sabato 20 dicembre 2014

THE ORIGIN OF PROTEINS: The fundamental problems. Part One





Post n. 19 English

The water is made up of hydrogen and oxygen. We know the electronic structure of these two elements, their chemical-physical properties, but from this knowledge, we do not have information on the properties of water. The fact that water is liquid at room temperature is an emergent property that is not contained in the individual parts, which are hydrogen and oxygen. What is valid for the water is valid for all substances, whether they consist of a few atoms or from thousands of atoms. Ultimately with the term "emergence" we mean the appearance of a new property that is not contained in the individual parts. We also refer to an emergence when a number of complex substances, each with its own properties, are part of a complex interacting system. For many scientists life is an emergent property that is generated by a complex system of interactions of all the molecular species present in a cell. The emergence has to be understood as the way Ernst Mayr wrote in "The uniqueness of biology", 2005: «The appearance of unexpected characteristics in complex systems». «It does not enclose any kind of metaphysics implications». «Often in complex systems properties that are not obvious appear (nor can be predicted) even though we know the individual components of these systems».
The current organisms are very complex. Even the most simple uses thousands of species of organic macromolecules: nucleic acids, proteins, lipids, carbohydrates. It is always subject of debate, which ones and how many of these organic compounds were part of the primitive interacting complex system from which emerge we have homeostasis, ie a cytoplasm that gave birth to a proto body. Scientists, who deal with the problem of the origins of life, however all agree that two complex molecules couldn’t have been absent: the nucleic acids, probably the RNA, and proteins. These two macromolecules are interdependent in the sense that the nucleic acid contains the program to synthesize proteins. But the nucleic acid alone is unable to synthesize itself, it needs the proteins to do so. That is because they are interdependent: one always needs the other.
The origin of these fundamental macromolecules to this day is a mystery.
As Pier Luigi Luisi clarifies in "Sull’origine della vita e della biodiversità" in 2013, about the theories on the origin of life: «They all share a major problem: each of these theories must begin with a series of more or less arbitrary assumptions». Moreover, in reference to the fundamental macromolecules, he adds: «In fact, the vast majority of hypothesis ignores the main problem, that of the biogenesis of macromolecules with an ordered sequence in many identical copies».
But if the main problem is the genesis of the fundamental macromolecules, then the first objective of a theory for the origin of life must be to understand the origins of nucleic acids and proteins in the prebiotic era.
The RNA constituents are nucleotides. They are formed by a phosphate group, the ribose which belongs to the family of sugars and the nucleobases (adenine, cytosine, guanine and uracil). As we have already fully described in previous articles, sugars and nitrogenous bases in the prebiotic era did not exist. All research on these compounds are laboratory experiments without any connection to the prebiotic environment.
On the other hand, except for some astrophysicist, all those involved in the origin of life agree in considering plausible Miller's experiment. It is therefore to be considered that in the prebiotic era, starting from simple molecules such as methane, ammonia, water and other simple molecules thousands of organic compounds were formed and among them were amino acids too.
The presence of amino acids in the prebiotic era was confirmed by the analysis of meteorites dating back to the time of formation of the solar system. In particular, in the carbonaceous chondrites there was a presence of amino acids similar in quality and quantity, to that found by Miller in his experiment.
Since amino acids are the constituents of proteins, it is reasonable to conclude that in the first prebiotic era, the fundamental macromolecules to appear were just proteins. The formation of these complex molecules is therefore an important step towards the origin of a primitive cytoplasm and therefore towards the origin of life.
As we already discussed in other articles, protein synthesis however is problematic, but to be complete to those with less competences, it will be useful to repeat with some examples. 
it.wikipedia.org


1) Our hands are a mirror image of each other, right and left, and there is no visual correspondence if stacked. Forms, which are mirror images, not superposable, are called chiral. Alanine is an amino acid constituent of our proteins. If we want to prepare in laboratory 1g of alanine, we won’t get 1g of a single molecular, but 0.5 g of a right-handed (D) and 0.5g of its mirror image left-handed (L). The amino acids are therefore chiral and in fact, the amino acids obtained by Miller in his experiment are chiral. And chiral amino acids are also found in meteorites. Also amino acids formed in the prebiotic era, about 4 billion years ago, were surely chiral. There were two structures L (levo) and its mirror image D (destro).


