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A short story of life

Understanding the origin of life is much more than a scientific adventure. Understanding the origin of life, it is up (part of) the veil that slyly hides its meaning. Why are we here ?

Are we here

  • by chance, as argued by Richard Dawkins (The God Delusion), Nietzsche, Laplace, Darwin or Michel Onfray ?
  • as a product of an intelligent design, as claimed by the great monotheisms and therefore liable to a « creator »?

The ramifications, we see, are multiple, scientific of course, but also metaphysical and religious. It’s a battle which opposes :

  • on one side, the Creationists (supporters of intelligent design);
  • and on the other the laity (supporters of chance).

The debate is still (an will for ever) going..

The origins of life: the debate rages

Great scientists, like the astrophysicist Trinh Xuan TUAN, or a little smaller like Bogdanov, are convinced of the existence of an intelligent design:  the universe is governed by some fundamental constants (speed of light , gravitational force, electromagnetic force interaction, mass of the electron, Planck’s constant …), perfectly adjusted to allow the emergence of life. The models have shown that if you change a fraction of the value of these constants, the universe becomes unstable and therefore sterile. For example, increase the force of gravity and the universe will close on, in a devastating Big Crunsh. Decrease it and expansion will be so rapid that Universe will disappear in a great eternal cold, before life have a chance to emerge.

The value of these constants seem given: we do not explain it. Why the speed of a photon is 300 000 km/s ? We don’t know.

NEWTON had commented about his laws of mechanics by insisting they allowed to explain « how » large objects (planets) worked, but certainly not « why ». Like Voltaire, we can then imagine a great watchmaker settled this beautiful mechanics…

The origins of life: towards entropy

Entropy measures the disorder of a system: a tidy room has lower entropy than the same room after the passage of a teenager. And the more time passes, the worse the room: covered with dust and lurking dirty linen. If one believes the second law of thermodynamics, a system still sees its entropy increase (in the example of the room if we do not provide it with energy (eg repeated work of a woman cleaning), room will naturally go towards disorder.

Life is an organizational masterpiece. It is the culmination of a path from the disorder (frantic atoms) to the complexity (a perfectly organized genetic code : us). It is therefore a contradiction to the second law. But not that much. This second principle must be understood at the scale of the entire universe: at this sacle, the order appears somewhere on time, for example in a puddle. Elsewhere, in the Universe, disorder increases. And that’s exactly what happens. Our brain is now identified place in the universe where matter is best organized. So it is a singular point that deserves special attention. A matter of chance ?  Or is it the result of a organised plan ? Is the disorder of the universe at the service of the organization of our brain?

Chance, morality and meaning of life

If chance is king, then there is no meaning of life and even less moral obligations. The Marquis de Sade could then be the spokesman of the chapel which recognizes no limits, no shackles, leaving total freedom to his impulses. Dostoevsky recalls in this respect in the Brothers Karamazov : « If God does not exist, then everything is permitted. » Indeed: no fear of a last judgment, no concept of good and evil! Then we can go to their heart.

If there has been a creator, however, the history of morality is different. Two major families of legal consequences are to be distinguished; two irreconcilable thought that schools are the Deists and Theists :

  1. Deists, as the Epicureans, the Christians, but also great names of philosophy as Voltaire, Leibniz and Kant, science as, Newton, Einstein or Trinh Xuan Tuan, are committed to the principle of a « God-watchmaker » ; a designer, an architect who would have settled everything at first, then that would let the world go at will, giving the man a free will , the power to do good or evil; man is free, he is responsible for his actions and can therefore be judged. Here we see the interest of religion to postulate that free will to better present themselves moralizing and possibly inquisitor; this is the story of Cain who tells us the best in Genesis ;
  2. Theists, who believe that God not only created everything, but still rule everything: the operation of the lower wheel of the universe, the slightest breath of air: an omniscient and omnipotent God. LAPLACE had thus shown the illusion of free will by considering a genius knowing all the parameters of the Universe today would deduce, by the simple laws of physics, the universe tomorrow. In this context, the man can not be free because everything is written in advance. The moral point of view, man can then be held accountable. Spinoza, with his formidable pantheism, is part of this school, like Nietzsche or Schopenhauer.

