Giovanni Occhipinti
PREBIOTIC CHEMISTRY AND
THE ORIGIN OF LIFE
(New Edition)
To my students
Introduction
Ilya Prigogine won, in 1979, the Nobel Prize for his studies on the distant systems of the thermodynamic equilibrium.
When I arrived at the Magistri Cumacini of Como, in 1982, the echo of his theory on the origin of life had not yet died out. With my students we discussed the instability of Benard, dissipated structures and oscillating reactions. As the students were interested, we decided to order the reagents for this type of reactions.
Only after about twenty years did I execute the oscillating reactions.
Some observations on the interfacial tensions and the electric phenomena, which are linked to them, took me very far away from the ideas of Prigogine.
The appendix 1 of this book is about the result of these observations, presented by three students of Magistri Cumacini at the international Philips concourse. From this endeavour, from these simple observations, the research contained in this book had its origin.
In 1984, I started the construction of the instrument for the measurement of the flux potential. My end was to verify if double electric strata of argil, sand, and glass in contact with solutions would have accumulated in their interior the amino acids.
Such an event could have been a strong indication on where life would have had its origin.
The construction of the instrument, its application and finding the physical-chemical conditions of the experiments, took much more time than I had predicted.
The experiments with argil and sand did not give convincing results, and with a glass diaphragm no useful results were obtained. I stopped experimenting until I had the idea, after about two years, to use quartz diaphragms.
In the summer of 2001, I read in Le Scienze an article on “L’acqua nel sistema solare” by Thérèse Encrenaz. Thus, I learned that water molecules are not all identical… one never stops learning. From that day on, I never abandoned the idea that the problem of molecular asymmetry of living organisms is a determinist problem and is linked with the inorganic world.
Thus began the preface to the 1st Edition.
From 1984 to 2009, I was mainly concentrated in experimental research. So in the 2010 edition some important problems, in particular the origin of the genetic code, of the proto-organism, of the descendants and of the mind, I had left them in track. In the ten years since publication, the only significant research regarding the origin of life has been the formation of the nucleic acid constituents in the presence of clay published by two Italian researchers. During this long period, I had the opportunity to reflect and read a lot. In particular, I expected to find robust hypotheses in the scientific literature with reference to the above problems. I was surprised to find that although much had been written, in the end it was still valid as Niels Eldredge's report: "I agree with George Williams when he says that scientific problems are not solved as much as they are quietly abandoned in favour of some new set of questions that come to absorb the interest of a discipline”.
At the molecular level, life uses the same molecules in quantity and quality, and of the same symmetry both for proteins and for the genome. This led scientists to conclude that all extinct and living organisms on our planet are descended from a single ancestral living organism: the universal progenitor. This would also explain an indisputable truth: life is unitary.
But life is not unitary only at the molecular level, life is unitary in all its manifestations. All living organisms are in possession of metabolism, they evolve and all, from higher organisms to microorganisms, have two fundamental characteristics: the instinct of survival and the mind. So I ventured to give an answer to the problems listed above. Overall, an organic picture of the origin of life from simple molecules to the cell through the laws of nature emerged.
In this edition, I have tried to make the topics, in particular those of physical chemistry, as simple as possible by eliminating almost all mathematical equations and enriching the topics with examples of everyday life. Many images have been inserted to help the reader in understanding the processes and also some formulas of chemical compounds but only to make the reader understand how complex some molecules are, in particular the constituents of nucleic acids. The different chapters contain repetitions also of images and this in order to render every chapter partially independent from the others, so as to enable the reader to discover the global unity.
To conclude I must thank many colleagues and laboratory technicians for their great critical and practical contribution.
A particular thanks goes once again to the director of Magistri Cumacini Eng. Enrico Tedoldi, who put at my disposition the place where I carried out my experiments and who always demonstrated interest and faith in my work.
I confirm the dedication of the first Edition "to my students" with whom I spent part of my best time.
Chapter 1
What is life?
Before addressing the topic, perhaps it is worth doing a brief introduction.
The definition of the concept of life and living beings is of course a very difficult task whereby inaccuracies and misunderstandings are round the corner. At times, wanting to be accurate and rigorous ends up running the risk of being dogmatic and fall into paradoxical conclusions, such as those that lead to doubt the status of a Mule as a living being just because it is sterile and cannot reproduce.
The following are, therefore, considerations that have a predominantly terminological end (which is to avoid discussions, due to the use of similar terms, and giving them different meanings) and methodological (to circumscribe the analysis of the subject, strictly in a scientific-experimental manner).
If you look at a barking dog and a stone, immediately you recognize which one is alive and which inanimate. However, giving a conclusive and scientific definition that distinguishes the living from the inanimate world that is, how to define life through macroscopic observations and common sense, which is a difficult task. In the early seventies of the last century, they began to make a list of characteristics of the living beings. So a living organism was considered a system able to feed, grow, reproduce and react to stimuli. The issue is that these functions are found even in the inanimate world. The granules of a crystal “feeds" off the particles in solution and grows, can break and reproduce another crystal. Also different mechanical systems that react to a thermal or electric stimuli are known. It was then thought to place a condition, to define a living being that was the simultaneous presence of all the characteristics listed above. But, if your dog is then seriously ill and no longer able to feed on its own? And hybrids like the mule that do not reproduce?
The matter was then moved to populations and in fact, Maynard Smith in "La teoria dell’evoluzione" in 1975, wrote: «A so arbitrary list serves us little. Fortunately, Darwin’s natural selection theory gives us, however, a satisfactory definition. We consider living beings a population formed by entities that have the multiplication property, inheritance and variability». The problem of hybrids that do not reproduce still remains.
In the early 80's, Alessandro Minelli in "Gli albori della vita" Le Scienze 1984, writes, it is preferable to leave aside the temptation to define the phenomenon of "life." Towards the end of the same decade Manfred Eigen, in "Gradini verso la vita" 1987, devotes the first chapter to this subject and finally concludes: «The question: "What is life?" has many possible answers, none of which is satisfactory [...]. Too large is the mass of complex phenomena, too diverse are the characteristics and the behaviours of the living beings, for a general definition to make sense».