                                             L(levo)                                   D (destro)


These two molecular forms have the same chemical-physical properties and always travel together. Since both the D-form and the L-form were dissolved in water in the prebiotic era, the molecular disorder would produce cross-reactions between L and D amino acids and given birth to proteins containing the two forms, but of no biological interest.
The issue is that in all living organisms, proteins are made up of only L-form amino acids. 

                                                                         L(levo)


Since the existing living organisms descended by evolution from primitive organisms, also the proteins of primitive organisms had to be constituted by L amino acids. But then, if the two molecular forms having the same chemical-physical properties and were inseparable, how come the choice fell on L amino acids and what happened to the Destro?

2) In the prebiotic era a large number of different amino acids were surely available. In Miller’s experiment, for example, about 60 different amino acids were found as many as in meteorites.
But in the current living organisms, only 20 amino acids are necessary for the formation of proteins.
How did the choice of the 20 amino acids occur?

3) The reaction between amino acids for the formation of proteins takes place with the elimination of H2O.

 In prebiotic conditions, in an aqueous environment, this reaction is not spontaneous because it goes against the second law of thermodynamics. It would like seeing a rock spontaneously rolling up a hill.
These problems are interconnected and it makes no sense to imagine to solve three different models. You cannot think that for the first problem it was just by chance, for the second based on an evolutionary process and the third due to a puddle in evaporation.
On these issues Giuseppe Galletti and Valentina Sorgi in "Astrobiologia: le frontiere della vita" in 2009, identified the centrality of the problem when they say: «These features should be explained, possibly with a single initial model».
In addition to these three specific points, there are other general questions that need be answered.
A) As Miller's experiment showed, in the prebiotic era there were many other organic substances. Most of these substances were definitely useless, if not harmful and would jeopardize the formation of polymers.
B) The concentration of amino acids, dissolved in water, was certainly very low and, in such conditions, the synthesis of the polymers would have been impossible.
It is therefore logical to conclude that in the prebiotic era, chemical and physical constraints of the prebiotic environment worked as an organized principle for selection and concentration of substances essential for the origin of life and subsequently catalyse the formation of the macromolecules necessary for life.
It is also not possible that these processes took place in the North Pole, on the equator and another on the South Pole. These processes must be located in the same spot.
But the location alone is not enough. As suggested by Paul Davies in relation to these issues, selection, concentration and catalysis must take place simultaneously. You can not think that amino acids at a given moment are selected, then the Levo are selected after a month and after one year the catalysis occurs.
Ultimately, the unique initiation pattern must contain: selection, concentration and catalysis, and all must have be a simultaneous and localized processes.
Science has long highlighted that the planets, the stars and the entire universe are the product of chance and natural laws: chance and necessity. And no doubt that the evolution of living organisms is the result of chance and necessity too.
Did chance and necessity govern the first steps of the origin of life, specifically, the synthesis of biopolymers? If the steps listed above are part of a single coherent model, there are two possibilities: either the events were all random or were all deterministic. Introducing here and there, with discretion, some random event, or to use the new terminology some "frozen accident", it is just an expedient ad hoc to support theories which lack credibility. But the probability that all the steps listed above were random events and coincidence is like screaming out a miracle. Therefore, the events that led to the origin of the proteins must have all been deterministic.
Well, is there a theory that gives us an organizing principle and allows us to build a coherent model exclusively through deterministic processes?
In a century of research on the origin of life, the only scientist who suggested a solution was J. D. Bernal in 1951. As known clays are formed of various stacked crystalline layers. Each layer consists of two sub layers, one of silica tetrahedrons (Si2O52-) the other of octahedrons of hydrated alumina   
Al2(OH)42+]n. Without going into details, due the presence of electric charges the various layers or under layers are neutralized at a distance. Between one layer and the other or between an under layer and another there are empty spaces whereby water molecules or molecules that exhibit electric dipoles like the fundamental constituents of the macromolecules, can settle it. It is calculated that in a cm3 of clay the surface of these empty spaces is equivalent to almost the area of ​​a football field. Bernal suggested that the clays could select and concentrate the essential ingredients for the origin of life and subsequently catalyze the formation of the macromolecules necessary for life. He also suggested the importance of quartz in the formation of primitive molecules. Quartz in fact is found together with clay and presents, just like amino acids, a D and L form, and could have caused a prefered adsorption, separating the Destro from Levo. Since inside the clay there would be simultaneity and location, the hypothesis of Bernal gives us, in fact, a consistent model.                                                                                                              

