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

Interesting article published at Wired Magazine, under the title “Evolution’s New Foe: Timid School Administrators” (you can see it at

http://www.wired.com/wiredscience/2010/04/evolution-controversy/comment-page-1/#comments

Following the article are the coments and I am trying to participate. Below the posts for which I answered till now:

Posted by: tahos | 04/23/10 | 11:06 am |

Evolution belongs in philosophy and religion classes alongside creation. The “science” of evolution is tenuous and controversial, and should be explained as such. Presenting it as scientific fact rather than speculation and at best theory does the scientific method a disservice and establishes a pattern of thinking in young people that is dangerous and close-minded.

This is coming from someone who spent several years as a research scientist (cell and molecular biology).

Posted by: Morelli | 04/25/10 | 7:06 am |

Tahos: You should be right saying that “The Neo-Darwinian Theory of Evolution establishes a pattern of thinking in young people that is dangerous and close-minded”. Transformation of some species by Darwin’s three postulates – VSI: Variation, Selection, Inheritance – is a fact. But the fact finishes here. There are thousands of data showing that there is genetic variation, some of them are selected because produces better adaptation and then, is naturally selected. But these proved transformations do not means that Evolution is a Universal Law and the Darwin postulates means Evolution. Let’s see a sample: about reptiles the transformations went from lizards to crocodiles to dinosaurs. After reptiles there are mammals. But… for sure, mammals did not come from dinosaurs. Then, they say: “a meteorite came from the sky killing the dinosaurs, then, evolution departure from smaller reptiles to mammals.” Oh, com’ on! What about lions, elephant, eagles, whales… every developed giant from each species are going to extinction. In the future we will need a lot of tales about meteorites!
There is the possibility that smaller reptiles evolved to mammals. There are a lot of fossil showing animals that are half reptiles/half mammals. It is “almost” certainly that reptiles evolved to mammals. But, there are no observations of occurrence and not a proved link. Then, the “almost” is not a scientific statement yet. And it is almost certainly that the Darwin’s transformations do not explain the occurrence. It explains the variations or to say “evolution” from smaller to bigger, but the bigger were a dead end, then there were no evolution if the final result was not evolution.
The transformations from reptiles to mammals – and maybe from primates to human beings – need another kind of universal postulates. The Darwinian three postulates are not enough. Here is the danger, brilliant pointed out by you. These students, like the neo-Darwinians, will be closed –minded, turning around a non-complete natural process, then, they never will be able to find the whole picture.
I have a theory that suggests new explanations for these topics. But my theory has – besides the three Darwinian postulates – four more postulates, that came from Cosmological Evolution and physical ancestral thermodynamics systems. The theory suggests that Darwin’s theory is only half of the whole history. If these people become close-minded they never will get the whole picture. You are right.

Posted by: danielpauldavis | 04/23/10 | 2:52 pm |

”If you’re not looking to teach children the best science, that harms their education.” Crick and Watson really believed they were proving their atheism when they discovered the double-helix DNA molecule. What they actually did was prove that random assembly of ANY life was impossible because that double-helix structure required that EVERY DNA molecule be laevorotary: have the hydrogen atom on the left side. Any molecule with the hydrogen atom on the right side would stop all molecular processes at that point and kill the cell (which is what strychnine is all about.) While every atheist and evolutionist likes to point to Miller’s experiments about random DNA production, they always leave out two facts of that experiment. The first is that Miller, et al. included a trap to separate any formed molecules from the rest of the mix before they disassembled as spontaneously as they assembled. Second is that all the molecules were–being random–randomly laevorotary and dextrarotary. In other words, the experiment proved that intelligence was absolutely required for any life to actually exist. Without that intelligence separating the molecules from the mix AND separating laevo- from dextra rotary, inorganic chemistry could never become organic chemistry.

Posted by: Morelli | 04/25/10 | 7:52 am |

danielpauldavis, You said: “In other words, the experiment proved that intelligence was absolutely required for any life to actually exist. Without that intelligence separating the molecules from the mix AND separating laevo- from dextra rotary, inorganic chemistry could never become organic chemistry.”
I don’t agree, I think there is a natural mechanism that does not requires intelligence. If you go to my website you will see a model of a closed system (which seems to be the building block of astronomic systems). In a closed system, the flow of energy begins clockwise and at the top down ( in a watch this should be the mark of 6 hours); the flow goes to 12 and then is shared in two flows; one flow goes back towards 6 and another flow go normally to 1. Then, this flow designs the complete circumference, going to 6. It means that a face is shared into two half faces. Every time you have a complete left face, the flow will build the right one, obeying the bi-lateral symmetry.
Now, going back to DNA. The fundamental unit of information or the building block of DNA is the left/right pair of nucleotides. But, the nucleotides are exact a copy of the astronomic building block. Then, when you have the left nucleotide, and there are enough ingredients around, the flow of energy that goes through the left side falls to the surrounding soup building the right side. No intelligence is required here.

Posted by: Morelli | 04/26/10 | 5:53 am |

cardshoot,
You said: “Your argument is flawed from its start because evolution didn’t have to follow the path you expound.”

My answer: The path that I expound is the same of Wikipedia: “It is likely that cynodonts were at least partially if not completely warm-blooded, covered with hair, which would have insulated them and helped to maintain a high body temperature. The mammal-like structure of cynodonts hints that all mammals have descended from a single group of eucynodonts.” And cynodonts is still a reptile, the size of a alligator and not dinossaur. Are you saying that evolution did not follow from alligators to dinossaurs?! It should be the opposite?

