Archive for the ‘Irreducible Complexity’ Category

The Cellular ATP Motor came from the Galaxies’ Rotational Motor?!

Thursday, January 24th, 2013

This article is more detailed and complete in Portuguese section, here:

http://theuniversalmatrix.com/pt-br/artigos/?p=333ATP Sintase: Como a Terra Copiou do Céu esta Extraordinária Engenharia! )

That’s fantastical! About a hundred years, people has watching an incredible working motor inside the living cell, and we had no idea how, or from where, Nature got it. It will be very good if you watch the motor working, in the movie/animation at

http://vcell.ndsu.nodak.edu/animations/atpgradient/index.htm

Look to the complex called “ATP Synthase”. Isn’t stupendous, whimsical?! From where came this object, this phenomenon? How did it to being?! Do you believe – as many believers – that, the stupid matter of this lost planet did it, alone? Or do you believe that the matter of other planet or constellation did it? If so, is it a magic planet? Or do you believe that God – or other non-natural being – came here to Earth and did it by magic?

We found a theoretical solution, well developed and logical, rational.  The matter of Earth did it (but, not alone), the matter of others constellations also collaborated for doing it. Everything should be possible, but, we now know how was the natural process that made it, and from where it came from: it came from the body of LUCA, the Last Universal Common Ancestral!

Ok, let’s see the ” body of LUCA”: ( these drawinings were made in the jungle with pencils and papers, so, sorry by the bad quality. It means that an unique matricial systemic circuit rules the formation of astronomical systems, cells systems, and we had mimicked it when making the basic electric circuit of ours homes because it was encrypted into our DNA-memories):

And now, let’s see this extraordinary engineering natural job, the motor called ATP Synthase:

Ok. Seeing the two pictures, side by side, and understanding how each works, is almost automatically: we see at the astronomical ancestral proto-system a kind of proto-motor, doing the same job that the cellular machinery is doing. The picture of LUCA has a nuclei, inside the nuclei has a quasar composed by dusty and debris from stellar decomposition, and below the quasar there is the black hole. 4 billions years of Evolution, changing from celestial space and matter composed only by solid and gaseous state of matter, to Earth surface, with matter earning a new state of matter,the liquid state, and then, the chemical reactions… and finally we see the whole process of transformation at the picture below ( click on it for seeing better):

Understanding the method of investigation:

To those does not know what this website is about:

I am suggesting a theoretical model of LUCA – The Last Universal Common Ancestral.

LUCA does not leave at Earth, but it is surrounding Earth and contains Earth. The picture shows the seven known kind of astronomical bodies, but LUCA is every body. The picture shows the Life’s Cycle of LUCA, at least, his seven principal shapes in any lifetime. The seven pieces are connected as each shape of a human body in its lifetime are connected together. The LUCA’s Life’s Cycle – when reproducing and fixing its several shapes – becomes a closed perpetual motor, but not a system, yet. The systemic closed circuit of mass and energy carries the flow of information (genetic information of LUCA), but it exists only in relation to time; it does not exists visible in the space (like the several shapes of a human body during its lifetime can not be visible arranged as system in the space).

LUCA – its complete Life’s Cycle – becomes the building block of astronomical architectures, like galaxies. The picture of LUCA above can be seeing as the same picture of a base-pair of nucleotides, the fundamental unit of information of RNA/DNA. Extracting the circuit of energy as flow of information, from LUCA’s picture, we got the same picture of a unit of the DNA. By the process of Macro-Evolution, which is performed by seven variables – having among them the three variables of Darwinian micro-evolution - Nature applies “nanotechnology” transforming astronomical architecture into micro architecture. After several mechanisms and processes revealed inside this theory, LUCA is transformed into biological systems, and those becomes plants and animal systems, like human beings. Over the homo-erectus’ brain, the theory sees a new jump of macro-evolution, the elaboration of “consciousness” which we have a theoretical model suggesting its anatomy as natural system. That’s it…

Well… I am afraid I will need stopping now ( it is time for beginning work with my auto-cab in New York, so, we need stopping this historical discover…) But, after the work journey, I will came back, if God wants… Ah?! God? How I said that? Which God? Where? Hummm… maybe here at our side… or not?)