In 2000, in "Da dove viene la vita", Paul Davies tried to give a clear idea of what life is, and once more proposes a list. He lists ten essential characteristics for defining a living being and concludes: «I can summarize this list of quality by saying that, in a broader sense, life seems to involve two crucial factors: metabolism and reproduction». And hybrids?
Iris Fly returns the futility of any attempt to "define" life. The author, in the "Origini della vita sulla terra" 2002, after attempts to define life by scientists, concludes: «Whoever at least tried to produce a definition of life has had the frustrating experience of realizing that either the list of its properties is too large and applies to non-living systems, or it is too narrowed down and it excludes some living beings. A functional definition that focuses on nutrition, metabolism and excretion may also apply to a car, but not to a dormant seed».
Ernst Mayr, referring to the quest for life in space, in "L’unicità della biologia" 2004, returns to the need to give a definition of "life" and writes: «Personally I accept a broad definition: life must be able to replicate itself and use the energy obtained from the sun or some available molecules, such as the sulfuric compounds present in ocean fumaroles».
The problem of seeds and hybrids remains.
Also Pier Luigi Luisi in "Sull’origine della vita e della biodiversità" 2013, considers it useful to isolate and define a common denominator that unites all living beings. The author, as he himself writes, uses a semi-serious metaphor. He imagines a little green man, coming from a very far stellar system with a list of terrestrial things containing living and non-living things. The little green man meets a farmer who he asks to separate the living from the non-living on the list. After a series of objections and clarifications, they finally reach an understanding and the little green man concludes: «A system is defined by you as alive if it is capable of transforming external nutrition into an internal process of self-maintenance and production of its components». Pier Luigi Luisi highlights how a definition of living being was achieved without disturbing molecular biology. The definition does not, however, contemplate reproduction, because there is the mule that does not reproduce in the list that the little green man shows to the farmer. It is a shame that in the list presented by the little green man, just to a farmer, there were not any seeds.
Perhaps the farmer would have seen the seed as a plant and therefore life. But then life would be what you perceive as life, a feeling. So, if the seed is a living being for a farmer, perhaps it is not for those who live in the city. Moreover, we still have to define the sick dog.
In conclusion, list or no list, from a scientific point of view there is no clear and shared definition of what life is. So for some, the seed is life while for others it is not, and the same applies for a sick dog that cannot feed nor auto-sustain itself. Some definitions finally lead to the absurd conclusion of considering the mule non-living.
(https://it.answers.yahoo.com/question/index?qid=20100427124519AAZJMyS)
Why can’t one define what is life?
I think these attempts to define life all contain a fundamental error: every time that metabolism, reproduction and evolution appear on a list, they are always projected towards the future, but natural selection does not know the future. There is no meaning for a definition of life that looks to the future if the future is not known. So, we will use a metaphor too and see, without any pretence, if common sense we can suggest a definition of life.
In a warm summer evening, a couple sit on the veranda lit by a weak light. The wife says to her husband: “I haven’t seen the cat for some time, it always comes to ask me something every day”. Her husband confirmed: “It is true, I have not seen it for at least three or four days, do you think it is dead?” “I do not know - his wife answered - it certainly wasn’t young. And then, it has always been an imprudent stray, constantly around the neighbourhood, the streets around here, day and night, and you know how these streets are busy nowadays”. The couple stayed silent for a long time, but each one asked himself: what is the state of the cat, is it alive or dead? After a while, from the darkness appears the cat that, with swirling footsteps, crosses the veranda and vanishes again in the dark. The couple watched each other with satisfaction, the cat is alive.
How did they determine the state of the cat? Through observation. So in order to decide what is life requires an observer. But the observer is a subjective an aleatory element, that is why there is no agreement on the seeds, the sick dog and the hybrids. To define living beings, we are therefore forced to provide the observer with more elements.
So, let us continue with our metaphor.
As we have described, the cat crosses the veranda and returns into the darkness beyond the hedges.
The wife tells her husband, “Why did it go away, if it were hungry I could have given it something to eat”. “It is its instinct” - replied her husband - to survive, it must hunt for food”. But feeding means knowing how to use nutrition, i.e. transforming it into energy and useful components to the body, ultimately the possession of a metabolic system. But we do not know if the cat will find nourishment, it may not find it and die. We know, however, that the cat has the ability to feed and metabolize, whether or not it is related to the future, but nobody knows the future. Since there is no sense for a metabolism without nourishment, the term metabolism also means the ability to feed.
Metabolism must necessarily fall under the definition of living beings.
Now, we know that millions of years ago, the cats’ ancestors crossed those places and they had to reproduce to attain our days. But we do not know if our cat will have the possibility or the ability to reproduce. However, we know with certainty that he is a product of reproduction and that certainty must help define a living being.
Reproduction contains a copy of the parents’ genome. The parents’ genome had to replicate right before reproduction. There is no point in talking about reproduction without the genome replication. The reproduction term must therefore contain the replication.
Natural selection has affected reproduction and allowed the cat’s ancestors to evolve. But natural selection does not know the future nor do we know if the cat will evolve. However, we know with certainty that living beings are the product of the evolution of their ancestors, that certainty must help define a living being.
So, life is a state of matter. Since there are only two states, life and death, life is life until it turns into the state of death, that is, until you recognize the "new" state, the state of inanimate matter. The state of matter we call "life" is based on three fundamental properties: it must possess a metabolic system and be a product of reproduction and a product of evolution.
Matter that does not simultaneously present these three fundamental properties is inert matter.
No one in a car or in a crystal recognizes a metabolic system and the product of reproduction and evolution. The salt crystals formed on the rocks after the evaporation of water are identical to those that formed billions of years ago, no difference, and no evolution.
The sick dog is temporarily debilitated but has a metabolic system. It is a product of reproduction and evolution. The sick dog is a living being.
The mule survives with the help of a metabolism. It is irrelevant whether it reproduces or not, but it is a product of the reproduction and evolution of its ancestors, the mare and the donkey. The mule is a living being.