You said: “You’re right in that mammals didn’t evolve from dinosaurs, but your implication that evolution is wrong based on that premise is wrong.”

My answer: “I am not saying that evolution is wrong. I am saying that the Darwin’s theory based upon those three variables is not complete for explaining the history of evolution of biological systems (aka, living beings).

And maybe, the idea of evolution is controversial. If I am a small microbe living inside a pregnant womb, watching the transformations that happen with the fetus, certainly I should believe that evolution is whole picture. But it is not: it is a process of reproduction. Then, we are like microbes watching the transformations of Cosmos and living beings. But… is not scientific established that are watching the supreme process. Maybe we are seeing the evolution inside a process of reproduction… the reproduction of that something that triggered the start of the Universe. Who knows? Maybe this Universe is only a cosmic egg and here is being nurtured the son of something beyond the Universe. You can call it God, no problem with that. My theoretical models are suggesting that it is a natural system, non able to do magic, and suggesting that this Universe is a genetic production. But, Science has no data for deciding this question, yet.

You said: “Your idea of what happened due to the meteor impact that wiped out the dinosaurs is mistaken also. Mammals already existed at that point in time but were small creatures.”

My answer: “I know that. I am suggesting that nature does not need meteorites for applying a natural law, observed at each species: every creature that evolves in a wrong way, not supported by the parallel evolution of the environment, becomes extinct, no matter if it last a long time. It is because the creature super-specializes in a way of existence, becomes a closed system itself, a branch of the evolutionary tree that has no future. it is happen with whales, the giant of the oceans, with the lions, the giant of the jungle, with eagles, the giant of the sky… But the deep explanation is a mechanism inherited from our ancestral physical thermodynamic non-living systems, which I cannot expose here.”

You said: “I have no idea where you are coming up with these wild ideas unless you have been taking as gospel the stories of someone else as little informed on the topics as you are”

My answer: “That’s just the danger behind the teaching of Evolution to children. You should a good sample. You did not pay attention when I said that the Darwin’s theory and the neo-Darwinian theory does not explains the history of evolution because it is not complete. This idea is so strange for you that you mistakenly understood “non-complete” as “wrong”. It is totally different. You did not pay attention when I said that the history of evolution is not explained only by three variables, but, seven variables. The normal, natural, rational reaction here should be: “What?! I never heard something like that! Are you dreaming? But… how did you get there? Which are the four variables that we don’t know?!”

Then you go straight to conclusions: wild idea, gospel, you are not informed… that’s just the reaction of the Inquisitors facing Galileo, the Islamic religious facing evolution theory, the scientific establishment facing Boltzmann, etc. Our children nurtured in these textbooks are going to the same way. Ok, maybe the Modern Evolution Theory explains everything, then, will have no problem with the textbooks. But…I am telling you: I was not educated in a scientific school, and then I have the theory of evolution, biogenesis, Big Bang, gravity, under suspicions. I am reasonable informed about modern scientific data, from physics to chemistry to biology, etc. But I was living in Amazon jungle, the Nature there is suggesting a lot of things, mechanisms and processes which can build a bigger evolutionary theory. Why every scientific minded person that I tried to explain the theory does not want to hear? No one of them has showed a scientific data that is contradictory with any detail of the whole theory. Explanation? Close-minded. That’s the danger pointed out brilliantly by tahos ( 04/23/10 | 11:06 am).

Posted by: cardshoot | 04/26/10 | 6:55 pm |

@morelli
I’m not going to try to teach you how evolution works but to set you straight on an aspect or three of it where you seem to be looking at it from the wrong viewpoint.

1st. The answer to the question of whether evolution went from crocodiles to dinosaurs or from dinosaurs to crocodiles is neither. They are two different branches of a family tree that originated with a long distant common ancestor. And you can add mammals into that family tree also, but that doesn’t mean that mammals evolved from dinosaurs or crocodiles. It only means that they had at some point in the distant past the same ancestor.

2nd. The meteor and aftermath causing the death or extinction of the large dinosaurs doesn’t have to explain the death of other large organisms and in itself might only be partially responsible for the extinction. But before the meteor impact there were big dinosaurs and shortly afterwards there weren’t any more as evidenced in the fossil record. If other animals go extinct it doesn’t have to be from a meteor strike; it could easily be another factor causing it and you don’t have to resort to a meteor impact to explain them. But when you have a boundry layer left by a meteor that is a distinct dividing point between there being large dinosaurs and there not being large dinosaurs in the fossil record it is pretty likely that the meteor impact had something to do with it. There were other extinction events and theories about what caused them too, just look up extinction events. They seem to drive or cause a temporary speeding up of evolution.
3rd Major evolutionary change takes time on a timescale that you cannot personally observe in real time in any major way in a group of organisms, other than microorganisms, partially due the time between generations and the time a characteristic in a portion of a population actually becomes a determining factor in survival of the individuals in the population.

As far as Darwin’s theory being wrong or not complete enough because it is based on three principles, I can give one principle that explains all evolution. Populations of organisms change over time due to the genetic differences within the population affecting the reproductive success of descendents. But to see what the modern theory of evolution is look up ‘modern evolutionary synthesis.’ Neo-Darwinism originated in the late 1800’s so it isn’t really pertient except people continue to use term and confuse it with modern evolutionary synthesis.