Giovanni Occhipinti

Translated by: Sydney Isae Lukee

lunedì 15 dicembre 2014

L'ORIGINE DELLE PROTEINE (Prima Parte)




Post n. 19

L’acqua è costituita da idrogeno e ossigeno. Noi conosciamo la struttura elettronica di questi due elementi, le loro proprietà chimico-fisiche, ma da queste conoscenze non possiamo desumere le proprietà dell’acqua. Il fatto che l’acqua è liquida a temperatura ambiente è una proprietà emergente che non è contenuta nelle singole parti, cioè nell’idrogeno e nell’ossigeno. Ciò che è valido per l’acqua è valido per tutte le sostanze, siano esse costituite da pochi atomi o da miglia di atomi. In definitiva con il termine “emergenza” si intende la comparsa di una nuova proprietà che non è contenuta nelle singole parti. Si parla anche di emergenza quando un certo numero di sostanze complesse, ciascuna con le sue proprietà, fanno parte di un complesso sistema interagente. Per molti scienziati la vita è una proprietà emergente che si genera da un complesso sistema di interazioni di tutte le specie molecolari presenti in una cellula. Emergenza la si deve intendere nel significato dato da Ernst Mayr in “L’unicità della biologia” 2005: «La comparsa di caratteristiche impreviste in sistemi complessi». «Essa non racchiude nessuna implicazione di tipo metafisica». «Spesso nei sistemi complessi compaiono proprietà che non sono evidenti (né si possono prevedere) neppure conoscendo le singole componenti di questi sistemi».
Gli attuali organismi viventi sono molto complessi. Anche i più semplici utilizzano alcune migliaia di specie di macromolecole organiche: acidi nucleici, proteine, lipidi, carboidrati. Quali e quanti di questi composti organici  facessero parte di un primitivo sistema complesso interagente da cui emerge l’omeostasi, cioè un citoplasma che ha dato origine ad un proto organismo, è sempre oggetto di dibattito.  Gli scienziati che si occupano del problema dell’origine della vita sono però tutti d’accordo nel ritenere che due molecole complesse non potevano mancare: gli acidi nucleici, verosimilmente l’RNA, e le proteine. Queste 2 macromolecole sono  interdipendenti nel senso che l’acido nucleico contiene il programma per sintetizzare le proteine. Ma l’acido nucleico da solo non riesce a sintetizzarsi e ha bisogno delle proteine per essere sintetizzato. Ecco perché sono interdipendenti: l’uno ha sempre bisogno dell’altro.
 L’origine di queste macromolecole fondamentali è però, a tutt'oggi, un mistero.
Come chiarisce Pier Luigi Luisi in “Sull’origine della vita e della biodiversità” 2013, in merito alle teorie sull’origine della vita: «Tutte condividono un problema  principale: ognuna di queste teorie deve partire da una serie di assunzioni più o meno arbitrarie». E in riferimento alle macromolecole fondamentali aggiunge: «Infatti, la grande maggioranza delle ipotesi ignora il problema principale, quello della biogenesi delle macromolecole a sequenza ordinata in molte copie identiche».
Ma, se il problema principale è la genesi delle macromolecole fondamentali, allora il primo obiettivo di una teoria per l’origine della vita deve essere quello di capire l’origine, in epoca prebiotica, di acidi nucleici e proteine.
I costituenti dell’RNA sono i nucleotidi. Essi sono formati da un gruppo fosfato, dal ribosio appartenente alla famiglia degli zuccheri e dalle basi azotate (adenina, citosina, guanina e uracile). Come abbiamo già ampiamente illustrato in precedenti articoli, zuccheri e basi azotate, in epoca prebiotica non esistevano. Tutte le ricerche condotte su questi composti rimangono esperimenti di laboratorio senza nessun collegamento con l’ambiente prebiotico.
D’altra parte, ad eccezione di qualche astrofisico, tutti coloro che si occupano dell’origine della vita sono d’accordo nel ritenere plausibile l’esperimento di Miller. È da ritenere quindi che in epoca prebiotica, partendo da molecole semplici come metano, ammoniaca, acqua e da altre molecole semplici si siano formati migliaia di composti organici e tra questi gli amminoacidi. La presenza di amminoacidi in epoca prebiotica è stata confermata dall’analisi delle meteoriti risalenti all’epoca della formazione del sistema solare. In particolare nelle condriti carbonacee è stata riscontrata una presenza di amminoacidi simile, per qualità e quantità, a quella trovata da Miller.
Poiché gli amminoacidi sono i costituenti delle proteine,  è ragionevole concludere che in epoca prebiotica le prime macromolecole fondamentali ad apparire fossero proprio le proteine. La formazione di queste molecole complesse rappresenta quindi un passaggio fondamentale  verso l’origine di un primitivo citoplasma e di conseguenza verso l’origine della vita.
La sintesi delle proteine  pone però dei problemi, già illustrati in altri articoli, ma che per completezza è utile riproporre con qualche esempio per rendere le cose più chiare ai non addetti ai lavori.