What about the seeds to which we can also add spores? Like predators that hide between herbs and bushes waiting for the right moment to attack their prey and survive, seeds and spores stay protected within their shells and wait patiently for their time, surviving. Seeds and spores have a metabolic system and are produced by the reproduction and evolution of plants, fungi and bacteria. Seeds and spores are living beings.
Summing it up: Life is a state of matter that is based on three fundamental properties: it must possess a metabolic system and be a product of reproduction and evolution.
The definition of life cannot be a perception of the observer, but part of Darwin's natural selection theory.
The bacterial cell has a metabolic system, it is a product of reproduction and evolution, it is the smallest living entity, the first stage of life.
But there are organisms that are smaller than the bacteria: the Virus. The debate is often open if the viruses are to be considered living or non-living organisms.
Luis P. Villareal, a virological expert in “I Virus sono vivi?” Science 2005 compares viruses to seeds in which the potential of life can shed.
Dorothy Crawford, a microbiologist among the top experts in viruses, has an opposite view and in her essay, “Il nemico invisibile. Storia naturale dei virus”2002, writes: «Unlike bacteria, Viruses cannot do anything on their own. They are not cells but particles, and they do not have a source of energy or any of the cellular equipment needed to produce proteins. Each of them is simply composed of genetic material surrounded by a protective cap shell called “capsid”. [...] But in order to use it, they must penetrate into a living cell and take control of it. [...] As soon as a virus can enter a cell, it reads the genetic code of the virus who orders “replicate me” and the cell gets to work.
In this way, viruses invade living beings, highjack cells, and transform them into factories for the production of viruses». Furthermore, as Crawford tells us again, out of the host cell the Virus cannot survive for long because they do not have a metabolic system of a cell and therefore are not able to feed.
The definition of life outlined above definitively closes this debate. Viruses are not living organisms because they do not present one of the life-defining factors: metabolism.
But if the Viruses are not living but particles, are they like stones?
As the Norman Pirie virologist wrote in 1934, they are systems that are neither clearly living nor clearly inanimate. If the term Virus is unsatisfactory, it is necessary to define another term.
We have given a macroscopic definition of life and identified the smallest vital entity in the bacterial cell, but within the cell at the molecular level, what is life? Is there an "Elan vital" inside the cell, a vital spirit?
No scientist has ever claimed to be able to answer this question. In addition, life cannot be identified with one or a group of molecules. Life is "emergency". The term emergency must be understood in the meaning given by Ernst Mayr (cited work): «The appearance of unexpected features in complex systems». «It does not contain any metaphysical implications». «Complex systems often present properties that aren’t evident (nor can be predicted) even by knowing the individual components of these systems». So life emerges from complex systems, but at the level of simple systems, the inanimate world has similar behaviours to the living beings.
Myosin is one of the proteins involved in transporting materials into the cell. Observing the myosin moving along the actin filaments inside the cell, it looks like a small two-legged creature. If myosin is brought out of the cell it becomes motionless, but if fuel is supplied it starts moving. Myosin is not alive and has no purpose, it is a molecular machine, and it only performs functions, like catalase which decomposes hydrogen peroxide and like thousands of other proteins.
Pier Luigi Luisi in his essay (quoted work) highlighted how vesicle derived from fatty acids can reproduce with mechanisms typical of living organisms.
As we will see when we will deal with the synthesis of polypeptides, drops of different compounds located next to each other seem to us to have familiar behaviours. Water seems to run away in the presence of ethyl alcohol, the sulfuric acid surrounded by drops of water seems to be looking for an escape route. These phenomena have been denominated “non-living chemiotassis" (appendix 1). The term chemiotassis indicates the response of bacteria in the presence of nutrients or repellents.
But as early as the middle of the last century Oparin had pointed out that too many copolymers of polymers (coacervates) tended to divide. Even Sydney Fox has produced coacervates thermal proteins and observed that these divided when too big similar to the bacteria. Fox’s protein coacervates had weak enzymatic capabilities as well.
There are some analogies that call for vital processes in molecules and aggregates, but all these facts have a scientific explanation. Therefore the conclusion of Richard E. Dickerson, expressed in “L’evoluzione chimica e l’origine della vita” Le Scienze 1976, is always valid: «The experiments of Oparin and Fox are just analogies of vital processes but are evocative. They demonstrate like the extension of vital behaviours are rooted in physical chemistry and illustrate the concept of chemical selection for survival».
Concluding, there is no "Élan Vital", the behaviour of vital processes are rooted in physical chemistry.
Chapter 2.
Introduction to the origin of life and the natural laws
2.1 The constituents of a primitive cytoplasm
But not only vital behaviours are rooted in physical chemistry, the very origin of life must have been a chemical-physical process.
All cells are made of a cellular membrane, or plasma membrane, which separates and protects 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 "Origini della vita" 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. Without homeostasis there can’t be orderly metabolism, nor an almost stationary equilibrium, in short, nothing that deserves to be called life». Then, a homeostasis, inside a cytoplasm even if primitive, had to exist already when life began. Therefore, in order to understand the origin of life, we must:
Know, first of all, in their general lines, which chemical-physical laws allowed the appearance of life and then go in search of the origin of the components of this elemental cytoplasm, which gave rise to a proto-organism from which the cell emerged. How elementary the primitive cytoplasm must have been is always a matter of debate. Certainly, they could not miss:
1) Small organic molecules, especially the constituents of nucleic acids and proteins.
2) Proteins.
3) Nucleic acids, RNA and DNA
4) A closed environment that protects the cytoplasm.
And then specify the following steps:
5) The proto-organism, definition and origin.
6) From the proto-organism to the cell: origin of offspring and origin of the mind.
During this process, as we will see later, we have to solve some problems considered, by many researchers, insurmountable.
Furthermore, 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, an “organizing principles” or constraints must have existed which selected the right substances for life; to use a metaphorical expression, something must have directed the traffic.
A theory on the origin of the genetic code, that is the law of correspondence between nucleic acids and amino acids for the synthesis of proteins, will also be presented. A chapter will be dedicated to the choice of the amino acids that make up our proteins.