As far as the theory of evolution causing people to be closed-minded, being closed-minded isn’t necessarily a bad thing when the thing someone is wanting you to open your mind to is without merit( or unprovable). I am not going to entertain for a moment that the sun is really a giant ball of Jello. I am absolutely closed-minded to that idea, at least until someone goes there and brings back a bowlful.

Posted by: Morelli | 04/27/10 | 4:03 am |

cardshoot

You said: “I’m not going to try to teach you how evolution works but to set you straight on an aspect or three of it where you seem to be looking at it from the wrong viewpoint.”

My answer: “To me it seems that you are looking how evolution works not by the wrong viewpoint, but from a non complete one. Darwinian evolution or even modern evolutionary synthesis is about micro-evolution, only about biological systems evolution. But the process of Evolution – the mechanisms of this process – was not created by the stupid matter of Earth and not beginning in a deep ocean mixed soup. Before that the matter in this Universe was under the principles of Cosmological Evolution and from this dimensions are coming the mechanisms. In that time we had the so (and mistakenly) called non-living systems, like atoms, stellar, galaxies systems. The planet Earth and its matter is a production from the cosmological laws and mechanisms, then, if we want really understand any natural mechanism here at our biosphere, we need to understand its origins from the sky. Because evolution as transformation among species ( and not variations and selection of individuals inside the specie) have used the Gold punctuation jumps, and these jumps are influences from the forces coming from systems hierarchy superior, like the immediate astronomic system to which our planet belongs. The transformation from a reptile (cynodonts?) to a mammal is all about the sexual reproductive process: till reptile every species lay eggs out, at cynodonts happened the big jump that built the extraordinary engeenery of womb and pregnancy. Which was and where were the forces in Nature, in the environment or in the reptile itself, which made this spectacular transformation?

When I am telling about the danger of a non-complete knowledge closing the mind that denies the search for the whole picture is just about this. Evolution is a fact, period. We know the formula VSI, and it explains everything. So, from now to the infinite we have only to search the data that completes the history of evolution, and fighting those that does not believe in it. We stops using our mind searching alternatives to evolution, which is correct, like you said, we are not going to think that the sun is a ball of Jello. But… we have fossil telling the history about the skeleton transformation from reptiles to mammals. We don’t have fossil about the soft anatomy of reptiles transforming to mammals. And VSI is not enough for to explain it. Which motive leads a reptile to develop the modern reproductive process, the stage of pregnancy, if the new state means a big sacrifice, losing abilities to survivor and to hunt? How could natural selection to choose the worst adaptive intermediate creatures? These kind of questions does not appears in a brain of a trained evolutionist.

The modern theory of evolution has broken evolution in two separated blocks- Cosmological Evolution, from the big Bang to 10 billion years ago and Biological Evolution in the last 3,7 billion years – with no links, no connection between them, so, for to fill the big abysm between then, we appeals to variations by chance. This could be a mythos, the principles of a religion, the not-to-be-magical-thinking.

I am not a scientist but I learned a lot myself about natural philosophy, studying from Hippocrates to Euclides to Mendel to Darwin, they were not scientists also, merely natural philosophers trying to apply the scientific method isolated at very hard and poor circumstances. While Darwin spent 4 years observing small details like the birds, I spent seven years isolated in the jungle observing the bigger details, trying to understand macro-evolution. But is impossible getting reasonable answers if we do not consider the sun’s light and the astronomic context influencing biological evolution. Then we have new ideas, new theoretical models, even the surprising event when we have a theoretical model of an astronomic system where we can see, only among the connections among spheres and vortices in the sky, a system that lays eggs out and at the same time keep the eggs inside showing a thermodynamic structure identical the modern mammals womb. But, if it is thru, then, the mechanisms of atoms, galaxies need be increased upon the three Darwinian variables for to explaining the whole picture, included how and why a reptile became mammal.

It is not interesting from the natural systems viewpoint, loosing time with the meteorite influencing living species at that time. From the controversy around 1860-1960 among Maxwell’s demon, Szilard’s cost of information, Brillouin’s positions about dissipation, Bennett’s positions, etc., we knows today that any system that gets information beyond the limits of its physical possibilities, will pay the hard price for discarding it. Obtaining information does not cost ( at least in the path from alligators to dinosaurs if the environment is properly), forgetting it is the problem. It happens with any system, be it atoms, stellar, galaxies, plants or a human body. So, the pathways of evolution that leads the first reptiles to dinosaurs and then, going back to an alligator for to follow the path to mammals were obeying thermodynamic laws, macro-evolution laws, because the dinosaur had to forgetting the wrong informations they got. The pregnancy phenomena, the womb anatomy were written in the stars, thermodynamically, billion years before life’s origins, and those mechanisms are inside us, at our genetics, and above us, surrounding us, modeling the planets environment. It does not need religion, neither supreme intelligence, neither creationism nor Intelligent Designer for to explain Evolution, but, it does not need also the atheist mythos of Nature variations by chance selected for evolution. Open-mind, continuing to search at larger horizons, this is the right thing to teach our beloved children. But, ok, if you are parent and want another way, it is not me that will try to change your mind. I expose this theory trying to change informations, to see critical thinking against the theory, because, I am sure, my worldview is not complete either.

Posted by: Morelli | 04/27/10 | 4:24 am |

cardshoot ,

Correction: Instead “Gold punctuation” I wanted to write about the Stephen Jay Gould and Niles Eldrege punctuated equilibria theory. Sorry.

