapted to express entropy balance for an individual cell as:

$$\frac{dS}{dT} = \frac{\dot{Q}}{T} + \sum_{B}S_B\dot{n}_B-S_X|\dot{n}_X|+\dot{S}_{gen} =0$$

Where

$$\frac{\dot{Q}}{T} = $$ heat exchange with the environment

$$S_B =$$ partial molar entropy of metabolite B

$$S_X = $$ partial molar entropy of structures resulting from growth

$$\dot{S}_{gen} = $$ rate of entropy production

and $$\dot{n} $$ terms indicate rates of exchange with the environment.

This equation can be adapted to describe the entropy balance of a cell, which is useful in reconciling the spontaneity of cell growth with the intuition that the development of complex structures must overall decrease entropy. From the second law, $$\dot{S}_{gen} > 0$$; due to internal organization resulting from growth, $$S_X$$ will be small. Metabolic processes force the sum of the remaining two terms to be less than zero through either a large rate of heat transfer or the export of high entropy waste products. Both mechanisms prevent excess entropy from building up inside the growing cell; the latter is what Schrödinger described as feeding on negative entropy, or "negentropy".

Implications for metabolism

In fact, it is possible for this “negentropy” contribution to be large enough that growth is fully endothermic, or actually removes heat from the environment. This type of metabolism, in which acetate, methanol, or a number of other hydrocarbon compounds are converted to methane (a high entropy gas), is known as acetoclastic methanogenesis; one example is the metabolism of the anaerobic archaebacteria Methanosarcina barkeri. At the opposite extreme is the metabolism of anaerobic thermophile archaebacteria Methanobacterium thermoautotrophicum, for which the heat exported into the environment through fixation is quite high (~3730 kJ/C-mol).

Generally, in metabolic processes, spontaneous catabolic processes that break down biomolecules provide the energy to drive non-spontaneous anabolic reactions that build organized biomass from high entropy reactants. Therefore, biomass yield is determined by the balance between coupled catabolic and anabolic processes, where the relationship between these processes can be described by:

$$\Delta_r G_s = (1-Y_{X/S}) \Delta G_{catabolism} + Y_{X/S} \Delta G_{anabolism} $$

where

$$\Delta_r G_s =  $$ total reaction driving force/ overall molar Gibbs energy

$$Y_{X/S} =  $$ biomass produced

$$\Delta G_{catabolism} =  $$ Gibbs energy of catabolic reactions (-)

$$\Delta G_{anabolism} =  $$ Gibbs energy of anabolic reactions (+)

Organisms must maintain some optimal balance between $$\Delta_r G_s $$ and $$Y_{X/S}   $$ to both avoid thermodynamic equilibrium ($$\Delta_r G_s  = 0  $$), at which biomass production would be theoretically maximized but metabolism would proceed at an infinitely slow rate, and the opposite limiting case at which growth is highly favorable ($$\Delta_r G_s  << 0  $$), but biomass yields are prohibitively low. This relationship is best described in general terms, and will vary widely from organism to organism. Because the terms corresponding to catabolic and anabolic contributions would be roughly balanced in the former scenario, this case represents the maximum amount of organized matter that can be produced in accordance with the 2nd law of thermodynamics for a very generalized metabolic system.

Entropy and the search for extraterrestrial life
In 1964, James Lovelock was among a group of scientists requested by NASA to make a theoretical life-detection system to look for life on Mars during the upcoming Viking missions. A significant challenge in this task was determining how to construct a test that would reveal the presence of extraterrestrial life with significant differences from biology as we know it. In considering this problem, Lovelock asked two questions: "How can we be sure that the Martian way of life, if any, will reveal itself to tests based on Earth's life style?", as well as the more challenging underlying question: "What is life, and how should it be recognized?"

Because these ideas conflicted with more traditional approaches that assume biological signatures on other planets would look much like they do on Earth, in discussing this issue with some of his colleagues at the Jet Propulsion Laboratory, he was asked what he would do to look for life on Mars instead. To this, Lovelock replied "I'd look for an entropy reduction, since this must be a general characteristic of life." This idea was perhaps better phrased as a search for sustained chemical disequilibria associated with low entropy states resulting from biological processes, and through further collaboration developed into the hypothesis that biosignatures would be detectable through examining atmospheric compositions. Lovelock determined through studying the atmosphere of Earth that this metric would indeed have the potential to reveal the presence of life. This had the consequence of indicating that Mars was most likely lifeless, as its atmosphere lacks any such anomalous signature.

This work has been extended upon recently as a basis for biosignature detection in exoplanetary atmospheres. Essentially, the detection of multiple gasses that are not typically in stable equilibrium with one another in a planetary atmosphere may indicate biotic production of one or more of them, in a way that does not require assumptions about the exact biochemical reactions extraterrestrial life might use or the specific products that would result. A terrestrial example is the coexistence of methane and oxygen, the latter of which would eventually deplete if not for continuous biogenic production. The amount of disequilibrium can be described by differencing observed and equilibrium state Gibbs energies for an observed atmosphere composition; it can be shown that this quantity has been directly affected by the presence of life throughout Earth's history. Imaging of exoplanets by future ground and space based telescopes will provide observational constraints on exoplanet atmosphere compositions, to which this approach could be applied.