2.2 The laws of nature
The laws, which allow the formation of a primitive cytoplasm, belong to thermodynamics and Chemical Kinetics.
While the 1st law of thermodynamics tells us that energy it is neither created nor destroyed but can be transformed, 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 gives physical-chemistry 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 way, 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 stone on a hill. If you push the stone, it rolls down to the valley and its energy, through friction, 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 is: 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 is 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 of disorder increases; spontaneous processes tend towards chaos.
The disorder, in physical chemistry, 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. In short, the processes physically allowed are those processes that involve an increase in the disorder, an increase in entropy.
The universe, began with the Big Bang at billion of billion of 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?
2.3 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 diminishes. Whether the new organism will be more suitable 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 “La nuova alleanza” 1981 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 for the origin of life it would take thousands and thousands of local orders and all closely related. It is 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 is 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.
Time passes and entropy increases, 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, i.e. the origin of a primitive cytoplasm and therefore the origin of life.
Yet life originated, how was it possible?
2.4 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 order out of chaos, but chaos from order.
But how is chaos from order produced spontaneously?
Take a look how salt flats work. 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 do not 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 disorder arrangement. The energy difference between the disordered and ordered structure is transferred to the surrounding environment increasing entropy.
The order generated chaos.
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 is order that generates chaos.
2.5 The laws of nature and time
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 stone up the hill, if pushed, will go down the valley. But if the stone is not pushed entropy must wait. 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, release the amino acids and increase the disorder, but that doesn't happen.
Ultimately, entropy, metaphorically called "the arrow of time", in fact does not contain time.
The time function, in chemical processes, is introduced by the Chemical Kinetics, that branch of chemistry that studies the speed of reactions. 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. In order for a reaction to take place, it is necessary to break the chemical bonds of the reagents; that is, an energy barrier must be overcome. It can be briefly stated that: necessary and sufficient condition for a reaction to take place is that there is a collision and that the collision is effective.
This statement can be represented graphically by placing the energy E on the ordinate axis, and the reaction coordinate indicating the course of the reaction on the abscissa axis.
When the reactants collide the kinetic energy, i.e. the movement energy of the reactants, is transformed into potential energy. If the collision is not effective, i.e. fails to break the bonds of the reagents, the energy barrier cannot be overcome. The potential energy is transformed back into kinetic energy and the reactants return to their initial state. It is for this reason that the reaction between most organic substances (for example fuels) and oxygen, although thermodynamically possible, does not actually take place at room temperature.
If the collision is effective, the kinetic energy is transformed into Ep, an energy zone is reached (called the zone of the activated complex), where the bonds of the reactants are broken and the products of the reaction are formed.
We can therefore conclude that in order for a chemical process to take place it must first be thermodynamically possible and then kinetically possible.
For certain chemical reactions, the presence of certain substances, called catalysts, lowers the activation energy and the reaction can therefore also take place at room temperature. As soon as the catalysts are eliminated the reaction stops immediately.
Although in a more complex way this is ultimately the function of enzymes in living organisms: they operate as catalysts lowering the energy barrier.
In fact, if the reactions that occur in living organisms do not reach the activated complex, the reactants would remain in the initial energetic state; there would be no vital process.
If the reactions that occur in living organisms spontaneously reach the activated complex, overcoming the energy barrier, the reactions would take place in an uncontrolled way, all the energy would be released in a short time and the organisms condemned to die.
This energy barrier is in fact the energy door of life, and it is the enzymes that allow life to cross that energy bottleneck of thermodynamically possible but kinetically impossible processes.
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 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 stone 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 that 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 "Il secondo principio" 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, which is the entropy.
The order generated chaos.
Subsequently the protein, due to the effect of certain interactions between different parts of the molecule, folds into a globular structure. 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. As we will see in more detail below, a primitive cytoplasm must have originated through the interaction between the protein molecules within the second law of thermodynamics, whereby it is order that 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 "Un’altra terra" 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, since the time of Steno in the mid-1600s and later Renato Haüy, scientists who started the study of crystals, no scholar of crystallography, mineralogy and geology has ever identified in crystals virtue magic or souls.
Inorganic matter is inert, inanimate.
When after six billion years after the origin of the universe, amino acids that give rise to proteins appear, the second principle follows the same scheme derives entropy by generating ordered structures. But proteins come with a surprise, there aren’t inert like crystals. Proteins have the ability to recognize molecules and perform functions and, while giving something to chaos, they work by building complex structures, living organisms, who oppose chaos.
The second law of thermodynamics has brought the devil into the house.
Chapter 3.
Origin of the constituents of nucleic acids and proteins
3.1 Do the nucleic acids and proteins constituents have extraterrestrial origin?
All living organisms are more or less complex structures but all cannot do without 2 fundamental macromolecules: nucleic acids or chromosomes consisting of a phosphate group and two organic compounds Ribose and Nucleobases, repositories of genetic information, and proteins, in particular the enzymes, that control the reactions that take place within all living organisms, whose constituents are amino acids.
The constituents of nucleic acids and proteins are the same, in quality and quantity, in all living organisms. This led scientists to conclude that all extinct and living organisms on our planet are descended from a single ancestral living organism: the universal progenitor. In English, it is called last universal common ancestor, (LUCA), the last universal common progenitor. This would also explain an indisputable truth: life is unitary. Nucleic acids and proteins are also interdependent in the sense that, nucleic acid (often identified as software) contains the program of how to synthesize proteins. But nucleic acid alone cannot synthesise and needs proteins (hardware) to be synthesized. That is why they are interdependent: one always needs the other.
The first organisms, although very simple, had to contain both. We must therefore go in search of the fundamental molecules, that is, the constituents, which gave rise to these macromolecules.
But do these constituents have an extra-terrestrial origin?
