Theory of Intelligent Design, the best explanation of Origins

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Irreducible complexity is a undeniable fact

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1 Irreducible complexity is a undeniable fact on Sat Jan 25, 2014 4:08 pm

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Irreducible complexity is a undeniable fact

http://reasonandscience.heavenforum.org/t1468-irreducible-complexity#2133

The argument of irreducible complexity is obvious and clear. Subparts like a piston in a car engine are only designed, when there is a goal where they will be mounted with specific fitting sizes and correct materials, and have a specific function in the machine as a whole. Individually they have no function. Same in biological systems, which work like factories ( cells ) or machines ( cells host a big number of the most various molecular machines and factory-like production lines ) For example, in photosynthesis, there is no function for chlorophyll individually, only when inserted in the light harvesting complex, to catch photons, and direct them to the reaction center in Photosystem one and two. Foreplanning is absolutely essential. This is a  simple fact, which makes the concept of  Irreducible complexity obvious concept. Nonetheless people argue all the time that it's a debunked argument. Why ?

In the same sense, as a piston has no function by its own, an enzyme in a prebiotic soup or hydrothermal vent would have no function on its own.

A piston has no use if not installed in the cylinder of the engine, and the engine is fully functional. Similarly, a protein has no function if not installed in the cell in the proper location, and the cell is fully functional. So why would a prebiotic soup, or hydrothermal vents, produce proteins that have no purpose by their own? A factory with machines, production lines, computers, software/hardware, waste bins, recycle devices, quality check , control and repair, communication lines, and internal delivery mechanisms etc., always has an inventor. The building instructions for a factory or machine always have an intelligent origin. Biological cells are factories, full of machines, computers, and building instructions, stored in DNA. Abiogenesis is impossible. Life can only come from life.

Biological systems are functionally organized, integrated into an interdependent network, and complex, like human-made machines and factories. The wiring or circuit board of an electrical device equals to the metabolic pathways of a biological cell. For the assembly of a biological system of multiple parts, not only the origin of the genome information to produce all proteins/enzymes with their respective subunits and assembly cofactors must be explained, but also parts availability ( The right materials must be transported to the building site. Often these materials in their raw form are unusable. Other complex machines come into play to transform the raw materials into a usable form. All this requires specific information. ) synchronization, ( these parts must be read on hand at the building site ) manufacturing and assembly coordination ( which required the information of how to assemble each single part correctly, at the right place, at the right moment, and in the right position ) , and interface compatibility ( the parts must fit together correctly, like lock and key ) . Unless the origin of all these steps is properly explained, functional complexity as existing in biological systems has not been addressed adequately.

How could the whole process have started " off the hooks " from zero without a planning intelligence?
Why would natural, unguided mechanisms produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product exist, are in place and do their job?
My conclusion is: The origin of biological cells, and life, can only be explained by the acting agency of an intelligent mind.



Soren Lovtrup, professional biologist in Sweden, said
"...the reasons for rejecting Darwin's proposal were many, but first of all that many innovations cannot possibly come into existence through accumulation of many small steps, and even if they can, natural selection cannot accomplish it, because incipient and intermediate stages are not advantageous."

Irreducible complexity keeps being a unsurmountable problem for the ones that propose unguided evolution and natural mechanisms to explain the origin of life and biodiversity in general. No attempt to refute and successfully debunk the argument has been brought forward so far. Every attempt, no exception, has failed. Why ? Because IC is an undeniable FACT, no matter what. And this FACT becomes obvious to the unbiased mind when we envision biological systems as complex molecular machines, that operate similarly to man-made machines, but far far more complex. Individual parts have no function by themselves. This is an important point to highlight.

What use does the wing of an airplane have alone? None. The engineer has to envision a function for the wing, used as essential part of the design of the airplane as a whole in order to fly, and its use once the airplane is fully built with all parts in place.  The wing must be made with the right specifications, size, materials, form, and placed and mounted at the right place in the right way. And the wing itself requires complex machines to be made. The right materials must be transported to the building site. Often these materials in their raw form are unusable. Other complex machines come into play to transform the raw materials into usable form.  All this requires specific information.   The precise same thing happens in biological systems. Even the most simple cell uses numerous parts, that have no use by their own. For what reason would natural mechanisms create these parts, if there were no use for them individually?

