See full article at: http://cienciadiaria.com.br

 And here’s the version of the Matrix

(translation needs correction)

A study conducted by scientists at the Georgia Institute of Technology, USA, shows that small molecules could have acted as a “molecular midwife” to help in building blocks of long chains of genetic material, as well as aiding in the selection of base pairs of double DNA helix. For researchers, there is evidence that, before there were enzymes of protein for the production of both small molecules present in the prebiotic Earth (before the emergence of life on the planet) would have helped in the formation of these polymers to promote their self-assembly.

During the experiments, the scientists observed that the molecule may help ethidium oligonucleotides (short fragments of a single strand of DNA or RNA) in the formation of polymers. One of the biggest challenges for obtaining a polymer is that as he grows, their tips begin to react with each other instead of forming long chains – a problem that is known as cyclization. But by using a molecule that binds between adjacent base pairs of DNA (known as Interleaved), it is possible to form short pieces of DNA and RNA to facilitate the creation of larger molecules. Now, researchers are seeking the true identity of this molecule “mother of all”, for the formation of the first genetic polymer from Earth. The molecule selfless that took the first step in triggering the complex and explosive emergence of life.

First version of the Matrix

This theme reveals how difficult was the struggle of nature to restore the descendants of LUCA here on Earth to evolution, to correct them of the addiction that took his heavenly ancestors to commit the original sin. A battle at the level of molecules where the agents of nature had to invade closed walls of fortresses where the descendants ended addicts and bring them out where the officers were waiting for us with outstretched hands to form a new and wider society.

Let’s analyze the phenomenon coldly, without impregnating it with our mystic. If you really understand what the text says, we are observing the past, before the origins of life, and we see a group of atoms connected to form a tape and we know that this molecule is the initial part of a great tape that would take later and called RNA or DNA. But even small changes the tape target, their tips are linked and form a ring. Goodbye RNA, was not this time yet. But we found another smaller group – that would inevitably bend their tips and close – and something strange happens: it appears around a small group of atoms known as ethyl molecule that grabs one end of the small molecule and preventing it from bending close, and brings other atoms connecting them at that point. It looks like the tip after some time changes its normal behavior, because now it does not attract more for the other end, and thus remains atoms added to it. Thus one day came to get a complete RNA molecule and hence the life appeared. In turn, the molecule of ethyl with his mission accomplished, quietly disappeared from the scene, does not expect reporters, television, the reward from the government, the fame of heroin, and will seek another molecule anonymous baby who help grow…

Gee … but we’re talking about atoms, a gang or random group of atoms! Atoms are sets of particles, they have no purpose, they do not move a finger unless they are lacking in energy and seek food in the form of an electron in the surface layers of other atoms. If you have a group of them acting differently, with abnormal behavior, and even more purposeful to help, the babysitting babies, midwives, it is clear they do not know what they do or why they do it. There must be some forces within or outside of them, with more power than the natural force of them, directing them. Either that or we undressed the coat of a scientist, sent Science go plant potatoes because the world is not logical.

I think only the existence of systems may explain these forces. It’s the only thing we know and proven that we know can act in the matter without being visible. An Arab who should be working and looking girlfriend suddenly fills with bomb and kills himself. An unreasonable behavior that came out of him: an invisible system known as Islam (or at least an ideological system of terrorists). Systems hierarchically higher or greater in complexity act on smaller systems outside or on their sub-systems or even the essence of a system that gives it its identity, which is the information overload of information beyond the sum of all its parts acts on its own shares. This excess of information that is not in any of the parts, resulting from the experiences of interactions between the parts is the mind’s invisible system. Just as in man there is an entity that is abstract, untouchable, called mind, which is substantially different from the body that produces it, is different from all parts of the body, but has the power to direct the body to where she decides. Atoms alone are not heroes or altruistic. Put billions of atoms connected and they form a stone, which does not move a finger, because the loose stones are pieces of a disconnected system.

But then, what’s and where’s the system that exists in that area at that soup of mud, leading a group of atoms to abnormal behavior? Nobody goes to see because there is not any system; everyone swears that there is no system there.

As a result, we are tempted to see small groups of atoms as if they were thinking entities with piracy! It is fashionable to say that genes have roles, which have knowledge of the future, because these other piles of atoms possess the ultimate purpose of self-perpetuation! Researches stopped themselves, totally to seek external forces to the atoms, gave personality to them. Lost his mind! We were laughing by the religious because they believe they know where the forces comes from forces: God.