However, there is a caveat in this idea related to the potential for chemical disequilibria to serve as an anti-biosignature depending on the context. In fact, there was probably a strong chemical disequilibrium present on early Earth before the origin of life due to a combination of the products of sustained volcanic outgassing and oceanic water vapor. In this case, the disequilibrium was the result of a lack of organisms present to metabolize the resulting compounds. This imbalance would actually be decreased by the presence of chemotrophic life, which would remove these atmospheric gasses without producing oxygen via photosynthesis up until the advent of aerobic metabolism.

Entropy and the origin of life
The second law of thermodynamics applied to the origin of life is a far more complicated issue than the further development of life, since there is no "standard model" of how the first biological lifeforms emerged, only a number of competing hypotheses. The problem is discussed within the context of abiogenesis, implying gradual pre-Darwinian chemical evolution.

Relationship to prebiotic chemistry
In 1924, Alexander Oparin suggested that sufficient energy for generating early lifeforms from non-living molecules was provided in a "primordial soup". '''The laws of thermodynamics impose some constraints on the earliest life-sustaining reactions that would have emerged and evolved from such a mixture. Essentially, in order to remain consistent with the second law of thermodynamics, self organizing systems that are characterized by lower entropy values than equilibrium must dissipate energy so as to increase entropy in the external environment.'''

Early biosynthetic pathways were probably selected towards their ability to avoid high entropy states. '''One consequence of this is that low entropy or high chemical potential chemical intermediates cannot build up to very high levels if the reaction leading to their formation is not coupled to another chemical reaction that releases energy. These reactions often take the form of redox couples, which must have been provided by the environment at the time of the origin of life. In today's biology, many of these reactions require catalysts (or enzymes) to proceed, which frequently contain transition metals. This means identifying both redox couples and metals that are readily available in a given candidate environment for abiogenesis is an important aspect of prebiotic chemistry.'''

'''The idea that processes that can occur naturally in the environment and act to locally decrease entropy must be identified has been applied in examinations of phosphate's role in the origin of life, where the relevant setting for abiogenesis is an early Earth lake environment. One such process is the ability of phosphate to concentrate reactants selectively due to its localized negative charge.'''

'''In the context of the alkaline hydrothermal vent (AHV) hypothesis for the origin of life, Michael Russell employed a framing of life as “entropy generators” in attempt to develop a framework for abiogenesis under alkaline deep sea conditions. Assuming life develops rapidly under certain conditions, experiments may be able to recreate the first metabolic pathway, as it would be the most energetically favorable and therefore likely to occur. In this case, iron sulfide compounds may have acted as the first catalysts. Therefore, within the larger framing of life as free energy converters, it would eventually be beneficial to characterize quantities such as entropy production and proton gradient dissipation rates quantitatively for origin of life relevant systems (particularly AHVs).'''

Other theories
The evolution of order, manifested as biological complexity, in living systems and the generation of order in certain non-living systems was proposed to obey a common fundamental principal called "the Darwinian dynamic". The Darwinian dynamic was formulated by first considering how microscopic order is generated in relatively simple non-biological systems that are far from thermodynamic equilibrium (e.g. tornadoes, hurricanes). Consideration was then extended to short, replicating RNA molecules assumed to be similar to the earliest forms of life in the RNA world. It was shown that the underlying order-generating processes in the non-biological systems and in replicating RNA are basically similar. This approach helps clarify the relationship of thermodynamics to evolution as well as the empirical content of Darwin's theory.

In 2009, physicist Karo Michaelian published a thermodynamic dissipation theory for the origin of life in which the fundamental molecules of life; nucleic acids, amino acids, carbohydrates (sugars), and lipids are considered to have been originally produced as microscopic dissipative structures (through Prigogine's dissipative structuring ) as pigments at the ocean surface to absorb and dissipate into heat the UVC flux of solar light arriving at Earth's surface during the Archean, just as do organic pigments in the visible region today. These UVC pigments were formed through photochemical dissipative structuring from more common and simpler precursor molecules like HCN and H2O under the UVC flux of solar light. The thermodynamic function of the original pigments (fundamental molecules of life) was to increase the entropy production of the incipient biosphere under the solar photon flux and this, in fact, remains as the most important thermodynamic function of the biosphere today, but now mainly in the visible region where photon intensities are higher and biosynthetic pathways are more complex, allowing pigments to be synthesized from lower energy visible light instead of UVC light which no longer reaches Earth's surface.

Jeremy England developed a hypothesis of the physics of the origins of life, that he calls 'dissipation-driven adaptation'. The hypothesis holds that random groups of molecules can self-organize to more efficiently absorb and dissipate heat from the environment. His hypothesis states that such self-organizing systems are an inherent part of the physical world.