lunedì 29 settembre 2014

INTRODUCTION OF THE ORIGIN OF LIFE: Cytoplasm and chemical-physical laws




Post n. 18 English

All cells are made up by a cellular membrane, or plasma membrane, which separates the cell from the external environment. Inside the cell there is a fluid, cytoplasm, which contains the genetic material, various organelles, enzymes, and small molecules. And it is within the cytoplasm that the homeostasis or regulator circuit develops, as Freeman J. Dyson writes in "Origins of Life" in 2002: "Homeostasis is that set of chemical controls and feedback loops that allows each molecular species within the cell, to be produced in the correct proportion: not too much nor too little.
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Without homeostasis there can’t be metabolism, nor an almost stationary equilibrium, in short, nothing that deserve to be called life”. So homeostasis began with the life and is generated by the cytoplasm. Therefore, in order to understand the origin of life, we must dig deeper in to the origin of the components of the cytoplasm. Certainly, the cytoplasm is much more basic than the ones of nowdays, within a secure environment, locked within a rudimentary homeostatic mechanism. What should have been the primary primitive cytoplasm it is always a topic of debate. Certainly, there had to be:

1) Small organic molecules, especially the constituents of nucleic acids and proteins.
1) Proteins such as enzymes, at least a few hundred species according to Dyson.
2) Molecules of nucleic acid, presumably RNA.
4) A closed environment that protects the cytoplasm.

In order to develop a theory on the origin of life, it’s important to know the origin of these components in mind two questions:
First, as we have already explained elsewhere, in the prebiotic era on our planet thousands and thousands of organic substances originated. Many of these substances were of no use; some were even harmful for the origin of life. Then, as we will see from the next article, the regulative principles or constraints must have existed which selected the right substances for life; to use a metaphorical expression, something must have directed the traffic.
Also you need to know, the guidelines, such as chemical-physical laws which allow the formation of a primitive cytoplasm.
These laws belong to thermodynamics and ChemicalKinetisc.

While the 1st law of thermodynamics tells us that energy it is neither created nor destroyed but can be transformed, it is the second principle that seems to set limits to the origin of life. Thermodynamics distinguishes if a process takes place in an isolated system, closed or open, and the resolution of specific problems involving  these processes give physical-chemical students quite a hard time. However, with appropriate approximations to make them more accessible to non-experts, these laws are easy to understand because all the phenomena that we will observe, in a more or less obvious, must follow these laws. Understanding these laws will help us understand to which the extent the origin of life can be explained in terms of the physical sciences.
Imagine a rock on a hill. If you push the rock, it rolls down to the valley and its energy through friction; it is transformed into heat that is dispersed into the surrounding environment. A stone has never been seen spontaneously recovering heat from the environment and roll up the hill.
We can imagine a moving electric train, which is a power failure. The train slowly stops and, through the friction between wheels and rails, and the friction with the air, its “motion” energy is transformed into heat which dissipates into the surrounding environment. An electric train with a power shortage has never been seen running spontaneously without stopping. Finally, imagine a container with water boiling on a burner. If you turn off the heat, the hot water slowly cools to room temperature and the heat is dissipated into the surrounding environment. You will never see the water naturally heat up and reach boiling point on its own.

These examples illustrate the second law of thermodynamics and can be expressed in many ways. Since this principle was discovered in the mid-nineteenth century by studying the thermal machines, it statements: the heat cannot pass spontaneously from a cold body to a warm body.
It seems obvious as statement but its implications are of utmost importance and apply to all physical processes, for life and to the entire universe.
Meanwhile, as it’s clear from the above examples, in spontaneous processes we go from a higher energy state to a lower energy state. The difference in energy is transformed into heat which dissipates into the surrounding environment in the form of chaotic movement of the particles and is no longer usable. Therefore, in nature there is a spontaneous tendency of energy to pass from a useful form, which is neat, to a form useless and disordered.
This trend implies that in all spontaneous processes the level disorder of increases, spontaneous processes tend towards chaos.             
The disorder, in chemical-physics, is called Entropy and is clearly related to the second law of thermodynamics. In fact, another way of stating the second law is: in spontaneous processes, entropy is always increasing.
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In short, the processes are physically allowed are those processes that involve an increase in the disorder, an increase in entropy.
The universe, began with the Big Bang at a million billion degrees, in the phase of expansion it cools and, perhaps in 50 or 100 billion years, will reach the maximum entropy and thus the "Heat Death". Entropy is associated with the loss of structures. A house, for example, although well built, if abandoned by the time deteriorates until it completely loses its structure.
Since the spontaneous processes, over time, are progressing towards an increase in the disorder, entropy is often metaphorically called "The arrow of time." Time, really, flows in only one direction, towards the increase of the disorder and the loss of structures, towards the increase of entropy.
But then, if all goes towards an increase in entropy, as it is possible that living organisms have gone in the opposite direction, towards greater structural complexity?