This is a problem that stretches through all biology, from the simplest to the most complex. Biological systems do only achieve specific tasks, once a number of individual parts are made upon  specific complex instructions, frequently through other specific machines or even factories and assembly lines, that have no other tasks than to build these specific parts, and all this through the instructions of the  blueprint in the genome, and then other specific instructions provide the information of how, when, and where to mount the parts to form the complex machine. Same as done when building human-made machines. And all these processes must be strictly controlled, with error check and feedback mechanisms, and if something is not built to the right specification, complex repair machines fix the problem. These checking and repair systems must be fully operational from day one, otherwise, the organism dies. And the energy in usable form must also be provided , and the making of energy requires also complex machinery which by itself requires energy to be made ( chicken-egg problem ).

Furthermore, internal and external communication networks must be established.  Also, all these machines are made to self-replicate, which adds a huge amount of further complexity into the picture. Self-replication is far from simple. It demands the most complex molecular machinery, which works in an astonishing, beautiful, orchestrated, regulated and controlled manner. Why at all would natural unguided, non-intelligent chemical reactions have the need to produce living biological systems, and keep them existing through self-replication?

History of the idea 3

The idea of irreducible complexity can be traced back to the 1st century AD. The early authors used it as support for the reality of God. The argument was first used to attack evolution by Gustave Cuvier in the early 19th century. As Cuvier put it:
The entirety of an organic being forms a coordinated whole, a unique and closed system, in which the parts mutually correspond and work together in the same specific action through a reciprocal relationship. None of these parts can change without the others changing as well. (Cuvier, 1831, p 59)

A list of irreducible complex systems
http://reasonandscience.heavenforum.org/t2166-a-list-of-irreducible-complex-systems

Catch22, chicken and egg problems in biology and biochemistry
http://reasonandscience.heavenforum.org/t2059-catch22-chicken-and-egg-problems

Evolution and the Problem of Non-Functional Intermediates
http://reasonandscience.heavenforum.org/t2317-evolution-and-the-problem-of-non-functional-intermediates

Objection: Intelligent Design is based on gaps of knowledge and ignorance
Answer: It's not.

1. High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.
2. Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
4. Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems. 

Stephen C. Meyer, Not by Chance: From bacterial propulsion systems to human DNA, evidence of intelligent design is everywhere
Natural selection preserves or "selects" functional advantages. If a random mutation helps an organism survive, it can be preserved and passed on to the next generation. Yet, the flagellar motor has no function until after all of its 30 parts have been assembled. The 29 and 28-part versions of this motor do not work. Thus, natural selection can "select" or preserve the motor once it has arisen as a functioning whole, but it can do nothing to help build the motor in the first place.
This leaves the origin of molecular machines like the flagellar motor unexplained by the mechanism-natural selection that Darwin specifically proposed to replace the design hypothesis.Is there a better alternative? Based upon our uniform and repeated experience, we know of only one type of cause that produces irreducibly complex systems, namely, intelligence. Indeed, whenever we encounter irreducibly complex systems--such as an integrated circuit or an internal combustion engine--and we know how they arose, invariably a designing engineer played a role.
http://www.discovery.org/a/3059

Thus, Behe concludes--based on our knowledge of what it takes to build functionally-integrated complex systems--that intelligent design best explains the origin of molecular machines within cells. Molecular machines appear designed because they were designed.