Who is right ? We never will know. The mathematician Kurt Gödel has demonstrated the impossibility of any to show in particular the existence of God (Kant, without mathematics, arrived almost at the same conclusion, Nietzsche also with depths that hide deeper depths also).

So ? Should we continue to look for the origin of life? Without a doubt. With the firm conviction that doubt remains. John Paul II, parodying this PASTOR at the occasion, had recalled  » a little science away from God (this is what happened in the enlightened minds of the revolution as Condorcet or Diderot ) and a lot of science in closer (as is the case in the head of many scientists (as Newton or Einstein) who discover little by little the vastness of our ignorance and our fatal inability to know everything).

Worms in the fruit

But back to the origin of life. PASTOR, in 1865, showed dramatically the impossibility of spontaneous generation. Organizations can emerge from inanimate matter as it was believed it at the time.

It was Aristotle who paused the basics, then made the success of the theory of spontaneous generation : the opportunity to emerge from inert matter a living without ascending. Democritus, the father of the atomic materialism and the great inspirer of Epicurus, had already raised the possibility that the atoms (the smallest possible fraction of matter) can be assembled to form tiny living beings. It was by observing the mold, especially on food, that Aristotle was convinced of his theory that suffered no challenge for two millennia ! It was surprising that the Church (St. Augustine) went on his own theory:

« Let the waters bring forth abundantly the moving creatures that have life » (Genesis 1:20).

Mice could well emerge from a pile of garbage! PASTOR in 1865 demonstrated the manifest error of Aristotle. If to appear is that they are already there, in the form of embryos. Pasteurization eliminates these germs and prevent any appearance of living beings.

Sentimental atom

Yet it is clear that life originated on Earth. What happened ? How « non-living » (the prebiotic or inert matter) became « alive » (biotic). How is it that a broth of atoms to organized matter capable of replicating? The mind, intellect, feelings emerged from these large assemblies of molecules, made of carbon, hydrogen and oxygen (among others) love. An atom acn laugh or cry.

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DNA

The code carried by DNA, includes the complete plan of being (of all living creatures) and its mode of operation. This code is written with four letters only and is entirely contained in the cells of a few microns. Was it assembled by chance? Difficult to design because the probability of such an event is ridiculously low. It was formed under the constraints imposed upon him the environment? Or, like a computer code ? He needed then an « encoder » as think Bill Gates.

The brief history of life is just beginning. It will not close. But can we start writing, as LAPLACE, that is to say without using the assumption God?

The origins of life

How did it happen?

How we pass from the inert to the living. How are atoms assembled to form the impressive buildings that are the cells (see image below) and then a giraffe? Where are the building blocks of life (proteins)? Why have they organized to form cells? How is made:

  • the nucleus , which encloses the genetic material;
  • ribosomes, protein assembly plants;
  • mitochondria that supply energy to the cell?

This is a series of questions that could go on forever about the mystery of the first moments of life …

The origins of life

There are 5 billion years

Life as we know, implies some invariants:

  • water in liquid form to encourage chemical reactions;
  • the presence of large quantities of carbon atoms (C), oxygen (O), hydrogen (H), nitrogen (N) but also phosphorus (P) of sulfur (S) and few others such as iron (Fe), to assemble the first « organic » molecules.

Luckily (or necessity to paraphrase Jacques Monod?), these elements are present in large quantities on Earth. At its formation, there are five billion years, under the effect of gravity, the heavy compounds sank into its depths, leaving the free surface free for light elements that formed the first simple organic molecules. The carbon is thus assembled with four molecules of hydrogen to form methane (CH4), nitrogen with three molecules of hydrogen to form ammonia (NH3).