There is a complete system, very big, huge even, in a shapeless mass of very tiny cells. I refer to the genetic code within a morula or blastulae in the middle of amniotic soup from which will develop a human being. The human being is the system that is driving the behavior of atoms within that soup, but there are no human beings inside the small egg. He was transfigured, decoded, and placed as a molecule composed of atoms within the amorphous mass. So if we have a proven solution here on Earth, why we should issue identity cards for molecules or demote God from the heights to come here and be playing with mud? Why not seek a larger system out of the soup?!

It was the conclusion I arrived at Amazon. When crouched turning mud of the swamp, thinking the system, I lit this little light, I thought about it, let the mud and looked up, searching the surrounding area, risking an investigator to look into the heavens … I never went back to the mud to find the answers to the origins of life. Surely they were not there, like my father and mother were not in person inside the tiny egg from my early days.

So … if I fight for this idea, now I at least must to suggest who’s the unknown system and where the system are.

 When the scientific text says “A major challenge to obtain a polymer is that as he grows, their tips begin to react with each other instead of forming long chains – a problem that is known to cyclisation.” We can understand it in the language of the Matrix. Prior to remember that “polymer” atoms are connected together to form a tape, as if it were a worm and they came together because the sun’s energy and substance of the earth’s core inoculate the atoms of light particles called photons, which are units of information from the LUCA’s Matrix/DNA. These photons are trying to create a body to incarnate itself as software, as we try to do a more advanced computer hardware to operate the latest software more developed than before. The photons act as subversive agents of a foreign regime on the particles of atoms leading them to connect in new ways. But photons inherited from LUCA are the supreme selfishness and so when they have aligned atoms sufficient to unite the two ends of the worm to they attempt transform it into a ring.

 Benzene, a simple compound cyclic.

The most primitive ring chemical benzene was discovered by Kekulée while traveling in a carriage and started to sleep but as the bumps of the carriage made her body dancing he dreamed of dancing atoms and forming wheels and cirandas. Suddenly he shouted to the coachman to stop, left the train, raised his arms to the heavens and shouted to the world: “I found the Benzene.” And gave an affectionate slap on the rump of the horse by saying “thanks buddy, to your trot! When we arrive you will have the best alfalfa ad and a week of vacation!”

Forming the ring LUCA’s genes closed the system, have retreated inside of him as the turtle is retreating into the shell inside and prepare to live eternally thermodynamic their paradise. But Nature does not want that, she has a mission far greater reach than just be balls or hard balls around in the sky, so she has to open those tips to add more atoms that are needed to build more complex systems and let them open to evolve. When she breaks up a ring it is called by chemists of “cyclization” and see an example:

 Ring opening metathesis Polymerisation

See details on Wikipedia. You see as a closed ring, when involved in a substance catalyst in a laboratory, it becomes an open line as a worm? Now for an opposite example, when a chain of atoms in the form of line – or open system – makes its points and sticking to react to form a ring, closed system:

Dieckmann condensation

In the scientists’ experiment the agent of Nature to correct the heirs of LUCA was a molecule of ethidium, which would be in place above the base-ROH. I think this example is not quite appropriate, but this haste cannot find another (if you have time you have a mission to help me with the opportunity to learn by yourself (a)). For as the text says: “… small molecules could have acted as a” molecular midwife “to help in building blocks of long chains of genetic material” – the action of ethidium molecule is not to attack and break rings after they were closed but she acts before the two ends of the chain of atoms come together, inserting these new tips atoms selected to fulfill a plan consisting of a larger and more complex. Therefore, the molecule of ethidium functions more as missionaries and psychologists dealing with young people seeking to become addicted trying to convince them to follow another path. Or as the message of the Matrix tries to transmit a healthier naturalist message to the young that lost the religious faith of parents and is about to be captured in the network transmitted by the theories of materialistic nihilism.

It said: “Now, researchers are seeking the true identity of this molecule” mother of all “, for the formation of the first genetic polymer from Earth. The molecule selfless that took the first step in triggering the complex and explosive emergence of life.” Well, that name “molecule of life”, or “mother of all” are advertising resources to enhance the materialist theory of abiogenesis. Believe that there would be a molecule or midwife creator of life? But will they have forgotten what lies behind the true meaning of the word “Life”? It is the most complex thing existing in these regions of the universe, an extraordinary engineering that we can never imitate, then who created this fantastic thing would have been a handful of atoms more stupid than a rock?! Now common! Anyway, I prefer the reasoning of Matrix Theory which suggests that many different molecules as agents for polymerization, these molecules are out pieces of the circuit LUCA ion affinity looking for other molecules that contain snippets of the past with neighbors, so as a Chinese arrived in New York will not seek to live in the Turkish quarter but the neighborhood that contains his countrymen from China.