1) Le nostre mani  sono una l’immagine   speculare dell’altra, destra e sinistra, e non sono sovrapponibili.
it.wikipedia.org
 Forme che sono immagini speculari e non sovrapponibili vengono dette chirali. L’alanina è un amminoacido costituente delle nostre proteine. Se noi vogliamo preparare in laboratorio 1g di alanina, non otteniamo 1g di una sola forma molecolare ma 0,5g di una forma destro (D) e 0,5g della sua immagine speculare sinistro (L). Gli amminoacidi sono quindi chirali e infatti, gli amminoacidi ottenuti da Miller nel suo esperimento sono chirali.
  E chirali sono anche gli amminoacidi trovati nei meteoriti. Anche gli amminoacidi formatisi in epoca prebiotica, circa 4 miliardi di anni fa, erano sicuramente chirali . Di essi esisteva, quindi, una struttura L(levo) e la sua immagine speculare D (destro).

                                        Ala L                   Ala D



Queste due forme molecolari presentano le stesse proprietà chimico-fisiche e viaggiano sempre insieme. Poiché sia la forma D che la forma L, in epoca prebiotica, erano sicuramente disciolte in acqua, il disordine molecolare  avrebbe prodotto reazioni incrociate tra amminoacidi L e D e dato origine a proteine contenenti le due forme, ma di nessun interesse biologico.
La questione è, che in tutti gli organismi viventi, le proteine sono costituite solo da amminoacidi della forma L.


Ala L



Poiché gli attuali organismi viventi discendono per evoluzione di organismi primitivi, anche le proteine degli organismi primitivi dovevano essere costituite da amminoacidi L. Ma allora,  se le due forme molecolari presentano le stesse proprietà chimico-fisiche ed erano inseparabili, come è avvenuta la scelta degli amminoacidi L e che fine ha fatto il Destro?

2) In epoca prebiotica erano sicuramente disponibili un gran numero di amminoacidi diversi. Nell'esperimento di Miller, per esempio, sono stati trovati circa 60 amminoacidi diversi e altrettanti nei meteoriti.
Ma negli attuali organismi viventi solo 20 amminoacidi concorrono alla formazione delle proteine.
Come è avvenuta la scelta dei 20 amminoacidi?

3) La reazione tra amminoacidi per la formazione delle proteine avviene con l’eliminazione di H2O.