What really happened 13,6 milliards of years ago, we do not know, yet we know that it happened and we called it the Big Bang. We also know that, after 380 thousands of years from the Big Bang, when the temperature of the then universe dropped to a few thousand degrees, the electrons (-) and the protons (+) linked, giving origin to hydrogen (H), Helium (He) and small quantities of Lithium (Li). The gravitational attraction between the atoms of these elements gave origin to the first stars. It was inside the massive stars, at a temperature of hundreds of millions of degrees through the nuclear fusion that, starting from hydrogen, other chemical elements were formed and among these Carbon (C), Nitrogen (N), and Oxygen (O), that is those elements that form the 99% of our body. The gravitational collapse of these stars, at hundreds of billions of grades, completed the picture giving origin to all the other natural elements. Therefore, for what concerns the elements, there is no doubt: we are “sons” of stars.
But are we also sons of space? That is, the substance fundamental for the origin of life, amino acids, sugars, and nucleobases come from space?
The idea, expressed at first by Juan Orò in 1961 and taken up again in the 70’s by F. Hoyle and C. Wickramasinghe, has a certain fascination in itself.
We know that our solar system originated 4,6 milliards of years ago, from the condensation of a cloud of gas and dust. Our planet was at the beginning very hot and hammered by impacts of meteorites and asteroids. Its surface was fused. With time, the impacts became less frequent but they never ceased happening. Some of these meteorites, precipitated in the last two centuries, had been gathered and studied. In total, over a thousand meteorites are conserved but only some, called “carbon chondrite”, are interesting for our ends. These meteorites dated 4,5 milliards of years ago, had their origin during the formation of the solar system.
The chemical analyses, done at the beginning of the 70’s, have shown the presence of amino acids, constituents of proteins. These amino acids present themselves in the two forms Right (D) and Left (L), as we will examine extensively later, and hence surely are extraterrestrial and not biological. Furthermore, hydrocarbons (made up of H and C) have been found with a molecular weight even high and demonstrated the presence of traces of purines and pyrimidine. These substances have a molecular structure fairly close to that of the nucleobases. In neither case was however discovered sugar and nucleobases that is the constituents of the nucleic acid, whereas it is now certain that amino acids are present. Hence from the depth of space, arrives evidence of the chemical processes that have given rise to fundamental substances of the origin of life. But it remains to be cleared if the organic molecules of the meteorites already made part of the gas cloud and dust, which gave origin to the solar system, or if these were formed during the condensation phase of the cloud itself through inputs of energy.
Around the end of the ‘70’s, the idea of an extraterrestrial origin of the substances fundamental for the origin of life, received a new impulse. In the interstellar clouds of gas (more or less ionized) and dust, radio astronomers have discovered various simple organic substances and among these formic aldehyde (HCHO) and hydrogen cyanide (HCN). A complete list of all the organic substances (about 40) found in space until the beginnings of the 80’s is contained in an article by Leo Blitz: Complessi giganti di nubi molecolari nella galassia, Le Scienze 1982. However no trace of molecules a bit more complex, important for the origin of life.
It was thought that they could be find in the near future, but it was not clear in what way these molecules could have arrived from space on our planet. As single molecules, they would have been destroyed by the solar ultraviolet, mortal not only for living organisms but also for the molecules fundamental for the origin of life. If the molecules had been contained inside asteroids fallen on our planet, they would have been destroyed by the enormous heat given off by the impact or remained prisoners inside the fragments.
However, around the middle of the 80’s, the majority of scientists implied in research on prebiotic chemistry, was of the opinion that the extraterrestrial origin of organic substances only demonstrated the ease with which these molecules can be synthesized in the presence of carbon, hydrogen, azote and oxygen.
Such an opinion was also well synthesized by Mario Ageno, pupil of Enrico Fermi and collaborator of Edoardo Amaldi, careful and profound scholar of Biophysics who in “Lezioni di biofisica 3”, 1984) concludes: «Even if a minimum fraction of it succeeded in the end in surviving and in joining in some way the hydrosphere of the planet, it would be difficult for the chemical evolution to go further up to the appearance of living organisms, without a continuous contribution and of a completely different order of magnitude of substances of new synthesis of local origin».
The discovery of organic molecules in space, implied however a reflection. If the interstellar clouds contain prebiotic organic molecules, these must have been present also in the cloud that gave origin to the solar system. It was hence thought that, during the formation of the solar system, in the planets close to the sun, because of the enormous heat, these molecules were destroyed. They were however saved in the colder zones that is at the limits of the solar system, where they were incorporated in the comets. Hence was diffused, among scientists, the conviction that comets were a residue of the nebulous, which gave origin to the solar system and that they contained the organic substances necessary for the origin of life
The hunt for comets begins.
Around the middle of the 90’s in the coma of the comets Hyakutake and Hale-Bopp, organic compounds are discovered and among these formic aldehyde (HCHO) and hydrogen cyanide (HCN).
However, still no trace of molecules a bit more complex, important for the origin of life.
Yet it has been observed that, when in the interstellar space water molecules, methanol, ammonia and hydrocarbons are deposed on silica dust, frozen grain are formed. According to some scientists, inside these grains, organic substances could have been accumulated, complex ones included, and the layer of ice would have protected them from the ultraviolet. Other researchers hold that, if the layer of ice had not been sufficiently thick, the ultraviolet rays would have broken the organic substances. The residues, as they could not disperse into space, could have reacted early or late giving origin to more complex molecules. When they enter into the atmosphere, the organic substances contained in the cavities of the granules are protected from overheating. Frozen granules have been reproduced in laboratory, and named “analogous to frozen granules”. In these “analogous granules” have been individuated simple organic substances like ketones, ethers and alcohols, but no trace of molecules a bit more complex. However when we reread the article of M. Bernstein, A. Sandford and J. Allamandola: ”Dallo spazio le molecule della vita (Le Scienze, 1999), apart from the emphasis, understandable for one who works at the NASA, there is no trace of molecules important for the origin of life.