Read More http://www.wired.com/wiredscience/2010/04/evolution-controversy/comment-page-2/#comment-107706#ixzz0mI12OjWU

Important issue published in the article below, I am recording for studying later and doing already some comments by Matrix/DNA Theory – which are in red. As we know, Matrix/DNA Theory is a new interpretation of Evolution, then, the “post-darwinism”.   

Article published in The Global Spiral

http://www.metanexus.net/magazine/tabid/68/id/10914/Default.aspx

 ( The Global Spiral  is an e-publication of Metanexus Institute. Through articles, essays, book reviews, and news, the Global Spiral  explores humanity’s most profound questions and challenges.)

By William Grassie -

A review of Ecological Developmental Biology: Integrating Epigenetics, Medicine, and Evolution,
By Scott F. Gilbert and David Epel (Sunderland, MA: Sinauer 2009).

As a combatant in the evolution wars here in the United States and abroad, I have penned and processed quite a few papers on the interpretation of evolution.¹ This means also reviewing the vast literature in evolutionary psychology, particularly its attempts to explain religious behaviors.² I am convinced that most of what is transmitted and consumed in the way of popular accounts of genetics and evolution by and for philosophers, theologians, and lay readers is pretty much bunk. This is not a question of whether evolution is true. The weight of the evidence for evolution is conclusive. The mythological literalism of the Young Earth Creationist is delusional and Intelligent Design is more of the same confusion.³ That is not what this review is about. The problem is that the popular accounts of how evolution and genetics actually work are so simplistic as to be misleading. These popular accounts then serve as the basis for philosophical and theological interpretations of evolution and genetics, so we, the philosophers and theologians, are getting the current state-of-the-science wrong. The simplistic views of evolution and genetics are also uncritically adopted in the emerging field of evolutionary psychology, where they are applied to understanding human behavior, including religious behavior. I have nothing against evolutionary psychology in principle; it is just that the paradigm being applied is too simplistic. And if it is not true of plants and animals, it certainly will not be true for complex human cultures.

Ecological Developmental Biology, the new textbook⁴ by biologists Scott F. Gilbert and David Epel⁵ is the antidote to these deficits in the public understanding and scholarly interpretation of biology. And while biologists and their students should certainly read this book, I want to make the case in this review for why philosophers, theologians, bioethicists, environmentalists, and evolutionary psychologists should be required to read this book. Anyone who purports to teach and interpret evolution and genetics to the public should read this remarkable book. Indeed, policy-makers and homemakers will find much relevant to public health and safety in these pages.

∞

The book is divided into three parts, involving ten chapters, a philosophical coda, and four appendices. Unlike most biology textbooks, this book actually has a plot and a dramatic denouement. Unique also is that Ecological Developmental Biology includes an insightful history of the evolution of evolution, which as a discipline has itself sometimes been “red in tooth and claw.” An outsider might otherwise have no idea about the interesting scientific and ideological battles waged within the field. Moreover, since the book is intended for a heterogeneous audience across the biological sciences, it carefully explains its vocabulary and contains numerous charts, diagrams, and photographs. This is important since the languages of science are not the languages of philosophy and theology. (It is amazing how many humanists in the academe have not cracked open a science book since high school.)

Part one examines “Environmental Signals and Normal Development,” which will charm the reader with many details of strange and familiar species that change their phenotype based on their environment. In chapter one, we learn how the environment signals an organism to develop different phenotypes. In chapter two, we learn how other organisms, for instance predators or siblings, also affect gene expression in the maturation of organisms. (Matrix notes: The Luca that’s encrypted in the planet, driving evolution throught environment, has as predator allways the following shape of a given shape. As the predator of a teenager is the adult, the predator of a planet is the pulsar, the predator of Function 4 is the Finction 5, etc. Why the environment signals an organism to develop different phenotypes? The answer is: since LUCA is being reproduced he controls the future anatomy of a given specie. But, since that any individual existing where there is no system yet, have free-will and its behaviour is going out of the planned reproduction, the Matrix uses real predators for doing the tasks of the next shape. In other words: the predator is allways an aberration of the next evolutionary step, used for to correct any misleading of the currently top evolutionary specie).   Chapter three explores the central role of symbiosis and co-development in the life of species. In chapter four, we learn of embryonic defense mechanisms.

Why should one care about these disciplinary details? The full story will not be apparent until part three, the coda, and the appendices, but Gilbert and Epel mention early on that genetics has been the dominant paradigm in biology since World War II. There has been a “marked antipathy against the notion of phenotypic plasticity and the inheritance of nonallelic phenotypic variations…” (8) They write:

…the environment is not merely a filter that selects existing variations. Rather, it is a source of variation. The environment contains signals that can enable a developing organism to produce a phenotype that will increase its fitness in that particular environment. This isn’t the view of life usually presented in today’s textbooks or popular presentations of biology (8). ( Matrix notes: these signals come from the system hierarcly superior to the surrounding environment. Ex: surrounding environment: Earth’s surface or biosphere; superior system: the astronomic building block. Note that it is not superior in complexity, since it is an ancestor, but it is superior in force, size, influence: it is being reproduced and every specie is merely a piece used in this reproduction process.)

The authors call this dominant view “geneticism.” James Watson, who won the Noble Prize for his part in discovering the Double Helix, writes:

We used to think our fate was in the stars. Now we know in large measure, our fate is in our genes”

( Matrix’s notes: “But,… but…, where came from the genes, if not from the “stars” and its systems? They were created here? I don’t believe and the models of Matrix makes sense. Where was the fate ( the future shape and identity) of any human embryo, if not in its parents?)  