Another issue related to this and what is fashionable eco is the fact that the industrial laboratory techniques discover how close lines or rings rather as open rings in rows, and the results of these experiments are materials such as nylon, polyethylene, etc.. A technique known as “Ring-opening metathesis polymerization of cycloalkenes” has important petrochemicals. Hence we can understand why some of these products are toxic pollutants or non-degradable, since we are creating new chemical compounds that can be deadly to those formed naturally, for both closed rings and opened molecules that would be used by evolution.

See here some useful definitions:

In chemistry, a cyclic compound is a compound in which a number of carbon atoms are connected into a loop or ring. [1] Benzene is a well known example. The term “polycyclic” is used when more than one ring form a molecule such as in naphthalene, and the term macrocycle is used for a ring containing more than a dozen atoms.

An organic chemical reaction that forms a cycle, i.e., produces a cyclic molecule from a non-cyclic compound is called cyclization reaction. A generic example to understand this type of reaction is the cyclization of hexane cyclohexane. An example of the cyclization reaction produces the Dieckmann condensation.

Regards,
Louis Morelli 

Synthetic Biology

Source: http://scicollege.net/archives/120

See article on Guardian.co.uk

http://www.guardian.co.uk/science/2010/may/20/craig-venter-synthetic-life-form

Craig Venter creates synthetic life form

Major milestone in the history of science and giant step for mankind!

In my opinion, what Venter did was skip the chapter initiated by Oparin and theoretically experienced by Mulley / Urey which consists in seeking the reduction of atmospheric and terrestrial conditions at the level that was four billion years ago to see if from the abiotic matter we obtain the basic components of life. This research is a bit abandoned because all that does not take the following evolutionary steps alone, i.e., amino acids encountered in Urey experiment are inert and do not bind polymers to form the next step, which would be the proteins. Besides the Urey’s amino acids are not the amino acids used by life. Then Craig chose to observe a genome done and copy it, taking atoms, combining them into amino acids and other components, etc..  Inserting the synthetic genome into a bacterium, it was reproduced by passing the synthetic genome of Craig to its offspring, which now must be offspring of the mother bacteria and father Craig. This offspring will have other offspring indefinitely, so a new species appeared on Earth, carrying a sign of Cain on his forehead, which are the four watermarks in the genome. Fantastic! But …

Most atheists and critics of religion came running to the media asking: “And now what about creationism? Huh?

In my case I immediately asked: “How are the Theory of Matrix / Universal DNA now? Huh? Does it come time to put everything in the trash and remove me from the scene? “

Of course, this event will require me to restudy the theory and compares it with the new situation. But it seems to me beforehand that the theory suffers no shock, on the contrary, it seems to leave the episode further strengthened. The Theory suggests that the atoms on the surface of the Earth are available to be penetrated by photons coming from solar energy, such that photons are bits of information from LUCA. The ultimate goal of the photon-genes is to replicate the system from which they came, as if the Chinese immigrants in New York, had enough money and material, would create a neighborhood to live replicating the environment of China, to the extent that would allow the materials and conditions of New York. Now Craig Venter used the surface atoms, which contains LUCA immigrants come from – which is the Earth plus the sun to form a proto-system. What he did was just replace the large environment – which also is produced by LUCA, like we produce all the medicine in the monitoring of the pregnant woman and then the delivery room. Craig did in 10 years the work that nature took billions of years to do in the last period of biogenesis, when she already had the ingredients.

But I think we could play a trick on Craig, just as Louis Pasteur got the advocates of the theory of spontaneous generation. Pasteur sterilized and hermetically sealed vials containing the material which said generating life forms like microbes. Was not generated anything, proving that the vital principles came through the air or something else. Likewise we could try to collect atoms in a certain region of the deep Earth that did not touch neither they nor their neighbors, with solar energy but which have not been otherwise achieved by substances that rise from the core of the planet. In our Matrix’s language, these atoms would be sterile, the vital principles comes from something else. We would give these atoms to Craig and ask him to repeat the experience. If the Theory of Matrix / Universal DNA are correct, he could never copy the genome. Had the same problem of the researchers in the lab trying to add pieces of polymers or proteins for small molecules that form in nature and should evolve into RNA or DNA but instead, when they reach a certain point, its two ends are attracted to bend and connect to form a closed ring forever.  Why? For simple atoms has its own attraction forces that deterministically leads to connect to specific atoms also constitute simple arrangements that result in rocks, water, inorganic things. But the atoms used by Venter are special, they contain the vital principle. We would have closed the bottle, proving that Craig’s material is sterile. It should be Pasteur in the head!

However, we will continue analyzing it all, is too recent for definitive conclusions.