Articles are being posted in Portuguese only

Saturday, January 15th, 2011

Sorry. Since I am not having enough time for translating from Portuguese, for seeing the articles one need to chlick the Brazillian flag above. Also, I understand that the site is not explaining almost nothing about the theory. It is because the site is under construction, I have a lot of writed material but had no time and the special computers skills for doing that. I hope will do it soon. Thanks…

Irreducible Complexity explained by Matrix/DNA Theory

Tuesday, September 22nd, 2009

 I don’t know answers to the phenomenas pointed out by Intelligent Designer as arguments for Irreducible Complexity (if somebody knows, please, tell me). Reading the Michael Behe paper below we really are compelled to see a cell and believe in designer. 

But, let’s go to think about an analogy:

A scientist friend of mine, put a human embryo freezed in a rocket and sent it to space. In Orion, Nebula, the life form existhing there which is iron-based and not carbon-based, found the embryo and after studying it they said: “This thing was designed!”

They were right. The embryo was designed by the mother body that was outside the womb, sorrounding the womb and was inside the embryo also, as the genetic code. The mother did not used any kind of intelligence for designing the embryo: Nature did everything.

Now we are seeing the complexity of a cell – could be the first living being, the first cell system – and we are compelled to say: it was designed. And we are right. The first cell was like the embryo sent to space and falls over Earth surface. The cell was designed by its parents, called LUCA, an hermafrodit that lives in the space, surrounding the planet and Luca is inside the cell also as it genetic code. 

So, the evolutionists does not need have fear that the Darwin’s Theory is threat, everything continues equal and the deists does not need have fear that evolution could threat their faith: the Matrix/DNA is only showing that it is possible that everything inside the Universe could be designed, since that the own Universe is a genetic production: the parents of the Universe are outside the womb and inside also, throughout the genetic code. You can call then as God, and thinking about then as God, the Matrix/DNA has no knowledge about this dimension.

Abiut the phenomenas pointed out as irreducible complexity, the Matrix/DNA theory has found that every phenomena cited above are reducible to the body of LUCA. Everything were there, joined, performing a proto/system. For instance, the cillia came from the comeds tail, which movies compelled by the magnetic fields in the spiral. It was used the motor of LUCA, the cillias inside LUCA, etc.

Since I have no time just now, thisn article will be open and later I will come back explaining everything. By now it is necessary to copy and register here the excellent artivle of Mr. Behe.  

Artigo editado em: 

Access Research Network
Michael Behe Files

http://www.arn.org/docs/behe/mb_mm92496.htm

In The Origin of Species Darwin stated 6:

If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.

A system which meets Darwin’s criterion is one which exhibits irreducible complexity. By irreducible complexity I mean a single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced gradually by slight, successive modifications of a precursor system, since any precursor to an irreducibly complex system is by definition nonfunctional. Since natural selection requires a function to select, an irreducibly complex biological system, if there is such a thing, would have to arise as an integrated unit for natural selection to have anything to act on. It is almost universally conceded that such a sudden event would be irreconcilable with the gradualism Darwin envisioned. At this point, however, ‘irreducibly complex’ is just a term, whose power resides mostly in its definition. We must now ask if any real thing is in fact irreducibly complex, and, if so, then are any irreducibly complex things also biological systems.

Consider the humble mousetrap (Figure 1). The mousetraps that my family uses in our home to deal with unwelcome rodents consist of a number of parts. There are: (1) a flat wooden platform to act as a base; (2) a metal hammer, which does the actual job of crushing the little mouse; (3) a wire spring with extended ends to press against the platform and the hammer when the trap is charged; (4) a sensitive catch which releases when slight pressure is applied; and (5) a metal bar which holds the hammer back when the trap is charged and connects to the catch. There are also assorted staples and screws to hold the system together.

Figure 1. A household mousetrap. The working parts of the trap are labeled. If any of the parts are missing the trap does not function.

If any one of the components of the mousetrap (the base, hammer, spring, catch, or holding bar) is removed, then the trap does not function. In other words, the simple little mousetrap has no ability to trap a mouse until several separate parts are all assembled.