Watson here is giving expression to genetic determinism, the myth of the “master molecule.” He has been aided and abetted in promoting these misconceptions by Richard Dawkins and a host of others. We learn that genetic determinism is a fallacy.⁶ We might just as well talk about environmental determinism. The distinction between nature and nurture is a false dichotomy in biology. It is nature-nurture and nurture-nature all the way down to the level of gene encoding and expression. Gilbert and Epel write:

In standard embryology, the focus has always been on the internal dynamics through which the genes of an individual’s cell nuclei produce the phenotype of the organism. Within the past century, we have discovered that cell-cell communication is the key to this phenomenon. By itself, the genetic information in a cell’s nucleus cannot directly produce the many differentiated cell types in a multicellular organism; cells must interact, reciprocally instructing each other as they differentiate (9).

It is not just cell-to-cell interactions that effect the differentiation of cell types in multicellular organisms, but all kinds of environmental factors as well. There are temperature-dependent pathways, nutritional-dependent pathways, pressure-dependent pathways, predator-induced pathways, maternal-care dependent pathways, and conspecific dependent pathways (the effects of siblings and close relatives). Depending on the kind of species, these environmental determinants can radically change how an individual looks, acts, and whether and when it develops into a male or female adult. Some of these environmentally induced changes in gene expression are heritable, passed on to the next generation, in violation of the “Central Dogma” still found in biology textbooks today. And that’s just the first two chapters of this book. All of this is normal biology and there are plenty of entertaining examples.

Chapter three we learn of developmental symbiosis. Far from being competitive, much of evolution is about cooperation. You need only consider your own body, a multicellular collaboration of trillions of eukaryotic cells coming in some 214 tissue types which began once upon a time as a single, undifferentiated zygote in your mother’s womb. However, it is estimated that 90 percent of the cells in your body, by number not mass, perhaps as many as 100 trillion (10¹⁴) are not “yours” at all, but are a rich ecosystem of up to 1000 different microbial species living in your intestines (98).⁷ These bacteria not only provide a number of nutritional benefits to us, as we do for them by consuming three-square meals per day, they also help regulate gene expression in the development of intestinal cells.

The boundaries of identity in modern biology are up for grabs. Whatever the individual organism may be, it is not contained within the boundaries of epidermis, membranes, or genomes. The individual is always internally and externally composite and interactive. The individual is always an interdependent variable. The organism is a “social construction.”

My favorite example from Gilbert and Epel’s book is the protozoan Myxotricha paradoxa, a symbiont found in the gut of an Australian termite, which helps in digesting cellulose. M. paradoxa, however, is itself a symbiont, containing within its cell membrane the separately replicating genomes of a protist and three species of bacteria (97).⁸ All of life is Anima paradoxa.

It would be nice to have a simple theory of evolution, as Darwin has provided in his elegant algorithm, but the catechism of random drift, universal struggle, survival, reproduction, and differential selection just doesn’t hack it anymore.⁹ It is time to embrace complexity, symbiosis, multi-level selection, contextuality, and as we will see, even some aspects of Lamarckianism.¹⁰ Along the way we can banish the geneticist dogma of “selfish genes,” because genes do absolutely nothing by themselves. Indeed, it is equally valid and descriptively accurate to talk about “sharing genes.”¹¹

Part two examines ecological developmental biology and diseases and it is here that the regulators, policy-makers, and homemakers should pay close attention, because birth defects, cancer rates, infertility, and intersexuality, as they relate to environmental pollutants take center stage. Chapter six on endocrine disruptors is particularly disturbing and worthy of careful study, because pollutants affect development differently at different stages. Most product safety testing, for instance, does not test the impact of chemicals on fetus development, but as we learn, the presence of trace chemicals in the environment can have dramatic impact on gene expression differentially at different stages in the development of embryos or young adults. This book documents the dramatic rise of testicular cancer, breast cancer, and hypospadias (deformity of the penis), all accompanied by an equally dramatic drop in sperm count (214). Such disorders are not primarily “genetic” in origin, but thought to be caused by endocrine disruptors in the environment altering gene expression, i.e., epigenetic. Compounds found in soy products (estrogenic chemicals), pesticides, herbicides (atrazine), sunscreen (4-MBC), plastics (bisphenol A or BPA), and electronics (polychlorinated biphenyls) are all thought to be involved in endocrine disruption in humans and other species. Note that all of these chemicals affect organisms differentially at different stages of development. Note also that some of these effects have been demonstrated to be transgenerational, i.e., the phenotypic effects are passed on to the next generation. It seems we are threatening our health, our fertility, and our survival with the proliferation of certain chemicals in our environment.

∞

Part two, however, is a side story to the main thesis, which the authors begin in part three – “Toward a Developmental Evolutionary Synthesis.” This section will most interest philosophers and theologians who try to interpret evolution, because it is here that Gilbert and Epel develop the idea that Neo-Darwinism – the combination of Darwinian natural selection with modern genetics also known as the Modern Synthesis – is no longer adequate biology. Chapter eight provides the history and theoretical background. Chapter nine argues that “without the integration of developmental genetics and developmental plasticity into [evolution], evolutionary biology has no complete theory of variation” (323). Here they focus on developmental regulatory genes (e.g., Hox complex). In chapter ten, they propose a “New Synthesis” between environment, development, and evolution.

The book contains four appendices of special interest: two are historical and two are technical. Appendices A and C are the historical pieces, fascinating essays that review the collapse of developmental biology in continental Europe (the indirect results of Stalinism and Nazism) and how developmental biology was written out of the Modern Synthesis in post-war Anglo-American science. These essays are fascinating behind-the-scenes glimpses at how ideologies and history impact the making of science and meaning in the modern world.

