domenica 5 febbraio 2017


Post n. 30 English

Before addressing the topic, perhaps it is worth making 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, individually, 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, he 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" Scientific American in 1984, writes, it is preferable to leave aside the temptation to define the phenomenon of "life." Towards the end of
the decade Manfred Eigen, in "Gradini verso la vita" in 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 authoress, 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 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 that you define is 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 weren’t 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.
 Why can’t one define what is life?
Because 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, whether with our 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 see 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 now days”. The couple stayed silent for a long time, but each one asks themselves: 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, ie 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 how 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 horse 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’s a product of reproduction and evolution, it is the smallest living entity, the first stage of life on which natural selection can act upon and is therefore subject to evolution.
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 that reads “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». Also, 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?
No scientist has ever claimed to be able to answer this question. 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, looks like a small two-legged creature. If myosin is brought out of the cell 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 functions as a catalase that decomposes hydrogen peroxide just like thousands of other proteins.
Pier Luigi Luisi in his essay (quoted work) highlighted how vesicle derived fatty acids can reproduce with mechanisms typical of living organisms.
In the article “THE ORIGIN OF PROTEINS: 3) Polypeptide Synthesis” we have seen how 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". 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 which is similar to the behaviour of bacteria. Fox’s coacervated proteins 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 the extent to which life-like behaviours are rooted in physical chemistry and illustrates the concept of chemical selection for survival».
Concluding, there is no "Élan Vital", a vital spirit, a life-like behaviour, the origin of vital processes are rooted in physical chemistry.
There are, however, inexplicable facts, real mysteries, which fall out of possible chemical-physical explanations.
At a molecular level, metabolism means thousands of chemical reactions that provide for the transformation of food into energy and components needed for sustainment and growth. But metabolism means basically enzymatic proteins. As we have shown in the article "Proteins: Molecular Machines", enzymatic proteins are assembly chains, guides, quality control and recycling, transport of materials, pumps and electro-motors. These molecular machines are the engine of life; they also control the genome and surely have always existed. They were certainly much more rudimentary, but they definitely had to be part of a “proto-organism”. Who is behind these machines, what are these exceptional macromolecules made of?
They are made up of exceptional, unique and universal constituents: amino acids. (See post 11 and 12)
The organic chemistry compounds are about 1.5 million and are ordered in groups. It is only by chance that the amino acid simultaneously have seven properties also highlighted as “seven shots at luck”, summarized as:
1) Simple and easy to synthesize
2) Soluble and stable in water.
3) Doesn’t react in water.
4) Must be linked to each other, giving rise to a peptide bond in resonance
5) Must be chiral.
6) Must contain a residual -Hδ+ on the nitrogen atom.
7) The residue R is not random.
No other group of organic compounds possesses similar characteristics, and if only one of these properties were missing, we do not know how life would have been, perhaps it would not have existed.
Where did the amino acids originate from? The inanimate matter.
In short, inanimate matter provided the material, amino acids, with all the right properties for life. It created all around a chemical vacuum so that there were not interferences during the formation of life. And it is from here, from amino acids that originates a particular kind of matter: organic matter, matter for life.
The secret of life, if it exists, is within amino acids, in their origin, and in these "seven shots at luck".
The question remains: how did amino acids originate from inanimate matter with all these properties, exactly those properties needed for life, while life was still in becoming?
To this question, science has no answer because it is out of its domain.

Giovanni Occhipinti.

Translated by: Sydney Isae Lukee

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