Because the mousetrap is necessarily composed of several parts, it is irreducibly complex. Thus, irreducibly complex systems exist.

Molecular Machines

Now, are any biochemical systems irreducibly complex? Yes, it turns out that many are.

Earlier we discussed proteins. In many biological structures proteins are simply components of larger molecular machines. Like the picture tube, wires, metal bolts and screws that comprise a television set, many proteins are part of structures that only function when virtually all of the components have been assembled. A good example of this is a cilium. 7

Cilium animation

Figure 2a. Animation of a Cilium

Cilia are hairlike organelles on the surfaces of many animal and lower plant cells that serve to move fluid over the cell’s surface or to “row” single cells through a fluid. In humans, for example, epithelial cells lining the respiratory tract each have about 200 cilia that beat in synchrony to sweep mucus towards the throat for elimination. A cilium consists of a membrane-coated bundle of fibers called an axoneme. An axoneme contains a ring of 9 double microtubules surrounding two central single microtubules. Each outer doublet consists of a ring of 13 filaments (subfiber A) fused to an assembly of 10 filaments (subfiber B). The filaments of the microtubules are composed of two proteins called alpha and beta tubulin. The 11 microtubules forming an axoneme are held together by three types of connectors: subfibers A are joined to the central microtubules by radial spokes; adjacent outer doublets are joined by linkers that consist of a highly elastic protein called nexin; and the central microtubules are joined by a connecting bridge. Finally, every subfiber A bears two arms, an inner arm and an outer arm, both containing the protein dynein.

But how does a cilium work? Experiments have indicated that ciliary motion results from the chemically-powered “walking” of the dynein arms on one microtubule up the neighboring subfiber B of a second microtubule so that the two microtubules slide past each other (Figure 2a and b). However, the protein cross-links between microtubules in an intact cilium prevent neighboring microtubules from sliding past each other by more than a short distance. These cross-links, therefore, convert the dynein-induced sliding motion to a bending motion of the entire axoneme.

Figure 2b. Schematic drawing of part of a cilium. The power stroke of the motor protein, dynein, attached to one microtubule, against subfiber B of a neighboring microtubule causes the fibers to slide past each other. The flexible linker protein, nexin, converts the sliding motion to a bending motion.

Now, let us sit back, review the workings of the cilium, and consider what it implies. Cilia are composed of at least a half dozen proteins: alpha-tubulin, beta-tubulin, dynein, nexin, spoke protein, and a central bridge protein. These combine to perform one task, ciliary motion, and all of these proteins must be present for the cilium to function. If the tubulins are absent, then there are no filaments to slide; if the dynein is missing, then the cilium remains rigid and motionless; if nexin or the other connecting proteins are missing, then the axoneme falls apart when the filaments slide.

What we see in the cilium, then, is not just profound complexity, but also irreducible complexity on the molecular scale. Recall that by “irreducible complexity” we mean an apparatus that requires several distinct components for the whole to work. My mousetrap must have a base, hammer, spring, catch, and holding bar, all working together, in order to function. Similarly, the cilium, as it is constituted, must have the sliding filaments, connecting proteins, and motor proteins for function to occur. In the absence of any one of those components, the apparatus is useless.

The components of cilia are single molecules. This means that there are no more black boxes to invoke; the complexity of the cilium is final, fundamental. And just as scientists, when they began to learn the complexities of the cell, realized how silly it was to think that life arose spontaneously in a single step or a few steps from ocean mud, so too we now realize that the complex cilium can not be reached in a single step or a few steps. But since the complexity of the cilium is irreducible, then it can not have functional precursors. Since the irreducibly complex cilium can not have functional precursors it can not be produced by natural selection, which requires a continuum of function to work. Natural selection is powerless when there is no function to select. We can go further and say that, if the cilium can not be produced by natural selection, then the cilium was designed.