Appendices B and D are technical discussions of the molecular level processes by which epigenetic changes occur in the development of an organism (i.e., changes in the DNA that alter the expression of the gene rather than the DNA sequence of the gene) and how these epigenetic changes can then be passed on as inheritable traits (i.e., what Eva Jablonka has called “Neo-Lamarckianism”). It turns out that gene function can be deleted more easily by altering its expression (epigenetics) than by altering its sequence (genetics).

I must confess that a lot of this technical material was very hard for me to follow given that I am not formally trained in biology. Fortunately, I was able to get a memorable tutorial on DNA methylation from my daughter, Maisy Grassie, now a second-year student in veterinary medicine at the University of Pennsylvania. Both the institution and my daughter are wonderful examples of Lamarckian evolutionary processes at work in human culture. That human culture evolves in a Lamarckian pattern throws a wrench in evolutionary psychology, which tries to explain complex cultural formations through the lenses of survival and reproduction.

∞

The real gem in Gilbert and Epel’s book, and the reason I am writing this review, is the coda entitled “Philosophical Concerns Raised by Ecological Developmental Biology.” If nothing else the philosophers and theologians really need to read this section, because it opens up the territory for much more realistic and productive reflections on the interpretation and meaning of evolution and genetics than we are normally exposed to in the popular and scholarly literature. This section is divided up into discussions of ontology, pedagogy, epistemology, and ethics. The longest section is on ontology, proving once again that metaphysics is politics by other means. How we interpret evolution has implications for everything from political economy to childrearing to religion.

The first problem in reconceptualizing ontology in light of the New Synthesis is that the individual has disappeared. “Individuality is illusionary,” write the authors. There is no spatial definition of an organism simply “contained” in an epidermis, a membrane, or a genome. “At the very least,” write the authors, “the prevalence of polyphenisms and reaction norms instructed by environmental agents abolishes any notion of a genetic determinism” (404). Actually I suppose many examples of genetic determinism remain – for instance, cystic fibrosis or Tay-Sachs disease – but these are now the exceptions and not the rule.

The authors favor integrative philosophical traditions, discussing the Buddhist concepts of co-dependent origination and no-self, and focusing especially on the process philosophy of Alfred North Whitehead, along with the phenomenology of Merleau-Ponty. They understand the organism to be “the concrete, fleshy nexus integrating (in time and space) the internal networks of developmental genetic interactions with the external networks of ecological interactions” (409). All processes are context specific and are examples of reciprocal induction. They quote Donna Haraway: “relationships are the smallest possible pattern for analysis” (410).¹²

Emergence, which has always been “normative in developmental biology,” is now normative in our understanding of evolution as well as in the new ontology. There can no longer be simple reductionistic explanations of complex phenomena:

Entities need to be thought of in terms of several geometries at the same time. They are defined by the braiding of down-top and top-down (as well as lateral and temporal) networks built from patterns of reciprocal causation (410).

Our understanding of competition and cooperation in nature is also due for revision. “[D]evelopmental symbioses are no longer relegated to marginal exceptional cases,” write the authors. “Rather, they are the norm” (404).

How we conceive of nature is a magic mirror for human society.¹³ The Anglo-American tradition of evolutionary biology finds in nature the ontology of Smith, Locke, Mills, and Hobbes. “Just as the wooden pencil was created from self-interested individuals, so was the tree from which the wood came.”

The tradition of embryology, however, was oriented toward the European continent and found its philosophical underpinnings in the emergent forms of Immanuel Kant and Wolfgang Goethe. Embryology embraced both mechanistic and teleological views of the organism. “Interdependence, harmony, and integration” is “a different perspective on nature than the autonomous, competitive nature of classical evolutionary biology.” Gilbert and Epel are not promoting an either/or choice, rather “in addition to Locke and Hobbes, we have Kant and Goethe” (406).

Group selection theory, an “outlier” in Anglo-American biology, is now central to any adequate evolutionary theory:

Both traditional evolutionary biology and existentialism grow from the soil of Hobbesian competition and individuality. While ecological developmental biology similarly postulates that we are defined, in part, by the “other,” it depicts our identities as becoming with the “other.” (407)

The authors have given us a new dialectics of nature: process and relations, emergence and reduction, self and no-self, individuals and groups, cooperation and competition. If that seems like a muddle, it is because that is what life turns out to be. As Whitehead warned:

The aim of science is to seek the simplest explanations of complex facts. We are apt to fall into the error of thinking that the facts are simple because simplicity is the goal of our quest. The guiding motto in the life of every natural philosopher should be, Seek simplicity and distrust it.¹⁴

It is time to jettison the simplicity of the Darwinian algorithm and geneticism. Life is a “social construction” of interdependent variables. This insight provides a much more interesting possibility space for doing constructive and realistic philosophies and theologies of nature than we have been led to believe was the case by the sometimes shrill proponents of ultra-orthodox Darwinism.¹⁵

∞

All of this has implications for education and research. In terms of pedagogy, Gilbert and Epel call for the integration of developmental biology into the teaching of evolution, genetics, ecology, and medicine. While I can appreciate the integration of developmental biology in these other disciplines, I would also be interested in how the pedagogy itself, as opposed to the content thereof, might actually be transformed by these insights.