The early Earth was quite different from the blue planet we know today. Its atmosphere consisted mainly of water vapor (H2O). Its surface was dotted with molten rock, volcanoes letting out toxic gases such as sulfuric acid (H2SO4). No life was possible: In addition to water vapor, the atmosphere contained ammonia (NH3), methane (CH4), carbon dioxide (CO2). The gradual cooling has the appearance of more complex molecules such as:

  • formaldehyd (HC=O);
  • hydrocyanic acid (HCN);

two essential molecules for the rest of the story and that form spontaneously when a power source is present (see below MILLER experience ). In particular, Juan ORO showed that the synthesis of a major nucleotide (adenine) is possible from hydrocyanic acid. This adenine is also one of the constituents of ATP and is, as such, capital in the energy supply to the cell.

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Condensation of water vapor brought torrential rains to cause a leaching of primary rocks, bringing ocean training mineral compounds in significant quantities and especially silica (Si). The atmosphere was devoid of oxygen and rich in CO2. The greenhouse temperature stabilized and maintained a sufficient temperature for liquid water (at that time the sun was feeble and its influence was not enough). Despite its low activity, the sun’s UV bombarding Earth’s surface that were not, as now, stopped by stratospheric ozone (O3). This bombardment prohibited any molecular stability by destroying the first buildings. Only the ocean floor was spared. It is therefore not surprising that life has emerged under the sea.

The origins of life

Under the ocean

The underwater volcanoes, but also hydrothermal vents, allowed the rise of heavy elements including iron (which solution is expressed in ferrous ion Fe 2+), but also phosphate and sulfuric acid. The ocean was so primitive:

  • very hot due to volcanic activity, but also the bombardment of the surface by UV ;
  • very acid , because concentrated sulfuric acid;
  • rich in organic elements and minerals, due to the leaching of soils and the contribution of hydrothermal vents and volcanoes.

This explosive cocktail has the pretty name of primordial soup .

We see, until then, no need for the intervention of something other than chance and necessity.

The origins of life

The primordial soup

This soup was still hot. Its temperature exceeded 100°C. Atmospheric pressure, particularly high at that time, kept it in a liquid state. The atmosphere was the seat of permanent electric shocks, linked to the strong telluric activity (lightning). The heat and energy have then allowed the formation of the first molecules. The  UV bombing of the surface also had its importance in reducing CO2, that is to say, snatching an oxygen molecule and replace it with hydrogen, nitrogen or carbon. This is the type of reaction that is at work in photosynthesis, plants forming organic matter from reduced CO2 and energy from the sun. This reduction in CO2 was also result of enriching the oxygen atmosphere.

Amino acids: the first building blocks of life

In 1953, Miller showed that a mixture of ammonia (NH3), methane (CH4), water vapor (H2O) and CO2, exposed to electric shocks, spontaneously formed organic molecules such as acids amino.

As its name suggests, an amino acid is an acid (HOOC- group) carrying an amin (NH2). Their combination provides a molecule with an acid head and a basic queue, providing the ability to create chains of amino acids: The head of the first acid is assembled with the tail of the next link in a so-called « peptide » . The chain then carries the polypeptide name.

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The peptide bond releases a water molecule

The equations of life

The atmosphere is so rich in nitrogen (N2) and ammonia (NH3) and methane (CH4). It is bombarded with UV rays from the sun. Gas energy supplies is in some cases sufficient to separate a pair of atoms:

N2 -> 2 N

These freed atoms are very energetic and are attacking their fellows including methane giving rise to the famous hydrogen cyanide (HCN), which will play a fundamental role later:

N + CH4 -> HCN +3/2 H2

The other essential molecule, formaldehyd (HCOH) appears in turn:

CH4 + H2O -> H2 + 2 HCOH

Now if we mixture formldehyd (HCOH) and hydrocyanic acid (HCN), with a little water an amonia, we obtain an amino acid !

HCOH + HCN + NH3 -> Amino nitrile (+ H2O) -> amino acid + ammonia (gas)

This reaction is known as the « Strecker synthesis ». It remains only to assemble amino acids to form channels that become proteins.