The best of Behe's book :  Darwins Black box

Darwins Black Box page 40:

http://reasonandscience.heavenforum.org/t2115-the-best-of-darwins-black-box#3760

So let us attempt to evolve a bicycle into a motorcycle by the gradual accumulation of mutations. Suppose that a factory produced bicycles, but that occasionally there was a mistake in manufacture. Let us further suppose that if the mistake led to an improvement in the bicycle, then the friends and neighbors of the lucky buyer would demand similar bikes, and the factory would retool to make the mutation a permanent feature. So, like biological mutations, successful mechanical mutations would reproduce and spread. If we are to keep our analogy relevant to biology, however, each change can only be a slight modification, duplication, or rearrangement of a preexisting component, and the change must improve the function of the bicycle. So if the factory mistakenly increased the size of a nut or decreased the diameter of a bolt, or added an extra wheel onto the front axle or left off the rear tire, or put a pedal on the handlebars or added extra spokes, and if any of these slight changes improved the bike ride, then the improvement would immediately be noticed by the buying public and the mutated bikes would, in true Darwinian fashion, dominate the market. Given these conditions, can we evolve a bicycle into a motorcycle? We can move in the right direction by making the seat more comfortable in small steps, the wheels bigger, and even (assuming our customers prefer the «biker» look) imitating the overall shape in various ways. But a motorcycle depends on a source of fuel, and a bicycle has nothing that can be slightly modified to become a gasoline tank. And what part of the bicycle could be duplicated to begin building a motor? Even if a lucky accident brought a lawnmower engine from a neighboring factory into the bicycle factory, the motor would have to be mounted on the bike and be connected in the right way to the drive chain. How could this be done step-by-step from bicycle parts? A factory that made bicycles simply could not produce a motorcycle by natural selection acting on variation—by «numerous, successive, slight modifications»—and in fact there is no example in history of a complex change in a product occurring in this manner.
So far we have examined the question of irreducible complexity as a challenge to step-by-step evolution. But there is another difficulty for Darwin.  If the base were made out of paper, for example, the trap would fall apart. If the hammer were too heavy, it would break the spring. If the spring were too loose, it would not move the hammer. If the holding bar were too short, it would not reach the catch. If the catch were too large, it would not release at the proper time. A simple list of components of a mousetrap is necessary, but not sufficient, to make a functioning mousetrap.




What type of biological system could not be formed by “numerous successive, slight modifications?” Well, for starters, a system that is irreducibly complex.

By irreducibly complex I mean a single system composed of several well-matched interacting parts that contribute to the basic function, wherein the removal of any one of the [core] parts causes the system to effectively cease functioning.



But today, there are many such cases observed in nature.

High information content machine-like irreducibly complex and interdependent structures,  of which photosynthesis, the eye, the human body, nitrogenase, the ribosome, the cell, rubisco, photosystem II, the oxygen evolving complex etc. are prime examples, are commonly found in nature.
Since Evolution is unable to provide an advantage of adaptation in each evolutionary step and is unable to select it,  1) Darwinism’s prediction is falsified; 2) Design’s prediction is confirmed.


Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information, irreducible and interdependent biological systems. 
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information, irreducible and interdependent systems of all sorts. 
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information and irreducible complexity in the cell, and interdependence of proteins, organelles, and body parts, and even of animals and plants, aka moths and flowers, for example.  

1. High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.
2. Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
4. Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems. 1


For certain phenomena -- especially functionally specific, complex organisation and associated information [[FSCO/I] -- the only empirically observed adequate causes are intelligent ones. 1

For Behe the inadequacy of the neo-Darwinian synthesis consists in the fact that it cannot even in principle explain the origin of irreducible complexity. He argues that the existence of irreducible complexity at the molecular machine level points unmistakably to intelligent design: ‘To a person who does not feel obliged to restrict his search to unintelligent causes, the straightforward conclusion is that many biochemical systems were designed. They were designed not by the laws of nature, not by chance and necessity; rather, they were planned. The designer knew what the systems would look like when they were completed, then took steps to bring the systems about. Life on earth at its most fundamental level, in its most critical components, is the product of intelligent activity.’ In addition, Behe emphasizes that his conclusions are inferred naturally from the data, and not from sacred books or sectarian beliefs. They require no new principles of logic or science, but flow from the evidence provided by biochemistry combined with a consideration of the way in which we normally make design inferences.