In 2002, twenty years after the publication of the article by Leo Blitz and hence, after another twenty years of research in radio astronomy is published by P. Ehrenfreund and others: “Astrophysical and astrochemical insight into the origin of life, (Rep. Prog. Phys. 65 (2002) 1427-1487, a list up to date, about 70, of organic substances found by radio astronomy in space. Among these substances Ehrenfreund includes Glycine, a very simple amino acid that makes part of our proteins, but he adds an interrogation. Also in this new list, there is not yet the trace of complex molecules important for the origin of life. In the same article, Ehrenfreund publishes the list of the substances found in the comets Hyakutake and Hale-Bopp, about 35, even fewer than 70 radio astronomy substances and almost all already identified in the interstellar space. Hence, it does not seem that inside the comets particular reactions of synthesis take place. In the Ehrenfreund table, Glycine is still included but this time without any question mark. Reading through his comment on the table, he writes: «Glycine, the simplest amino acid, has not yet been detected, […]».
In 2006 was brought to earth the dust of the comet Wild 2, taken by the Stardust mission. Analysis has shown the presence of amine and molecules made of long chains of carbon atoms. In 2009, after three years of the publication of the first data, NASA announces with much emphasis, that in the dust of Wild 2, when the analysis had been redone, also traces of Glycine has been found.
What can one conclude? Finally, they did it.
It is opportune, to conclude, to add some points starting with some parameters.
The massive stars that form inside the immense clouds of gas and dust, have an average life of about 3 million years and the greater part of their energy they give it out under form of ultraviolet rays. Also our sun gives out ultraviolet rays which would destroy amino acids and nucleobases up to the threshold of the solar system. When the sun had its origin, the intensity of radiation was thousands times superior to the actual situation. Space is hence permeated by rays lethal not only for the living organisms, but also for molecules important for the origin of life.
In the interstellar clouds, matter is extremely rarefied. At the temperature of -260°C, the average density is 100 molecules of hydrogen per cm3 and small fractions of azote, oxygen, and carbon. These elements atomized or ionized by the ultraviolet rays, through casual impacts have given origin to very simple substances like methane, ammonia, water and formaldehyde, hydrogen cyanide, ammines too. Part of these substances are destroyed by ultraviolet rays and then maybe reformed later in other places. Now, the molecules fundamental for the origin of life like amino acids, sugars, and nucleobases, even if they are molecules with a molecular weight relatively low, they are not so simple, but have their own complexity. What is the probability that molecules of this type could have formed in space, from atoms and ions extremely rarefied through casual impacts and at such a low temperature? And what is the probability that they could have resisted against the ultraviolet rays? The good sense of Cartesian memory suggests that such probabilities are practically zero.
And then even if some molecule, useful to the origin of life should form, what could be its usefulness? The quantity of molecules necessary to the origin of life is of such an order of magnitude that space should be permeated, and instead space is permeated with rays that destroy these molecules.
Therefore, for what concerns substances fundamental for the origin of life, we are not “sons” of space.
Space with its ultraviolet rays is the dwelling of death. The first living organisms on earth knew something about that, being obliged to live in mud or, as we will see later, in water deeper than 10 meters. Only after two billion years the oxygen, produced by autotrophic microorganisms and released into the atmosphere, it gave rise to the Ozone shield (O3), that blocked ultraviolet rays, and life managed to wrest a few kilometres of space from death and occupy the surface and atmosphere of the planet.
However, living organisms exist thanks to the fact that space is the kingdom of death. Life was possible on earth thanks to the fact that the ultraviolet rays sterilized space.
The organic substances known by us are now, on the earth, more than 1,5 million. Let us imagine if in space, through casual impacts and in the absence of ultraviolet rays, the substances fundamental for the origin of life had originated and hundreds of thousands of other organic substances most harmful to the origin of life. Having arrived on earth, in an oceanic melting pot, from these substances only a miracle could have given origin to life.
And then, the organic molecules which radio astronomy finds in space are nothing but the ashes of a perennial cremation thanks to which life has been able to originate on earth.
That which has been exposed above, makes one conclude that space is not the seat of the origin of the substances fundamental for the origin of life.
The comet impacts on our planet have probably restored in the prebiotic epoch the primitive atmosphere; they have added water to our planet and probably also some simple organic substances like formic aldehyde, hydrocyanic acid, etc.
It is also probable that during the phase of contraction of the primitive cloud, from compounds present in the cloud like Methane, Ammonia, Hydrogen and Water, through addition of energy, many organic substances were produced, and among these the amino acids. Some of these amino acids were imprisoned in the meteorites, other have been destroyed by the solar ultraviolet and the high temperature of contraction of the cloud.
Therefore, the conclusion to which scientists had come to in the 80’s is still valid: natural processes, in prebiotic conditions, on our planet, are able to produce the substances fundamental for the origin of life, and the contribution of simple organic substances, coming from space, if ever it existed, is to be considered without influence.
3.2 Do the nucleic acid and protein constituents have a terrestrial origin? The theory of primordial broth.
Proteins make up tissues and organs, allow cells to communicate, control what needs to enter and leave the cell, act as antibodies.
All living organisms have a complexity of independent functions that permit them nourishment, growth, reproduction, evolution, reaction to stimuli, death. All these vital functions have in common the metabolism; that is, that process of chemical reactions that co-operate with proteins (enzymes) which permit the living organisms to function. Inside the cell, thousands of enzymes can be found which rule and program thousands of chemical reactions. No biological reaction and none of the functions mentioned above can happen without their intervention, not even the synthesis of the nucleic acids.
The proteins are macromolecules whose constituents are the amino acids. But the amino acids, in the prebiotic era, were present in our planet? And then, were the organic constituents of nucleic acids, Ribose and Nucleobases also present?
Around 1870 in a letter to a friend Darwin wrote: «If ( and it is an if very big) we could imagine that in a small puddle hot, rich in ammonia, phosphorous salts, light, heat, electricity etc., a protein compound was formed chemically, ready to pass through variations still more complex[…]». However, Darwin’s official position was firm and clear: at the actual state of knowledge, it is not possible (ultra vires) to formulate a theory on the origin of life.
In 1924 A. I. Oparin, who at the time was professor of biochemistry at the university of Moscow, translated this idea in a sort of scientific theory and published it in a book, “L’origine della vita” 1924 (Ed. 1977).