Now, by mixing:

  • two formaldehyde, we get glycoladéhyde (HO (CH2) COH) which, when mixed with hydrogen cyanid , in turn, gives an amino acid (serine);
  • two hydrocyanic acid, by adding the UV and a little water, we obtain guanine, one of four letters of the genetic code;
  • two formaldehydes, by adding lime (chalk) in the presence of borate, we can forme sugar (ribose) of biological interest (pentoses: five-carbon sugars).

And God in all this? A complex prebiotic world may form naturally by simply reproducing the conditions of the primitive atmosphere. All these syntheses (and many others) have been conducted in human laboratories, perhaps « to uch human » Nietzsche would have said.

The proteins

Upon reaching a chain of more than ten amino acids linked by peptide bonds, we speak of proteins. These macro-molecules having high molecular weights, which can be folded to form three-dimensional objects. Everything in the human body is made of protein, except the DNA molecule that contains the genetic code (and the instructions to make proteins).

Catalysts

Certain chemical reactions can only be realized in the presence of a catalyst, a substance that causes the reaction, but that does not participatein it. This is the case of reactions involving organic substances. To assemble or transform, an organic molecule is generally free of O2. Now, in an aqueous medium, that is to say saturated with oxygen, it is impossible. Catalysts were needed and the particular iron risen from the bowels of the earth.

Iron suffered the bombardment of UV from the sun. This bombardment managed to snatch two electrons (negatively charged) of its electron cloud that turned far around its nucleus (positively charged).

UV + Fe -> Fe2+  +  2 e-

The iron, atom in the original neutral electrically, spread through the water as ion (Fe 2+) , positively charged (since lost two negative charges). The electrons (e-) goes freely in the soup where they combined with H+ ions to form an atom of dihydrogen H2.

2H+  +  2e- -> 2 H2

The hydrogen was then available and tore oxygen from organic molecules to form water. Iron has well catalyzed reaction known as « reduction » of the organic molecule giving it the ability to evolve.

Organic molecules have so proliferated to accumulate at the bottom of the ocean in thick layers. It was in this layers that polypeptides were probably made. DARWIN was then invited to the party. The most stable molecules have taken precedence over other unstable limited lifespan. It is believed that confined environments such as cavities in rocks or ponds, contributed to this concentration and thus the formation of more and longer chains. For billions of years, this prebiotic chemistry (before life) was at work randomly constituting a monstrous mash of various organic molecules. But we were still far from life. The formation of molecules was random, not directed by a code.

The origins of life

The code

In the soup, have been identified :

  • adenine (formed from the hydrocyanic acid), the first letter of the genetic code marked « A » ;
  • triphosphates acids (or ATP), formed from adenine which will later suppliers energy of the cell;
  • nitrogenous bases (guanine (G), cytosine (C), thymine (T)) , the other three letters of the genetic code.

The four letters (or nitrogen bases) tended by chemical affinity, to assemble them. This assembly gave them a competitive advantage because the letters, associated in pairs (A to C and G to T), protected themselves mutually.

DARWIN favored the constitution and chain letters. The molecule of RNA (ribonucleic acid) was born.

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Strand RNA

The chains stretched and twisted in all directions to form loops. This gesture offered to the molecule a second competitive advantage : it acquired the mechanical strength in addition to chemical stability. In parallel to this first string of letters, came clump of letters, depending on affinities already mentioned (A with C and G with T). A second chain thus formed in front of the first.

For the first time, the construction of an organic molecule was not a coincidence: the second string was the image « negative » of the first :

  • C instead of A (and vice versa);
  • and G instead of T, and (conversely).
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This was the first driven replication of an organic molecule. The RNA was able to self-replicate. Some strands are more stable than others, mobilized community resources and eliminated competitors. DARWIN yet! Nature is not perfect : replication errors opened the door to new molecules, more stable (or not) and especially with new properties such as catalyzing reactions.