In terms of epistemology and methodology, Gilbert and Epel suggest that we get away from using model systems. They note that six model systems have dominated biological research – the fly Drosophila, the frog Xenopus, the nematode Caenorhabditis, the mammal Mus, the bird Gallus, and the zebrafish Danio – and that each was selected for laboratory studies in part because of the absence of major environmental factors, so of course biologists failed to understand the ubiquitous role of the environment in gene expression and evolution (412). They pose a series of research questions:

What does evolution look like when the proper unit of analysis is not the individual but the relationship (at each different level)? What does evolution look like when selection may be on ‘teams’ of organisms and on the relationships between these teams? What does natural selection mean when the environment is not only an agent that selects adaptive phenotypes but also contains agents that help instruct the formation of adaptive phenotypes (and may undergo changes itself because of it?) Moreover, how do we revise our views about the environment and evolution when germline DNA methylation can effect the transmission of environmentally induced characters from one generation to the next? (414)

Finally, Gilbert and Epel wonder about the ethical and policy implications of the New Synthesis. Policy gets short shrift here, though they address those implications elsewhere in the book. They cite here only one example: 88 percent of breast cancer is thought to be caused by the environment. The so-called “cancer genes” BRCA1 and BRCA2, account for only 5 to 10 percent of breast tumors. They warn that “Our emphasis on the genetic component of this disease appears to be dangerously misplaced” (415).

I wonder whether we might enlarge this policy discussion substantially, including not only public health and safety, but ways that the New Synthesis might help address problems in the “science wars,” as well as the problem of general science literacy. The relational and process ontology explored here is much more conducive to romantic and even comic readings of evolution than the Stoic and existentialist interpretations promoted today.¹⁶

The take-home message and the ethical bottom line is that the stories that scientists tell matter! We need new and better stories about nature:

Scientists have a moral imperative to tell accurate stories. Scientific stories must always fall within the limits of the existing data. Evolutionary narratives are the most critical stories in biology, in science, and perhaps in Western civilization, so we had better get them in line with the biological data (415).

This brings me back to my opening observation. Many of the public interpreters of evolution are doing a disservice to the current state of the science and therefore also to our ontologies, our epistemologies, our pedagogies, and our ethics. These oracles of science are then read and debated by philosophers and theologians, replicating the distortions and distorting our interpretations. It is time to give Richard Dawkins a rest and read something new that is, if not revolutionary, at least evolutionary in our understanding of biological complexity and the theory thereof.¹⁷

“The image of man affects the nature of man,” observed Rabbi Abraham J. Heschel. “We become what we think of ourselves” (415). We cannot avoid the Naturalistic Fallacy; the only question is how to relate the “Is” and the “Ought.” Let’s be sure we use science to the best of our ability to get the “Is” of nature as accurate as possible, because we will surely morph that “Is” into political economy, social policies, behavioral norms, and child-rearing practices. Gilbert and Epel note that “If we think of ourselves as killer apes, certain behavioral phenotypes are acceptable that would not be socially allowed if we view humans as the current apex of an evolutionary trend towards cooperation” (415).

Gilbert and Epel are not just specialists in the intricacies of biology, but reveal themselves to be sage philosophers: “One has to know what is true in order to do what is good” (416). The truth of our planet, however, is changing rapidly and dramatically, as humans engage in large-scale environmental engineering and prepare to embark upon large-scale genetic engineering of the other species and ourselves. Humans are a Lamarckian wildcard in the Epic of Evolution. Our thoughts about nature not only transform our human nature, they are literally transforming our planet and therefore also the future evolution of all life. We live in the Anthropocene, a new era in evolution in which humans dominate the biosphere with unknown consequences. The authors call for an “ethics of flourishing and well-becoming” adequate for the Anthropocene:

Ecological developmental biology fosters an ethic that can integrate both selfishness and otherness, as one might expect of a discipline where self and other mutually construct each other (417).

∞

So I am bullish on Scott Gilbert and David Epel’s remarkable book, Ecological Developmental Biology (2009). My only problem is that it needs a better marketing strategy in our information-saturated world if it is going to have the impact they envision within and outside the guild. “Eco-evo-devo” won’t get very far. Better to sin more boldly and simply declare “Post-Darwinism” in this the two hundredth anniversary year of Charles Darwin’s birth and the hundred-fiftieth anniversary year of The Origin of Species. It seems to me that Post-Darwinism is a better designation for the New Synthesis and for what comes after Neo-Darwinism, by which I mean no disrespect for Charles Darwin, a remarkable scientist and human being, but surely evolution has evolved and we better, too.

Post-Darwinism does not mean that “Darwin is passé.” On the contrary, his name and ideas are appropriately enshrined in the very title, a title which is also a warning. The elegant simplicity of the Darwinian algorithm is misleading, as is the geneticism of Neo-Darwinism. Life is a “social construction” in innumerable, context specific biochemical, multicelluar, and ecological niches. There is even more grandeur in this new view of life!

Article Published in The New York Times, Sunday, August 23, 2009, page 9, Sunday Opinion

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 Robert Wright is brilliant on his thesis that natural selection could be made even before life’s origins and he reveal some arguments for that. Then he says that        “… God did his work remotely. His role in the creative process ended when he unleashed the algorithm of natural selection (whether by dropping it into the primordial ooze or writing its eventual emergence into the initial conditions of the universe or whatever).”

————————— 

 Of course, to say that God trusted natural selection to do the creative work assumes that natural selection, once in motion, would do it. This claim turns out to be scientifically plausible.