According to Oparin, on our planet carbon was linked to metals in the form of carbides. These, when they come into contact with water vapour, react giving origin to hydrocarbons and, in successive reactions, to many other organic compounds. When the temperature on the surface of earth has dropped below 100°C, water started to condense and all these compounds, contained in the atmosphere, were transported in a “primitive boiling ocean” where they started reacting, forming ever bigger molecules. The successive aggregation of these macromolecules would have given origin to particles of gel, “coacervates”. The organic coacervates would have absorbed and assimilated substances from the ambience and afterwards, dividing themselves, they would have given origin to primitive organisms some of which capable of creating metabolism. The evolution process and natural selection would have given origin, in the end, to all living organisms.
According to Mario Ageno (quoted work): «The fundamental idea is certainly very brilliant and it does not lose its interest even today. This, however, must not make us forget that such a “theory” passes in silence all the great problems, all the greatest defiance that the idea of an origin of life from inorganic substances, through natural causes, affronts our mind».
In 1929, J. B. S. Haldane, without knowing the ideas of Oparin, publishes a brief article on the origin of life.
According to Haldane the primitive atmosphere did not contain oxygen but, probably, H2 (hydrogen) H2O (water), NH3 (ammonia) and CO2 (carbon dioxid). More complex molecules would have been formed in the atmosphere due to the effect of solar radiations. These organic compounds, transported by the rain, would have accumulated in the primitive ocean, where, by reaction, they would have formed complex molecules, giving origin to a “hot dilute broth” and here the first organisms would have had their origin. The hot dilute broth was immediately translated into “primordial broth”.
Born the metaphor begins the theory.
Meanwhile methane (CH4) and ammonia were discovered in the atmospheres of Jupiter, Saturn and Uranus.
Around 1950 with H. Urey and S. Miller, an operative program of research starts. In particular, using a mixture of Hydrogen, Water, Ammonia and Methane, S. Miller, adding energy (electric charges) succeeded in producing amino acids, which are components of proteins, and many other organic substances. In this period is born pre-biological chemistry, which has the intent of individuating, over and above the amino acids already discovered, the formation of the molecules fundamental for the origin of life, and their synthesis in the ambiance similar to that of the earth at the period of the appearance of life.
The discovery created a great enthusiasm among scientists and it seemed that, very soon, they would have succeeded in unveiling the mystery of life.
In the years that followed several tests were carried out which confirmed the results of Miller’s experiment. Several researchers also have performed experiments both by varying the composition of the gas mixture and the sources of energy. All these studies have confirmed that in the prebiotic era, on our planet, the synthesis of a large number of organic substances was possible, and among these, amino acids were often present. Through those experiments was demonstrated the presence, in the prebiotic era, of about 60 different amino acids. Moreover also the presence of cyan hydric acid (HCN) precedent of purine, of formic aldehyde (HCHO) precedent of ribose and of other important organic substances among which urea have been demonstrated. The importance of these small molecules should not be underestimated, as they could have been the precursors of sugars, nucleobases and amino acids. In fact, Ribose, a fundamental molecule for RNA, is a pentamer of formic aldehyde (HCHO) in the sense that five aldehyde molecules could give rise to a ribose molecule. And adenine, a Nucleobase for nucleic acids, is a pentamer of hydrogen cyanide (HCN). In these experiments, however, Ribose and Nucleobases, constituting nucleic acids, have never been identified. However, they had to be present and, as we shall see, they probably formed by other ways. All this leads to the conclusion that on our planet natural processes may have produced the fundamental substances necessary for the origin of life.
It is remarkable that the same substances, in particular the amino acids, as we have already illustrated, were found in the meteorites going back to the era of the formation of our solar system. The discovery of the amino acids in Miller’s experiments and their presence in the meteorites demonstrates, according to scientists, the ease of synthesis of these compounds. Manfred Eigen, referring to experiments like Miller’s, in (quoted work), affirms: «That which renders significant these experiments is not so much the fact that in general amino acids form, but that their relative frequencies corresponds to those fund in nature, and in particular in the organic compounds discovered in the meteorites».
At the beginning of the 90’s, some research workers expressed doubt about the presence of a primordial atmosphere made up of CH4, NH3, H2O, H2. These research workers have supposed a primordial atmosphere made up of CO2, N2 and H2O, and in such conditions, the formation of the amino acids with application of energy does not take place. Miller has defined these studies hypotheses without sustaining data. No serious research has doubted of the presence of amino acids in the prebiotic era.
We can conclude that numerous and strong indications demonstrate the presence of amino acids in the prebiotic era. From the synthesis of these molecules, the proteins have their origin.
We are “sons” of the earth.
Despite these important discoveries, no further progress has been made in the following years. The problem is that Miller experiments seemed to confirm Haldane's theory in its totality, that is, of a primitive atmosphere free of O2, of the formation in the atmosphere of the fundamental substances for the origin of life and their collection in a ”Primordial Broth” where life originated. Almost all of the scientists accepted the hypothesis of the origin of life in a primitive ocean. But for over half a century it has been shown that the origin of life in a primordial ocean has posed basically four insurmountable problems. However, the metaphor of the "primordial soup" is so powerful that, even today, science cannot get rid of it.
But finally, what are these four insurmountable problems, and what the solutions proposed and the comments of noted scientists?
1) Our hands are a mirror image of each other, right and left, and are not superimposable. Forms, which are mirror images, not superimposable, are called chiral. The molecules of amino acids of which proteins are made, exist under two forms, Right (D) and Left (L), and they are one the mirror image of the other. If amino acids are prepared in laboratory, for example Alanine that which one obtains is 50% D Alanine and 50% L Alanine. Also the amino acids discovered by Miller in his now famous experiment were half Right and half Left, and as such also found in the meteorites. Hence, in the prebiotic world, the amino acids must have been half D and half L.
These two molecular forms have the same chemical physical properties, always travel together and their spontaneous separation in an aqueous medium is impossible.
L D
Since both the D-form and the L-form, in the prebiotic era, were definitely dissolved in water, 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: life is asymmetric.