Order from chaos

When we state that during a spontaneous process the entropy increases, we refer to the final result of the process and not what happens in every single point of the process itself. The stone, which fell from the hill, in the presence of a cataclysm, could end up back on the hill restoring the previous order, but at the end of the cataclysm, the disorder must be greater than the current order. The universe is expanding and its entropy is increasing. This does not exclude that locally a star can form with an ordered solar system, but implies that at the same time somewhere in the galaxy disorder must increase so that in total we have an increase in entropy. During the evolutionary process, a living organism can mutate and its structure become more complex, its entropy is decreased. If the new organism is be best suited for the environment, other organisms will no longer compete and become extinct. The increase of entropy due to the extinction exceeds by far the loss of entropy due to the new structure.
In conclusion, you can have order out of chaos.
Do these arguments, which apply to evolution, apply to the origin of life too? Can a local order within a chaotic process give rise to a primary cytoplasm and therefore to the life?
Ilya Prigogine was convinced that it was possible to explain the origin of life through a series of local orders in a chaotic process. He in the early seventies of the last century studied the chaotic systems, also called systems far from thermodynamic equilibrium. But soon it became clear that the origin of life would take thousands and thousands of local orders and all closely related. It’s like imagining that during a cataclysm thousands of stones are placed on a hill and all one above the other to form a column of stones, which is impossible. The matter is that if within a chaotic system a local order is added to another and another and so on, it’s highly the probable that the system collapses. Thus, after an initial enthusiasm that helped to give the Nobel Prize to Prigogine, the idea was abandoned.
The arguments summarized, and investigated by various scientists, find consensus and acclamation among scholars.
In summary:
The second law of thermodynamics is a fundamental law of nature, nothing can escape this law. It establishes that all spontaneous processes proceed towards disorder, to the loss of structures, to an increase in entropy.
The clock is ticking towards an increase of entropy; it is metaphorically called "the arrow of time."
In a spontaneous process, the origin of a local order and then a decrease in entropy is not excluded, but the total entropy must increase.
The local order helps us to understand the evolutionary process, but the second law of thermodynamics through the entropy seems to indicate the impossibility of the origin of a spontaneous structural complexity, ie the origin of a primitive cytoplasm and therefore the origin of life.
Yet life originated, how was it possible?


Chaos from order
If nothing can escape from the second law of thermodynamics, the origin of a primitive cytoplasm, which led to the origin of life, must have been a set of spontaneous processes that produced entropy: not from order out of chaos, but chaos from order.
But how is chaos from order produced spontaneously? Take a look how salt works. The seawater is contained in basins where it slowly evaporates and salt is deposited on the bottom. But the deposited salt is not an amorphous mass, meaning molecules of salt don’t pile on one another in random order. Salt molecules contain electrical charges, and if the disposal is disordered, for example positive charges in the proximity of other positive charges, the energy content would be too high, which is unstable.
The salt thus creates an ordered and rigorously geometrical structure, a perfect cubic structure, a crystalline structure where the positive charges are oriented towards the negative charges. The ordered crystalline structure is more stable, has a lower energy content than a chaotic ordering. The energy difference between the disordered and ordered structure is transferred to the surrounding environment increasing entropy. Order has created chaos though thus. This is the process by which all the beautiful crystals that we find in nature are formed. So, to understand the origin of a primitive cytoplasm, we have to go looking for a set of spontaneous processes of this type where it’s order that generates chaos.
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The second law of thermodynamics is a fundamental law of nature, it shows us the direction of an event but does not tell us anything about the time when this event will take place.
Thermodynamics states that the rock up the hill, if pushed, will go down the valley. But if the rock is not pushed entropy must stay put. According to thermodynamics, gasoline must react in the presence of oxygen, to produce other products and release heat. But we don’t observe any combustion. An enzyme protein is, initially a linear chain of amino acids. Let us leave aside for the moment how it could form a linear chain of amino acids. According to thermodynamics, in the presence of water and at room temperature this protein is unstable, it should decompose and release the amino acids, but it doesn’t.
Entropy, metaphorically called "the arrow of time", in fact does not contains time.
The time function, in chemical processes, is introduced by the Chemical Kinetics. Indeed, the chemical kinetics tells us that the gasoline reacts with oxygen, but the speed with which this reaction occurs at room temperature is almost zero. And the same goes for the decomposition of protein.
Ultimately, it takes energy to move the rock and roll it down the hill. It takes energy to break bonds within molecules of gasoline, and it takes energy to break the bonds between the amino acids in the protein molecule. Chemical Kinetics tells us that this energy, at room temperature, is not available and therefore, despite the predictions of thermodynamics, the reactions do not occur. And it is here, in this window of time, waiting for an event that should take place but never does, that a way out for life opens.
Returning to the first example, if the stone is not pushed it does not roll down, but if it rains the land becomes muddy and the stone spontaneously sinks into the hill, increasing the entropy. The rock is now more stable and it takes more energy to push down the valley.
In order to break the bonds between amino acids, in the linear chain of proteins, it takes energy which is not available at room temperature. So since the protein molecule has positive charges and negative charges, which establish new bonds among each other and create a helical structure which is more ordered. As Peter W. Atkins explains in "The second principle" 1996, Chapter 8, "The α-helix is ​​favoured over an irregular cluster of amino acids, as it corresponds to the situation of more chaos universe. The chain itself certainly has less chaos, because of the spiral arrangement of more ordered peptide bonds, but the universal chaos is greater because of the energy that is released at the time of the formation of strong hydrogen bonds”. The energy is released as heat which increases the agitation of the water molecules and thus the overall disorder, that is the entropy.