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”Matrix/DNA Theory Comments: “ Our models suggests that processes like natural selection were existing before the Big Bang. Resuming, when the models says that this Universe is a genetic production, he suggests that there is a father/mother of the universe, be it whatever system is. So, this Universe has the final purpose to reproduce his father/mother system. it means that what we see as evolution – be it Cosmological and Biological evolution – it is really, small steps in a big process of reproduction. And at any reproduction process there is natural selection: the final body of the father/mother drives the process to finally reproduce their own shape. So, among any events by chance, any species that arouse as sub product or in parallel to the real fetus, can be selected and gets his eternal place in the trunk of the evolutionary tree, or can be discarded by natural selection. The agent behind natural selection is the genome that came beyond the universe. But ( the good news for atheists) it not means that God did it. It means that an unknown system that was existing before is as natural as the universe and our land.But ( the good news for theists) it is plausible that beyond the natural creator of the Universe there is a God and He did it remotely… 

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…

Unifying The Animate And The Inanimate Designs Of Nature

From Duke University : http://news.duke.edu/2009/04/unification.html

By Richard Merritt

Tuesday, April 28, 2009

Living beings and inanimate phenomena may have more in common than previously thought.

At least that is the view of Duke University engineer Adrian Bejan and Penn State biologist James Marden.What they believe connects the two worlds is a theory that flow systems – from animal locomotion to the formation of river deltas — evolve in time to balance and minimize imperfections. Flows evolve to reduce friction or other forms of resistance, so that they flow more easily with time. This view has been termed the constructal law, which Bejan first stated 13 years ago.With the help of Marden, Bejan believes that he has now unified both the biological and geophysical principles of nature’s design through the constructal law, which can also be viewed as the physics of evolution.“This is an exciting development for physicists, but it should also resonate with biologists,” Bejan said. “The idea that organic evolution is analogous to the way form evolves in inanimate flow systems is a novel concept that has the potential to unite perspectives and approaches across disparate disciplines. We suggest that the constructal law provides a powerful tool for examining and understanding variation in both the animate and inanimate compartments of nature.”

The team’s findings were published online in the journal Physics of Life Reviews. It was supported by the U.S. Air Force Office of Scientific Research and the National Science Foundation.The story began with the two scientists trying to determine if the same laws applied to two very different forms of locomotion — the swimming of fish and the running or flying of animals. The commonly held belief among biologists was that fish locomotion was different than other animal locomotion. Since they live in water, the conventional wisdom held, fish were different because they would not be subject to gravity.The way Bejan saw it, birds and animals could be seen as weight-lifters, since their means of locomotion required effort with an unyielding base – the ground – and a limitless top – the air. He argued that as fish swim, they too have an unyielding floor – the sea bed. Hence, water flowed over and around them like the air over runners and flyers.So, fish too were weight-lifters, and these forms of locomotion are predicted by the constructal law, Bejan said.

“Our discovery that animal locomotion adheres to the constructal law tells us that – even though you couldn’t predict exactly what animals would look like if you started evolution over on Earth, or it happened on another planet – with a given gravity and density of their tissues, the same basic patterns of their design would evolve again,” Marden said.In numerous papers over past decade, Bejan has demonstrated that the constructal law predicts the design of a wide range of flow systems seen in nature, from biology and geophysics to social dynamics and technology evolution.“When thinking of evolution and Darwin, most people think of animals or trees,” Bejan said. “That’s too bad, because design features are everywhere in nature. The constructal law can be seen as a universal principle of evolution, which applies in many fields, from physics to economics.”He describes the law as an animated movie, where one screen is replaced by another screen on which the currents flow with greater ease. He sees the constructal law (www.constructal.org) as the time direction of the movie, flow configurations (designs, drawings) that flow more easily.”“The constructal law can be seen to cover ‘natural design’ phenomena across the board,” Bejan said, “as a compact summary of common observations, the tape of evolution running in one direction, which may be expressed in physics terms simply as: time and configuration.”——————————————————————————————————————

My comments:

Great! Finally people are thinking rationally. There are no shape and no mechanism/process over Earth surface and among biological creatures that was not existing in the world before abiogenesis. The Universe only can do things for which he has information, bits-information aquired with the Big Bang. There are no magics here. Dr. Bejan and Marden need to know the collection of links we have already in Matrix Theory, between cosmological evolution and biological evolution.

A few samples:

1 – A living male expelling spermatozoon is a projection, an extension, an evolutinary complexity from volvanoes expelling magma;

2 – A chicken keeping her offspring warm under her wings is an instinct coming from her ancestry, when stars were keeping planets (its offspring) warm under her gravitational “wings”; and so on, at every day we are discovring from where the phenomena among living bneings comes from.

3 – Another curious link between abiotic and biotic worlds:

Look to the placenta in the womb around a fetus and look to the map of any continent ( the better one is South America). The placenta has the same shape of a continent. The placenta has a principal vein, with a delta, the vein has several smalls branchs; the continent has a big river (Amazon, Nilo, Mississipi, etc.) with a delta, and several small branchs… What that means? Why the same shape? The placenta is the birth place of an individual and the continent is the birth place of a population those individuals. The similarity is because the two phenomena, biological and planetary, were built by the same universal systemic function, which is described in Matrix Theory.

I don’t understand why Dr. Bejan call “inanimate world”. And says about flow of systems, dynamics, in the “inanimate world”… I think there is no such thing… as inanimated dynamics !!! Ok, maybe English language has a different meaning for inanimate…

By the way this is an article needing study and development and if I have time I will be back here…