L
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. 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 Right?
According to Dickerson (quoted article): «[…] it is possible that at a certain period there was a primitive life, or the ancestors of it, based both on amino acids D and on amino acids L with a probability of 50%, and that, in the end, the amino acids L prevailed over the others».
It is already difficult to imagine the origin of one primitive life; to imagine two, one D and the other L is really hard.
2) The reaction between amino acids for the synthesis of proteins, all take part with the elimination of H2O.
In a watery ambiance, that is in the primordial broth, this reaction is practically impossible because it goes against the second principle of thermodynamics. It would be like seeing a stone that spontaneously goes up a hill.
According to S. Fox, the proteins would have formed close to volcanic zones at a temperature of 200°C, and only afterwards they would have been transported by the rain into the broth, where would have been formed microspheres resistant to the destructive action of water. In alternative it has been imagined, that the primordial broth was in reality puddles of water near the ocean and subject to continual evaporation. It has also been thought to resolve the problem imagining secondary reactions between amino acids with compounds rich in energy, but these passages multiply enormously the number of reactions. To obtain a polymer of 40 amino acids hundreds of reactions would have been necessary, and this appears not very credible.
In fact, the question is still open.
3) In prebiotic times, a large number of different amino acids were certainly available. In Miller’s experiments, about 60 different amino acids were found. But the amino acids of which are constituted our proteins are only 20. How did the choice come about, and why only 20 amino acids?
The explanation more often given is the most obvious: there were false departures that were extinguished, because they could not compete with the organisms that on the other hand survived.
4) The primitive atmosphere certainly did not contain O2 (oxygen) and hence the shield of O3 (Ozone) was absent. The ultraviolet rays, in larger quantity than the actual ones, attained the surface of the earth. In a primitive ocean, these attained the depth of 10 meters. Diffusion, thermic agitation and currents would have in the end carried all the organic substances to this zone and they would have been destroyed.
To resolve this problem, one imagines that the first organisms originated anchored to the bottom of shallow lagoons not less than 10 meters. For some researchers the problem does not exist, because life has had its origin in the deep of ocean bed near the hydrothermal sources.
Now, it is evident to all, that all the hypotheses, made to fill this void, are in reality modifications ad hoc, often even in contradiction one with the other and without any possibility of experimental verifying. Confirming the failure of the prebiotic broth theory In “Le radici della biologia” 1986, Mario Ageno writes «We can hence say that at the beginning of the ’80´s research on the origin of life has entered a crisis».
As already mentioned Nucleic acids and proteins (enzymes) are macromolecules fundamental for living organisms and without doubt, in a primitive organism, they could not be absent. Now, whereas nucleic acids contain the genetic information for the construction of proteins, these last are necessary for the construction of the nucleic acids. Nucleic acids and proteins are in this way interdependent, the ones are necessary to the others. And that which in Biophysics is called “The problem of the egg and the hen”: which appeared first?
When, at the end of the `60’s, became evident the failure of the synthesis of proteins in the prebiotic broth, researchers began taking an interest in the nucleic acids. It was in those years that the idea of the “RNA World” was being born. The original idea was that, in the primordial broth, molecules of RNA appeared first with the two functions in one: containing the genetic information, and having the function of enzymes catalyzing initially their own synthesis and subsequently the synthesis of proteins, that is being egg and hen at the same time. Experiments conducted by Sol Spiegelman of the University of Illinois and Manfred Sumper of the Max Planck Institut "L’origine del codice genetico", Manfred Eigen et al. Le Scienze 1984 gave a great impetus to this idea. It soon became clear, however, that spontaneous synthesis of RNA molecules in a primordial world is practically impossible.
In 1983, a great discovery brought back a temporary vigor to “RNA World” and to the theory of prebiotic broth. Thomas R. Cech and Albert Altman discovered that some types of RNA (Ribonucleic acid) are capable of behaving both as nucleic acids and as enzymes (that is they are egg and hen at the same time) and they have been called “ribozymes”.
Also the “RNA world” inspired much enthusiasm, but after about ten years, and in spite of contribution of many eminent researchers, the “RNA World” revealed itself, for the theory of prebiotic broth, another failure. In the mid-90s Christian De Duve in “Polvere Vitale” 1995, synthetizes: «It is honest to say that a mechanism which can explain in a satisfactory way the prebiotic synthesis of RNA has not yet been found, in spite of considerable efforts made by some of the best chemists in the world. Even the most faithful partisans of the “RNA World” have expressed pessimistic opinions on the future perspectives of this line of research». And after over a decade Christian De Duve in “Alle origini della vita” (2008) adds: «In spite of all those efforts, the tentative to reproduce the synthesis of the RNA in prebiotic conditions have had only limited success. The researchers have assembled short chains like the RNA through mineral catalyzers, for the most argil, with nucleotides artificially activated as precursors, and with some chosen matrix. The natural precursors, however, showed themselves less efficient, and their synthesis in plausible conditions has until now frustrated the ingenious of the researchers».
The theory of prebiotic broth, despite the contribution of many researchers, presents a bankruptcy balance and so after sixty years we are still at Miller’s experiments.
At the beginning of the new millennium, after having analysed if the first to appear were the protein or the nucleic acid, Paul Davies (quoted work) writes: «All the theories have in common the same idea: once that life had been born in whatever form, the rest came almost by itself, because Darwin’s evolution has been able to make its way. Hence, it is natural that scientists try to appeal to Darwinism starting from the very first phase of the history of life: whit his entry into the scene enormous progress is possible sustained only by the driving force of chance and selection. Unfortunately, though, so that Darwin’s evolution can begin it is necessary to have a minimum level of complexity. How this initial complexity attained? Put against the wall, the greater part of scientists wrings their hands and murmur the magic word: chance».
To introduce the concept of casualty in the origin of life seems to have been, in 1914, Leonard Thompson Troland, American physicist and psycho physiologist, as Iris Fly reports in her essay (quoted work).
From the times of Troland and up to the present day, the chance arises as an Arab Phoenix every time a theory on the origin of life shows its limits.
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