In condizioni prebiotiche, in ambiente acquoso, questa reazione non può avvenire spontaneamente perché va contro il secondo principio della termodinamica. Sarebbe come vedere un sasso che spontaneamente risale una collina.
Questi problemi sono anche interconnessi e non ha senso immaginare di risolverli con tre modelli diversi. Non si può pensare che per il primo problema sia intervenuto il caso, per il secondo un processo evolutivo e per il terzo un processo deterministico, cioè una pozzanghera in evaporazione.
In merito a queste problematiche Giuseppe Galletti e Valentina Sorgi su “Astrobiologia: le frontiere della vita” 2009, hanno individuato la centralità del problema quando affermano: «Queste particolarità devono essere spiegate, possibilmente con un unico modello di partenza».
In aggiunta a questi tre punti fondamentali specifici, ci sono altri problemi di carattere generale a cui è necessario dare una risposta.
A) Come l’esperimento di Miller ha dimostrato, in epoca prebiotica erano presenti molte altre sostanze organiche. La maggior parte di queste sostanze erano sicuramente inutili se non dannose e avrebbero ostacolato la formazione dei polimeri. 
B) La concentrazione degli amminoacidi, disciolti in acqua, era sicuramente molto bassa e in tali condizioni la sintesi dei polimeri sarebbe stata impossibile.
È quindi logico concludere, che in epoca prebiotica alcuni vincoli chimico-fisici dell’ambiente prebiotico abbiano funzionato da principio organizzatore per selezionare e concentrare le sostanze fondamentali per l’origine della vita e successivamente catalizzare la formazione delle macromolecole necessarie alla vita.
Inoltre non è possibile che uno di questi processi avvenga al polo nord, un altro all’equatore e l’altro al polo sud. Questi processi devono essere localizzati nello stesso punto. 
Ma la localizzazione da sola non basta. Come suggerisce Paul Davies in riferimento a queste tematiche, selezione, concentrazione e catalisi devono realizzarsi in simultanea. Non si può pensare che ad un dato istante vengono selezionati gli aminoacidi, da questi dopo un mese vengono selezionati i levo e dopo un anno si ha la catalisi.   
In definitiva il modello unico di partenza deve contenere, selezione, concentrazione e catalisi e tutti devono essere stati processi simultanei e localizzati.
La scienza ha ormai da tempo messo in evidenza come i pianeti, le stelle e l’universo intero siano il prodotto del caso e delle leggi naturali: caso e necessità. E indubbio che l’evoluzione degli organismi viventi sia anch’essa frutto del caso e della necessità.
Ma caso e necessità hanno governato anche i primi passi dell’origine della vita, cioè la sintesi dei biopolimeri? Se i passaggi sopra elencati devono far parte di un unico modello coerente si aprono due possibilità: o gli eventi sono stati tutti casuali o gli eventi sono stati tutti deterministici. Introdurre qua e là, a discrezione, qualche evento casuale o per usare la nuova terminologia qualche “accidente congelato”, è solo un espediente ad hoc per dare sostegno a teorie poco credibili. Ma la probabilità che tutti i passaggi sopra elencati siano stati eventi casuali e coincidenti è  come gridare al miracolo. E allora, gli eventi che hanno portato all’origine delle proteine devono essere stati tutti eventi deterministici.
Ma esiste una teoria che ci fornisce un principio organizzatore  e che ci permette di costruire un modello coerente attraverso processi esclusivamente deterministici?

In un secolo di ricerche sull'origine della vita, l’unico scienziato che ha suggerito una soluzione fu J. D. Bernal  nel 1951. Come noto le argille sono formate da vari strati cristallini sovrapposti. Ciascuno strato è costituito da due sotto strati,  uno di tetraedri di silice (Si2O52-)n e l’altro di ottaedri  di allumina idrata [Al2(OH)42+]n. Senza entrare troppo nei particolari, per la presenza di cariche  
elettriche i vari strati o sotto strati si neutralizzano a distanza. Tra uno strato e l’altro o tra un sotto strato e l’altro rimangono quindi degli spazi vuoti dove possono sistemarsi molecole di acqua o molecole che presentano dipoli elettrici come i costituenti delle macromolecole fondamentali. Si è calcolato che in un cm3 di argilla la superficie di questi spazi vuoti equivale a quasi la superficie di un campo di calcio. Bernal propose che le argille avrebbero potuto selezionare e concentrare le sostanze fondamentali per l’origine della vita e successivamente catalizzare la formazione delle macromolecole necessarie alla vita. Egli suggerì anche l’importanza del quarzo nella formazione delle molecole primitive. Il quarzo infatti si trova unito all'argilla, come gli aminoacidi presenta una forma D e una forma L e avrebbe potuto dare origine ad adsorbimento preferenziale separando il destro dal levo. Poiché  all'interno dell’argilla ci sarebbe stata anche simultaneità e localizzazione, l’ipotesi di Bernal ci fornisce, di fatto, un modello coerente.  

                                                                    Giovanni Occhipinti


Prossimo Articolo: Origine delle Proteine (2a parte), seconda metà febbraio

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.
www.reiaverdade.net
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.
www.sciezenoetiche.it

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