Regards,
Louis Morelli

Setembro | 27 | 2009

This is more one strong clue that the models of this theory could be right, or at least, the ones that is nearest to reality than any other nade till today. These formulas above help us to understand and how to interpret the Matrix/DNA formula, whem the universal matrix was in its evolutionary shape as astronomic structure, minutes before the origins of life at Earth. 

See the importancve of pyrroles in the following text:  

ASTROBIOLOGY MAGAZINE

Cooking Life’s Ingredients with a pinch of salt

Based on a European Planetary Science Congress news release

http://www.astrobio.net/pressrelease/3255/cooking-lifes-ingredients-with-a-pinch-of-salt

      “Approximately 4.5 to 3.8 billion years ago, the Earth was probably covered by a salty ocean, rich in organic compounds, dotted with active volcanic islands and short-lived continents. The team from the University of Hohenheim in Stuttgart has simulated some of the chemical processes that might have taken place along hot volcanic coasts during this Hadean era by evaporating solutions of artificial primordial seawater and then baking the salty residue in an atmosphere of nitrogen and carbon dioxide to volcanic temperatures of 350 degrees Celsius. They found that compounds such as pyrroles, which are contained in chlorophyll and haeme (the oxygen-carrying component of haemoglobin), are created.”

But… what are “pyrroles”? See Wikipedia:

     ” Pyrrole is a heterocyclic aromatic organic compound, a five-membered ring with the formula C₄H₄NH.^[1] Substituted derivatives are also called pyrroles. For example, C₄H₄NCH₃ is N-methylpyrrole. Porphobilinogen is a trisubstituted pyrrole, which is the biosynthetic precursor to many natural products.^[2]

Pyrroles are components of more complex macrocycles, including the porphyrins of heme, the chlorins, bacteriochlorins chlorophyll, porphyrinogens…”

Now, see the chemical compound at the picture above and keep side by side the model of LUCA, the hardware and the software diagram. Look how LUCA reproduces itself ’( translation will be continued soon)

em forma, como os fragmentos irradiaos de seu corpo-sistema penetram os atomos terrestres e dirigem-nos a se combinarem como reprodução da anatomia de LUCA. O Nitrogenio está fazendo a Função n.1, os quatro hidrogenios estão fazendo as funções 3,4,6,7. A função 5, (reprodutora, que é executada por cometas no nivel astronomico,  RNA no nivel cellular , uracila no nivel de nucleotideos, etc.) está aí representada pelo átomo de hidrogenio que está fora do circuito sistemico e ligado ao nitrogenio, assim como a uracila aparece de fora e esporadicamente no código genetico quando as outras quatro bases são sempre permanentes. Pyrroles são cópias transformadas de LUCA, pois enquanto este é um sistema fechado, suas cópias biológicas se tornaram sistemas abertos. Assim como o planeta precisa de uma estrela existente fora de seu ciclo vital para estimular seu nucleo a iniciar reações nucleares e se transformar em pulsar, ou assim como um atomo instavel aceita um eletron externo para se equilibrar, o pyrrole encontra o hidrogenio externo para euqilibrar-se e perpetuar seu circuito. O cometa permite o continuo reciclar de LUCA, e é exatamente isto que faz este hidrogenio externo. Não é por mero acaso que o pyrrole estava em abiogênese, na cena das origens da vida.

Pyrroles are structures rooted on the same precursors of aminoacids. The difference is about the structure speciation, like the nervous cells are different from the liver cells due to speciation. The central ring of aminoacids and pyrroles have the same shape derivated from LUCA.

About the question – “Why the pyrroles were formed earlier if they were used only latter, in photosynthesis and haemoglobin?!”- is answered by the processes about macro-evolution reproduction, like atoms systems to stellar systems, or from galaxies systems to biological systems. In macro-evolution the genes from the precursor are not transmitted in a closed envelope like the chromosomes does in micro-evolution. The genes, be them particles, photons, quantum bits-information, whatsoever, are spreaded free in time and space. So, the way they get linked together is very promiscuous, given to chance a lot of possibilities. That’s is the explanation for the great diversity of biological systems at Earth and elsewhere in the space.

( pretendo voltar e estudar melhor pyrroles e o artigo acima para desenvolver este conhecimento)

This article is a copy of my post in the “Richard Dawkins Forum, see: 

http://www.richarddawkins.net/forum

In the board “Evolution and Natural Selection” 

by Louis Morelli » Sat May 16, 2009 5:37 pm

Eversbane wrote: “The universe does not need explaining. The scientists you see around you are here only to describe it. No need to explain anything. Thanks anyway.”