Subsequently the protein, due the effect of certain interactions between different parts of the molecule, folds into a globularstructure. Even this structure, which is more ordered, releases energy that is dispersed into the environment leading to an increase of entropy. The molecule is more stable and more energy is needed to break these new bonds to decompose it. A primitive cytoplasm must have originated through the interaction between the protein molecules within the second law of thermodynamics, whereby it is order which generates chaos, formation structures to produce entropy.
The laws of physics are universal, in space and time. The second law of thermodynamics must have appeared ever since the beginning of the universe, about 13 billion years ago. But the universe at the beginning was made up of only of hydrogen and small amounts of helium and lithium. It is from these elements, after a few billion years, all other elements were formed in the stars. According to Dimitar Sasselov in "Another Earth" in 2012, it took at least 6 billion years for there to be enough of carbon, oxygen, silicon and iron sufficient to give birth to the rocky planets and the first carbon compounds. This means that the second law of thermodynamics has been operating for billions of years on inorganic chemistry producing entropy results of inert crystal aggregation. The crystals often make up beautiful and complex geometric structures or aggregates, which shine with the most various colours.
The initial difficulty in understanding the origin of the crystals has prompted various popular beliefs to attribute magical powers to crystals and some scholars have even attributed souls to the stones. But, as we have written elsewhere, since the time of Steno in the mid-1600s and later Renato Haüy, scientists begun to study crystals and no student of crystallography, mineralogy and geology has never identified in crystals virtue magic or souls.
Inorganic matter is inert, inanimate.
Six billion years after the origin of the universe, amino acids created proteins appear, the second principle follows the same pattern generating entropy due to ordered structures. But proteins come with a surprise, there aren’t inert like crystals. Proteins have the ability to recognize molecules and perform functions like building complex structures, living organisms, which are opposed to chaos, while contributing to the chaos.
The second law of thermodynamics is in the lion’s den.
The difficulty in understanding the origin of life has inspired and still inspires miracles and spirits. In fact what we haven’t understood yet is the secret proteins are hiding.
In the last twenty years, many researches have been performed to understand the structure, dynamics and function of proteins. Mike Williamson, a biochemist at the University of Sheffield, has summarized the results of this research in a book, "Come funzionano le proteine" 2013. According to Williamson, enzymes are not "special". Yet, as he tells us, in millions within the cell, proteins are in contact with each other and carry out various metabolic functions. Certain proteins, assembled into enzymatic complex, become real molecular machines that require a great deal of coordination and multienzymatic complex: the whole is more than sum of the parts. The cyclic reactions resemble a real production line, in which each enzyme performs its specific function and the sublayer is passed on from a specialist to the next. Enzymes are subjected to a system of quality control, through specialized proteins, and those that do not pass inspection are marked and subsequently degraded. Without forgetting symmetrical switches, pumps and sociology of the cell in relation to the dynamics of molecular complex. And finally, the selective pressure can derive into new functions through gene duplication; thus, a copy is maintained for the original function, while the second copy is subject to the action of evolution.
Ultimately, living organisms at the molecular level thanks to the proteins have been using the technology and procedures that man has invented in the last century, for more than three billion years.
How could proteins be not special?
Actually, amino acids are already special, unique compounds, with the right properties necessary for life; and enzymes are also, without their appearance life would not exist, and therefore organic chemistry.
Williamson writes in the first chapter: "What is the purpose of the protein? I hope it is that the recognized "purpose" of a protein is to fulfill some function that helps the host to reproduce the species (which means improving adaptability). Proteins have no other function that could better fulfill the definition of "purpose". [...] The proteins don’t have a "conscience" nor are "trying to reach" any purpose. [...] Consequently, when we try to understand what the function of a protein is, we need to think carefully. In real life ("in nature”) you can say that the task is to make the organism more and more suitable”. This conclusion, however, is simplistic and refers to proteins which, natural selection has developed specific functions for, during the process of evolution of living organisms. There is a basic fact that is ignored: the proteins perform their function even without the presence of the host. Eduard Buchner in 1897 already showed that the fermentation occurs all the same even if the yeast cells were destroyed. In 1926, James Summer succeeded in synthesizing the first enzyme, urease, which decomposes urea into carbon dioxide and water. In short, the function of the proteins is innate within the proteins; inside the cell natural selection is only manipulating the function. The key to the origin of life lies in this ability of proteins to recognize the molecules and to modify them even if they aren’t located within a cell. It is thanks to this function, necessary for life’s origin, the synthesis of complex molecules from simple molecules was possible. Now, as Williamson writes, within the cell the protein’s function is to improve the adaptability of the host; if the proteins are outside the cell, if the host is not there, for whom are the proteins functioning?


                                                                               Giovanni Occhipinti


Translated by:  Sydney Isaiah Lukee                                                                               

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