The argument by impossibility of gradual development
1. Proponents of neo-darwinism try to proof that the eye, ear, blood clotting and heart could develop in small steps.
2. But in this gradualistic concept each change has to provide some advantage.
3. Natural selection selects only for functional advantage.
4. Natural selection eliminates things that has no function and can even harm the organism.
5. Thus, the half functional blood clotting; flagellum of E-coli; heart etc are impossible scenarios.
6. These must have already existed in their full functionality to facilitate the survival of the living being.
7. Therefore, a creator exists.

http://www.asa3.org/ASA/education/origins/ic-cr.htm

Four Definitions of Irreducible Complexity
     1. Michael Behe's Original Definition — [an irreducibly complex system is] "a single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning." (Darwin's Black Box, page 39, 1996)
     2. William Dembski's Enhanced Definition — "A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function.  The set of these indispensable parts is known as the irreducible core of the system." (No Free Lunch, page 285, 2001)
     3. Michael Behe's "Evolutionary" Definition — "An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations).  The degree of irreducible complexity is the number of unselected steps in the pathway."  (A Response to Critics of Darwin's Black Box, 2002)
     4. My Revision of Behe's Original Definition — A system is irreducibly complex if there is no function for any system that is missing one part, i.e. if all "subsystems with one less part" are functionless.    { This revision, suggested in 2001, corrects a minor error in Behe's original definition;  the error does not affect the logic of claims about irreducible complexity if we use Definitions 2, 3 or 4. }

Michael Behe's "Evolutionary" Definition — "An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations).  The degree of irreducible complexity is the number of unselected steps in the pathway."  (A Response to Critics of Darwin's Black Box, 2002)

" 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."

In the quote above, Behe notes that there is a fundamental quality of any irreducibly complex system in that, "any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.” Behe elaborates upon this definition saying  "An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway."

On the one side you have an intelligent agency based system of irreducible complexity of tight integrated, information-rich functional systems which have ready on hand energy directed for such, that routinely generate the sort of phenomenon being observed.  And on the other side imagine a golfer, who has played a golf ball through an 12 hole course. Can you imagine that the ball could also play itself around the course in his absence ? Of course, we could not discard, that natural forces, like wind , tornadoes or rains or storms could produce the same result, given enough time.  the chances against it, however, are so immense, that the suggestion implies that the non-living world had an innate desire to get through the 12 hole course.

Since the publication of Darwin’s Black Box, Behe has refined the definition of irreducible complexity. In 1996 he wrote that “any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.”(Behe, M, 1996b. Evidence for Intelligent Design from Biochemistry, a speech given at the Discovery Institute's God & Culture Conference, August 10, 1996 Seattle, WA. http://www.arn.org/docs/behe/mb_idfrombiochemistry.htm). By defining irreducible complexity in terms of “nonfunctionality,” Behe casts light on the fundamental problem with evolutionary theory: evolution cannot produce something where there would be a non-functional intermediate. Natural selection only preserves or “selects” those structures which are functional. If it is not functional, it cannot be naturally selected. Thus, Behe’s latest definition of irreducible complexity is as follows:“An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.” (A Response to Critics of Darwin’s Black Box, by Michael Behe, PCID, Volume 1.1, January February March, 2002; iscid.org/)

microbiologist James Shapiro of the University of Chicago declared in National Review that (Shapiro 1996)

"There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations."

In Trends in Ecology and Evolution Tom Cavalier-Smith, an evolutionary biologist at the University of British Columbia, nonetheless wrote:

"For none of the cases mentioned by Behe is there yet a comprehensive and detailed explanation of the probable steps in the evolution of the observed complexity. The problems have indeed been sorely neglected--though Behe repeatedly exaggerates this neglect with such hyperboles as 'an eerie and complete silence.'" (Cavalier-Smith 1997)

What type of biological system could not be formed by “numerous successive, slight modifications?” Well, for starters, a system that is irreducibly complex.

By irreducibly complex I mean a single system composed of several well-matched interacting parts that contribute to the basic function, wherein the removal of any one of the [core] parts causes the system to effectively cease functioning.


But today, there are many such cases observed in nature.

High information content machine-like irreducibly complex and interdependent structures,  of which photosynthesis, the eye, the human body, nitrogenase, the ribosome, the cell, rubisco, photosystem II, the oxygen evolving complex etc. are prime examples, are commonly found in nature.
Since Evolution is unable to provide an advantage of adaptation in each evolutionary step and is unable to select it,  1) Darwinism’s prediction is falsified; 2) Design’s prediction is confirmed.


Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information, irreducible and interdependent biological systems.
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information, irreducible and interdependent systems of all sorts.
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information and irreducible complexity in the cell, and interdependence of proteins, organelles, and body parts, and even of animals and plants, aka moths and flowers, for example.  

1. High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.
2. Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
4. Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems. 1


For certain phenomena -- especially functionally specific, complex organization and associated information [[FSCO/I] -- the only empirically observed adequate causes are intelligent ones. 1

For Behe the inadequacy of the neo-Darwinian synthesis consists in the fact that it cannot even in principle explain the origin of irreducible complexity. He argues that the existence of irreducible complexity at the molecular machine level points unmistakably to intelligent design: ‘To a person who does not feel obliged to restrict his search to unintelligent causes, the straightforward conclusion is that many biochemical systems were designed. They were designed not by the laws of nature, not by chance and necessity; rather, they were planned. The designer knew what the systems would look like when they were completed, then took steps to bring the systems about. Life on earth at its most fundamental level, in its most critical components, is the product of intelligent activity.’ In addition Behe emphasizes that his conclusions are inferred naturally from the data, and not from sacred books or sectarian beliefs. They require no new principles of logic or science but flow from the evidence provided by biochemistry combined with a consideration of the way in which we normally make design inferences.

http://reasonandscience.heavenforum.org/t1546-chlorophyll-biosynthesis-pathway

Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eight last steps are used by specific enzymes uniquely in this pathway.
The pathway must go all the way through, otherwise chlorophyill is not synthesized.
Therefore, the Chlorophyll biosynthesis pathway is irreducibly complex.


What good would there be, if the pathway would go only up to the 15th step? none
What good would there be, if the pathway would go all the way through the 17th step ? Chlorophyll would be produced, BUT:
What good for survival would there be for chlorophyll on its own, if not fully embedded in the photosintesis process? none.
What good would there be for photosynthesis without chlorophyll in place, capturing light, and transmitting it to the photosystem? none, since capturing
light is essential for the whole process.

For a working biological system to be built, the five following conditions would all have to be met:
C1: Availability. Among the parts available for recruitment to form the system, there would need to be ones capable of performing the highly specialized tasks of individual parts, even though all of these items serve some other function or no function.
C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.
C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time, they are needed.
C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a system are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.
C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if subsystems or parts are put together in the right order, they also need to interface correctly.
( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)


All of these operations are contained within the DNA and have to produce machines that are shape dependent and form fitting to the DNA and RNA transcript that comes from it. 

Resumed: For the assembly of a biological system of multiple parts, following steps must be explained: the origin of the genome information to produce all subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super intelligent and powerful designer, rather than mindless natural processes by chance, or/and evolution since we observe all the time minds capabilities producing machines and factories, producing machines and end products.

everything *has* to be in place at once or else an organism has no survival advantage. The thing is, there's no driver for any of the pieces to evolve individually because single parts confer no advantage in and of themselves. The necessity for the parts of the system to be in place all at once is simply evidence of creation. A visual system missing one piece (like an optic nerve) is like a car missing just one piece of the drive train (such as a differential); it's not that it doesn't function as well - it doesn't function at all!
What does a box with a pinhole have to do with anything? A few photons traveling through a hole is not a visual system. There is no image receptor, no processing of an image, no decision-making based on the interpretation of the image, and thus nothing having to do with survival.


Leslie Orgel’s observation about the citric acid cycle: “In my opinion, there is no basis in known chemistry for the belief that long sequences of reactions can organize spontaneously – and every reason to believe that they cannot. The problem of achieving sufficient specificity, whether in aqueous solution or on the surface of a mineral, is so severe that the chance of closing a cycle of reactions as complex as the reverse citric acid cycle, for example, is negligible.
http://www.grisda.org/origins/60006.pdf

REVERSIBILITY IN EVOLUTION CONSIDERED FROM THE STANDPOINT OF GENETICS
http://onlinelibrary.wiley.com/doi/10.1111/j.1469-185X.1939.tb00934.x/abstract

http://bio-complexity.org/ojs/index.php/main/article/viewFile/BIO-C.2014.1/BIO-C.2014.1