My answer: “ Huh? The Blind Sciencemaker ?!…  Ok, it is not me that want change your mind, since that I know I am not the owner of the thru, and so, I am a blind seeker. I am very grateful to scientists that are experimentalist because I need the data they collects and distributes, my investigation in the jungle is supported over their shoulders. But… are you really right?! Let’s see an example about an interview with Stanley Miller, at http://www.accessexcellence.org/WN/NM/miller.php .

Question: Who came up with the idea of the reducing atmosphere?
Miller: “Oparin, a Russian scientist, began the modern idea of the origin of life when he published a pamphlet in 1924. His idea was called the heterotrophic hypothesis: that the first organisms were heterotrophic, meaning they got their organic material from the environment, rather than having to make it, like blue-green algae. This was an important idea. Oparin also suggested that the less biosynthesis there is, the easier it is to form a living organism. Then he proposed the idea of the reducing atmosphere where you might make organic compounds.
He also proposed that the first organisms were coacervates, a special type of colloid. Nobody takes that last part very seriously anymore, but in 1936, this was reasonable since DNA was not known to be the genetic material..
In 1951, unaware of Oparin’s work, Harold Urey came to the same conclusion about the reducing atmosphere. He knew enough chemistry and biology to figure that you might get the building blocks of life under these conditions.

Question: Tell us about the famous electrical discharge experiment.
Miller: The experiments were done in Urey’s lab when I was a graduate student. Urey gave a lecture in October of 1951 when I first arrived at Chicago and suggested that someone do these experiments. So I went to him and said, “I’d like to do those experiments”. The first thing he tried to do was talk me out of it. Then he realized I was determined. He said the problem was that it was really a very risky experiment and probably wouldn’t work, and he was responsible that I get a degree in three years or so. So we agreed to give it six months or a year. If it worked out fine, if not, on to something else. As it turned out I got some results in a matter of weeks.”

                                                          …………………………………………………………………………………………
So, dear EVERSBANE, either Oparin and Urey’s contributions were ideas emerged when seeking explanations for ultimate causes, which results in hypothesis and theories. Miller did not worked as a blind sciencemaker but he was guided by those ideas. See the words from Stanley Miller, below:
“In the 1820’s a German chemist named Woeller announced the synthesis of urea from ammonium cyanate, creating a compound that occurs in biology. That experiment is so famous because it is considered the first example where inorganic compounds reacted to make a biological compound. They used to make a distinction between organic, meaning of biological origin, and inorganic- CO2, CO and graphite. We now know that there is no such distinction…. However, it remained a mystery how you could make organic compounds under geological conditions and have them organized into a living organism. A number of people tried prebiotic experiments. But they used CO2F, nitrogen and water. When you use those chemicals, nothing happens. It’s only when you use a reducing atmosphere that things start to happen.”
So, I think it is clear that the method of unification of theories and experimentation was the guide for the brilliant Miller’s results and not the method of “blind experimentations”.
But, since the Miller-Urey’s experiments we never got the next step, making the aminoacids working alone for producing proteins or RNA. The Miller-Urey experiments remain a dead end, as said somebody here in the “abiogenesis forum”. I think that, again, Miller has the right explanation for “why?” we did not get it. See his words below:
“ The more important research are the experiments these days, rather than the trading of ideas. Good ideas are those that when reduced to an experiment end up working. Our approach is to do experiments and demonstrate things, not just talk about possibilities.”
If someone that make the job of naturalist philosopher and, in preference, in stranger lands, like the salvage Amazon jungle, does not try to organize the immense collection of data we have today, plus the inspiration get from the observation of crude nature, and try to organize it in models of a theory, we will not get the next step, I think.
By the way, the jungle is telling me that without the photons from sunlight and/or the materials from Earth nucleus, the amino acids of miller will not work alone. My models are suggesting some kind of laboratory experiments, I can’t do it from here.
There are something else I need suggest here: “ never think about, or never tell the words “origins” , “life” , “creation”, “spontaneous emergence”. There is no origin; there are no origins of life. The word “origins” means a broken event of natural flow of forces, means that cause-effect was broken by something non-natural, and we, here, in the jungle, never saw it happens. Instead using the word “ life” I use the word ‘biological systems’, facing ‘electro-magnetic systems’, ‘atomic systems”, ‘Newtonian mechanic system”, etc. The opposite of life is death and not non-living, there is no such distinction, I think. The word “origins” has been the cause of a lot of human mind deviation from the real nature, it is a cause for creating religions and erroneous ideas of “spontaneous generations”. The currently models in Astronomy are based upon the idea of “spontaneous generation of bodies in the sky”, and since I never have seen spontaneous generations here in the jungle, I don’t believe in it. Cheers…