Reading the code

But stability is able to kill evolution. Fortunately, a new start intervened when RNA was combined with an amino acid. This random combination revealed still more stable. We then saw the rise of RNA colony with an amino acid. These RNAs « carriers amino acid » clung (on the side of their nitrogen base) on RNA « code carrier ». At the other end, their amino tails came into contact and assembled. A chain of amino acids (polypeptides) could thus be read from the code on RNA « code carrier » through RNA called « transfer. » Nature had invented the code read head and the assembly line amino acids that form proteins was.

RNA from WIKIPEDIA

 The different types of RNA today :
  1.  messenger RNA (mRNA), which matrix are used for protein synthesis;
  2. ribosomal RNA (rRNA), which enter into the composition of the ribosome with the ribosomal proteins;
  3. transfer RNA (tRNA) , which are amino acids and make for proteins;
  4. RNA interference (siRNA, miRNA …) that allow gene expression, by targeting degradation of specific messenger RNA or by inhibiting protein translation.

Proteins and enzymes

Proteins consist of chains of amino acids (there are 20 different). They have the option to fall back on itself to form all kinds of assemblies which are all building blocks of life. This folding had two consequences: it allowed

  • a better stability of the long molecule;
  • an amino acid reconciliation hitherto separated. It thus played a catalytic role in promoting this assembly who otherwise would never have occurred.

These proteins favoring certain reactions (assembly of amino acids) bear the name of enzymes .

These enzymes-proteins may however encourage replication of all RNA, causing a dangerous competition for the code that was at its origin carrier RNA. So it had to shut to prevent it make benefit others of its catalytic powers.

The cell membrane

The partitioning of code (RNA) and the enzyme was provided by a membrane that separated the outside (soup) from the inside. The appearance of the membrane would change everything: it was a plus in the way of complexity. This wall would mark a difference between:

  • within organized allowing the creation of molecules increasingly complex (through energy import and export of waste);
  • and outdoors subjected to environmental fluctuations.

This membran was composed of fat:  Some of them (the phospholipids ) have in fact:

  • a hydrophilic end (loves water in Greek);
  • a hydrophobic end (who does not like the water always in Greek).

They stick to each other to form a barrier, pushing to one side the water and pulling the other. They eventually form a hollow sphere (coacervates). The envelope or membrane of the cell is born. Hydrophobic molecules from the external environment will naturally find refuge

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Cellular membrane

 

The prototype cells

When RNA code-promoting protein was wrapped within an insulating membrane, the game was won: the protein became exclusive. The membrabe encouraged more copy of RNA that was able to grow immune to competition.

Enzymes (ribozymes) could then promote the transition of RNA (chain single-stranded) to  DNA (two parallel strands in double helix). The RNA has the disadvantage of having a very energy-OH bond which made it unstable. The nature should snatch this toxic oxygen. DNA had the advantage of being more resistant and able to divide into two strands each with code.

Membrane passages

The system was not yet complete. Too tight membrane was useless. It was necessary to create passages which can filter the entries and exits. Long chains of sugars will be used to establish this function: polysaccharides. They reinforced (in the mechanical sense) the membrane. Cellulose is an example which gives the plant its rigidity.

Proteins were added to the building to filter the exchanges between the inside and outside of the membrane. A kind of customs is set up so that the cell can import and export its nutrients waste and regulate its vital parameters such as pH. For the latter parameter, the cell can export protons (H +) responsible for the acidity or contrary to import to maintain a neutral (pH = 7) condition.

The issue of energy

To operate the cell needed energy. It was for this, that it imports molecules of ATP (adenosine triphosphate), a valuable source of energy. This method proved ineffective.

ATP deteriorated into ADP (adenosine diphosphate), releasing energy but could be regenerated.

Afficher l'image d'origine

energy cycle by wikipedia

H2O + ATP -> ADP + Energy + HPO42-

Inverse reaction requires a supply of energy. Nature then found a much better way. Pigments (chlorophyll) appeared, giving the cell the ability to collect solar energy and regenerate as « free » ATP.