This paper has investigated a number of published models that claim to demonstrate the evolution of irreducibly complex systems and found that these models have failed on a number of fronts. Two of the models fail to satisfy the knockout test, in that they maintain functionality after parts have been removed. Almost all of the models use parts that are trivially complex, on the order of an amino acid rather than a protein in complexity. None of the models attempt to show why the mechanism used necessarily requires its parts. Finally, some of the models have been carefully designed to evolve. Thus, none of the models presented have demonstrated the ability to evolve an irreducibly complex system. In contrast, we do find irreducible complexity in the designed sensory system of the Tierran ancestor. This system is an example of what kind of system it would be necessary to evolve in order to falsify the claim that irreducible complexity is difficult to evolve. It has not been proven that the sensory system cannot evolve, but neither has it been shown that the sensory system can evolve. The prediction of irreducible complexity in computer simulations is that such systems will not generally evolve apart from intelligent aid. The prediction that irreducibly complex systems cannot evolve by a Darwinian process has thus far stood the test in computer models. Some have claimed to falsify the prediction, but have failed to follow the definition of irreducible complexity. However, it is always possible that a model will arrive that will falsify the claim. Until then, as a falsifiable prediction, the evidence for irreducible complexity grows stronger with each failed attempt.
http://translate.google.pl/translate?sl=pl&tl=en&js=y&prev=_t&hl=pl&ie=UTF-8&u=http%3A%2F%2Fbioslawek.wordpress.com%2F2014%2F02%2F18%2Fnieprzebyte-problemy-z-ewolucja-oka%2F&edit-text

The original argument for irreducible complexity was always probabilistic, meaning that like all claims in science, one never gets 100% proof. You never absolutely rule out with 100% certainty the possibility of an indirect evolutionary route. But science doesn't deal in the currency of absolutes. Is that Behe's problem or the neo-Darwinian evolutionists' problem? It's the evolutionists' problem because they claim these structures evolved by unguided mechanisms, and then they promote wildly speculative, perhaps even untestable indirect evolutionary pathways, to back that claim.
http://www.evolutionnews.org/2011/03/michael_behes_critics_make_dar044511.html

“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. But I can find no such case.”
― Charles Darwin, The Origin of Species

What type of biological system could not be formed by “numerous successive, slight modifications?” Well, for starters, a system that is irreducibly complex.

By irreducibly complex I mean a single system composed of several well-matched interacting parts that contribute to the basic function, wherein the removal of any one of the [core] parts causes the system to effectively cease functioning.
But today, there are many such cases observed in nature.
High information content machine-like irreducibly complex and interdependent structures,  of which photosynthesis is a prime example, are commonly found in nature.
Since Evolution is unable to  provide a advantage of adaptation in each evolutionary step, 1) Darwinism’s prediction is falsified; 2) Design’s prediction is confirmed.


The necessary precision and irreducible complexity found in nature all around us is indicative of expert design in the same way that a fine automobile indicates expert design in the way that the finely tuned parts work together, but a single error in construction in the wrong part could destroy the engine or transmission.

― Michael J. Behe
“The most essential prediction of Darwinism is that, given an astronomical number of chances, unintelligent processes can make seemingly-designed systems, ones of the complexity of those found in the cell. ID specifically denies this, predicting that in the absence of intelligent input no such systems would develop. So Darwinism and ID make clear, opposite predictions of what we should find when we examine genetic results from a stupendous number of organisms that are under relentless pressure from natural selection. The recent genetic results are a stringent test. The results: 1) Darwinism’s prediction is falsified; 2) Design’s prediction is confirmed.”

― Michael J. Behe, Darwin's Black Box: The Biochemical Challenge to Evolution
“In the abstract, it might be tempting to imagine that irreducible complexity simply requires multiple simultaneous mutations - that evolution might be far chancier than we thought, but still possible. Such an appeal to brute luck can never be refuted... Luck is metaphysical speculation; scientific explanations invoke causes.”