The Study of “Molecular Evolution”

Other examples of irreducible complexity abound, including aspects of protein transport, blood clotting, closed circular DNA, electron transport, the bacterial flagellum, telomeres, photosynthesis, transcription regulation, and much more. Examples of irreducible complexity can be found on virtually every page of a biochemistry textbook. But if these things cannot be explained by Darwinian evolution, how has the scientific community regarded these phenomena of the past forty years? A good place to look for an answer to that question is in the Journal of Molecular Evolution. JME is a journal that was begun specifically to deal with the topic of how evolution occurs on the molecular level. It has high scientific standards, and is edited by prominent figures in the field. In a recent issue of JME there were published eleven articles; of these, all eleven were concerned simply with the analysis of protein or DNA sequences. None of the papers discussed detailed models for intermediates in the development of complex biomolecular structures. In the past ten years JME has published 886 papers. Of these, 95 discussed the chemical synthesis of molecules thought to be necessary for the origin of life, 44 proposed mathematical models to improve sequence analysis, 20 concerned the evolutionary implications of current structures, and 719 were analyses of protein or polynucleotide sequences. There were zero papers discussing detailed models for intermediates in the development of complex biomolecular structures. This is not a peculiarity of JME. No papers are to be found that discuss detailed models for intermediates in the development of complex biomolecular structures in the Proceedings of the National Academy of Science, Nature, Science, the Journal of Molecular Biology or, to my knowledge, any journal whatsoever.

Sequence comparisons overwhelmingly dominate the literature of molecular evolution. But sequence comparisons simply can’t account for the development of complex biochemical systems any more than Darwin’s comparison of simple and complex eyes told him how vision worked. Thus in this area science is mute. This means that when we infer that complex biochemical systems were designed, we are contradicting no experimental result, we are in conflict with no theoretical study. No experiments needs to be questioned, but the interpretation of all experiments must now be reexamined, just as the results of experiments that were consistent with a Newtonian view of the universe had to be reinterpreted when the waveparticle duality of matter was discerned.

Conclusion

It is often said that science must avoid any conclusions which smack of the supernatural. But this seems to me to be both bad logic and bad science. Science is not a game in which arbitrary rules are used to decide what explanations are to be permitted. Rather, it is an effort to make true statements about physical reality. It was only about sixty years ago that the expansion of the universe was first observed. This fact immediately suggested a singular event–that at some time in the distant past the universe began expanding from an extremely small size. To many people this inference was loaded with overtones of a supernatural event–the creation, the beginning of the universe. The prominent physicist A.S. Eddington probably spoke for many physicists in voicing his disgust with such a notion 8:

Philosophically, the notion of an abrupt beginning to the present order of Nature is repugnant to me, as I think it must be to most; and even those who would welcome a proof of the intervention of a Creator will probably consider that a single windingup at some remote epoch is not really the kind of relation between God and his world that brings satisfaction to the mind.

Nonetheless, the Big Bang hypothesis was embraced by physics and over the years has proven to be a very fruitful paradigm. The point here is that physics followed the data where it seemed to lead, even though some thought the model gave aid and comfort to religion. In the present day, as biochemistry multiplies examples of fantastically complex molecular systems, systems which discourage even an attempt to explain how they may have arisen, we should take a lesson from physics. The conclusion of design flows naturally from the data; we should not shrink from it; we should embrace it and build on it.

In concluding, it is important to realize that we are not inferring design from what we do not know, but from what we do know. We are not inferring design to account for a black box, but to account for an open box. A man from a primitive culture who sees an automobile might guess that it was powered by the wind or by an antelope hidden under the car, but when he opens up the hood and sees the engine he immediately realizes that it was designed. In the same way biochemistry has opened up the cell to examine what makes it run and we see that it, too, was designed.

It was a shock to people of the nineteenth century when they discovered, from observations science had made, that many features of the biological world could be ascribed to the elegant principle of natural selection. It is a shock to us in the twentieth century to discover, from observations science has made, that the fundamental mechanisms of life cannot be ascribed to natural selection, and therefore were designed. But we must deal with our shock as best we can and go on. The theory of undirected evolution is already dead, but the work of science continues.

This paper was originally presented in the Summer of 1994 at the meeting ofthe C.S. Lewis Society, Cambridge University.