The cell had to overcome the energy problem and could conquer the planet.

Autotrophic and Heterotrophic

This cell was about to give birth to autotrophic beings, able to grow by drawing resources only in the environment (sunlight, CO2, nutrients); plants today are the great representatives of this class. Later appear the second class, the heterotrophic, who can not subsist in assimilating the first. Man, and more generally the animal kingdom, added mushrooms, are part of this second class.

The origins of life

In conclusion

The road is still long and the story is flawed. However, this test shows that the history of life can be written without using the assumption GOD. LAPLACE, the great mathematician of the Emperor, had already arrived at this conclusion:  » God? Sire, I have no need of that hypothesis « .

Heisenberg , German physicist, had shown in the early twentieth century that uncertainty is part of our world, that some phenomena escape and will for ever still escape the laws of mechanics. Had he demonstrated the existence of chance? Others, like Niels Bohr, confirmed this idea and opposed Einstein on this point repeated at will;  » God does not play dice « . Schrödinger , another German physicist of the same period, had speculated that the position of an electron could not be defined only from probabilities brief the electron was the image of randomness.

We can not end without also give the floor to Kurt Gödel, a mathematician who established the impossibility of demonstrating every thing: in particular the existence of God. For this purpose (demonstrate the existence of god), we must be outside of the universe, be greater than he, which of course is not possible …

The debate between creationism and atheistic can not be completed. This has been demonstrated mathematically.

The scientific community agrees on one point: the mystery of life is not ready to be resolved and some areas remain, despite our efforts, in the shadows. Everyone will have their own judgment, which will remain a profession of faith that escapes science.

The origins of life

The latest advances

The origins of life pose a number of paradoxes: to allow the emergence of life, a coding molecule (DNA) is needed to provide a protein building plan. But the cells can copy DNA without the help of proteins. To complicate everything, this replication is not possible in the presence of an incorporated lipid membrane. Another problem of the chicken and the egg appears as proteins function as enzymes are needed to make these lipids. Each needing the other to exist, the question of who was there first becomes inevitable.

Researchers now believe to have solved this paradox: a pair of simple chemical components, abundant during the first ages of the earth, is sufficient to give rise to a complex network of chemical reactions that produce the three families of molecules essential to end life :

  1. nucleic acids;
  2. amino acids;
  3. lipids.

Scientists have long argue about the likelihood of the roads leading to life. There are such proponents of RNA world, who think that this acid was a pioneer in allowing both:

  • to carry the genetic code;
  • and to function as a protein-enzyme catalyzing the reactions.

On the other side, advocates of the theory of « metabolism first » claim that simple metals, catalyzing their power, were able to create in the prebiotic soup of living bricks.

The hypothesis of an RNA world enjoyed its heyday in 2009. John Sutherland of the University of Cambridge (UK), published a paper in which he related that from simple precursor molecules (acetylene and formaldehyde ), it could cause a chain of reactions leading to the formation of two of the nucleotides present in the DNA, showing how RNA could be formed almost spontaneously, without the aid of enzymes. But critics have given the voice, both precursors John were already complex molecules whose origin was unclear.

In their recent study, Sutherland and colleagues then established a work program to identify contraflow « a road to the RNA », from more simple materials. And they succeeded! In a paper in April 2015 Nature, the team described an experiment to create nucleic acid precursors starting from hydrocyanic acid (HCN), hydrogen sulphide (H2S) and light (UV). Best of all, they also emerged the starting materials for the production of amino acids and lipids. Single molecule can, under certain conditions, be assembled to form the first blocks of life.

The Sutherland team also confirmed that the atmosphere of the earth origins was favorable to trigger such reactions: HCN was abundant in comets that bombarded for several hundred million years our young earth. The energy released by the impact was also sufficient to synthesize HCN from hydrogen, carbon and nitrogen. The H2S was meanwhile abundant because of intense volcanism. It is possible that copper is acted as catalyst.

 

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