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246854/
regarding the origin of the species and life (DNA), even Darwin commented, “If it could be shown that complex systems could not arise by small sequential steps, then my theory would completely break down.” Irreducibly complex systems involving thousands of interrelated specifically coded enzymes do exist in every organ of the human body. At an absolute minimum, the inconceivable self-formation of DNA and the inability to explain the incredible information contained in DNA represent fatal defects in the concept of mutation and natural selection to account for the origin of life and the origin of DNA. As new theories emerge that explain the origin of life, the inevitable emotional accusations of heresy and ignorance are not surprising in a period of scientific revolution. It is therefore time to sharpen the minds of students, biologists, and physicians for the possibility of a new paradigm.


http://www.genome.jp/kegg/pathway/map/map00195.html
In photosynthesis , 26 protein complexes and enzymes are required to go through the light and light independent reactions, a chemical process that transforms sunlight into chemical energy,  to get glucose as end product , a metabolic intermediate for cell respiration.  A good part of the  protein complexes are uniquely used in photosynthesis. The pathway must go all the way through, and all steps are required, otherwise glucose is not produced. Also, in the oxygen evolving complex, which splits water into electrons, protons, and CO2, if the light-induced electron transfer reactions do not go all the five steps through, no oxygen, no protons and electrons are produced, no advanced life would be possible on earth. So, photosynthesis is a interdependent system, that could not have evolved, since all parts had to be in place right from the beginning. It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts. In these systems, nothing works until all the necessary components are present and working. So how could someont rationally say, the individual parts, proteins and enzymes, co-factors and assembly proteins not present in the final assemblage,  all happened by a series of natural events that we can call ad hoc mistake "formed in one particular moment without ability to consider any application." , to then somehow interlink in a meaningful way, to form electron transport chains, proton gradients to " feed " ATP synthase nano motors to produce ATP , and so on ?  Such independent structures would have not aided survival. Consider the light harvesting complex,  and the electron transport chain, that did not exist at exactly the same moment--would they ever "get together" since they would neither have any correlation to each other nor help survival separately? Repair of PSII via turnover of the damaged protein subunits is a complex process involving highly regulated reversible phosphorylation of several PSII core subunits. If this mechanism would not work starting right from the beginning,  various radicals and active oxygen species with harmful effects on photosystem II (PSII) would make it cease to function.  So it seems that photosynthesis falsifies the theory of evolution, where all small steps need to provide a survival advantage.


http://reasonandscience.heavenforum.org/t1546-chlorophyll-biosynthesis-pathway
Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eigth last steps are used by specific enzymes uniquely in this pathway.
The pathway must go all the way through, otherwise chlorophyill is not synthesized.
Therefore, the Chlorophyill biosynthesis pathway is irreducible complex.


http://www.ebi.ac.uk/interpro/entry/IPR000392
Nitrogen fixing bacteria possess a nitrogenase enzyme complex that catalyses the reduction of molecular nitrogen to ammonia [PMID: 2672439, PMID: 6327620, ]. The nitrogenase enzyme complex consists of two components:

Component I is nitrogenase MoFe protein or dinitrogenase, which contains 2 molecules each of 2 non-identical subunits.
Component II is nitrogenase Fe protein or dinitrogenase reductase, which is a homodimer. The monomer is encoded by the nifH gene [PMID: 6327620].

the subunits are unique , and cannot be used in other proteins :

http://www.biologie.uni-halle.de/microbiology/general-mibi/sawers/basem_soboh/
The active site of [NiFe]-hydrogenase has one carbon monoxide and two cyanide ligands coordinated to the iron atom, a feature that is to date unique in biology.
Since the Nitrongenase enzyme is composed of two subunits, set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic  it can be considered  irreducible complex

The paradoxical urinary concentrating mechanism

Mammals and some birds concentrate urine (and thus conserve water) by a compact mechanism composed of several necessary and interdependent properties. It is an excellent example of ‘irreducible complexity’, a system which fails if only one component is removed. Its genesis poses a serious problem for gradualists. This is well illustrated by the 8-year resistance to adopting the current model of urine concentration by the leading renal physiologist of the time. He was a celebrated evolutionist, and opposed the model chiefly on the grounds that it violated gradualist principles.
MICHAEL BEHE:

In Darwin’s Black Box: The Biochemical Challenge to Evolution I devoted a chapter to the mechanism of blood clotting, arguing that it is irreducibly complex and therefore a big problem for Darwinian evolution. Since my book came out, as far as I am aware there have been no papers published in the scientific literature giving a detailed scenario or experiments to show how natural selection could have built the system. However three scientists publishing outside science journals have attempted to respond. The first is Russell Doolittle, a professor of biochemistry at the University of California at San Diego, member of the National Academy of Sciences, and expert on blood clotting. Second is Kenneth Miller, a professor of cell biology at Brown University and author of Finding Darwin’s God (Miller 1999). The third scientist is Keith Robison, who at the time of his writing was a graduate student at Harvard University.


1) Professor Doolittle argued that new laboratory work showed two components of the blood clotting cascade could be eliminated (“knocked-out”) from mice and the mice got along fine without them. However, Doolittle misread the laboratory work: the double knock-out mice have severe problems and have no functioning blood clotting system. They are not models of evolutionary intermediates.
Although anyone can misread a paper, in my opinion the fact that an expert cited a recent and contradictory journal article, instead of a publication directly addressing the evolution of blood clotting, shows that there are indeed no detailed explanations for the evolution of blood clotting in the literature and that, despite Darwinian protestations, the irreducible complexity of the system is a significant problem for Darwinism.
2) Although embedded in a lengthy description of how blood clotting and other systems work, Professor Miller’s actual explanation for how the vertebrate clotting cascade evolved consists of one paragraph. It is a just-so story that doesn’t deal with any of the difficulties the evolution of such an intricate system would face. Even so, in the one paragraph Miller proposes what looks like a detrimental or fatal situation, akin to the knock-out mice (above) that lack critical components.
3) Keith Robison proposed that a cascade might begin with a single enzyme with three different properties. Upon duplication of the gene for the enzyme, the duplicate loses several of the properties, resulting in a two-component cascade. Repetition of the scenario builds cascades with more components. Although intriguing, the scenario starts with a complex, unjustified situation (the enzyme with multiple abilities) that already has all necessary activities. What’s more, the proposed gene duplication and several steps needed to lose function are “neutral,” unselected mutations. Stringing together several very specific neutral mutations to build a complex system is vastly improbable and amounts to intelligent design.
http://www.trueorigin.org/behe03.asp

“Cornell geneticist Dr. John Sanford notes that “each part has no value except within the context of the whole functional unit, and so irreducible systems have to come together all at once, and cannot arise one piece at a time.” He adds that in the case of a mousetrap, even if all of the pieces are sitting neatly next to each other on the inventor’s workbench, they cannot properly assemble into a functional unit by chance—or by any feasible evolutionary mechanism. They must first come together simultaneously as a functioning system in the mind of the designer.”
http://www.uncommondescent.com/intelligent-design/michael-behe-has-not-been-bombed-either/

A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.

In the discussion section, we read: "Some readers might suggest that we 'stacked the deck' by studying the evolution of a complex feature that will be built on simpler features that were also useful. However, that is precisely what evolutionary theory requires..."

Well, no. The Lenski simulation requires that complex systems exhibiting complex functions can always be built up from  simpler systems exhibiting simpler function . Macro change needs to explain many de novo features, like the arise of wings, legs, body organs etc, starting from biological systems which did not have such features at all.  

http://www.ideacenter.org/contentmgr/showdetails.php/id/1319#critique

"The simulation by Lenski et al. assumes that all functioning biological systems are evolutionary kludges of subsystems that presently have function or previously had function. But there's no evidence that real-life irreducibly complex biological machines, for instance, can be decomposed in this way. If there were, the Lenski et al. computer simulation would be unnecessary. Without it, their demonstration is an exercise in irrelevance.

Following are the main critique points :
1.Stacking the Deck: It was pre-ordained that the complex function can be created from the less complex functions (they hand-coded a solution before even running the simulation)--but there is no such guarantee in biology that subsystems can be so easily combined to produce anything useful! The complexity gap between the smaller functions (NAND, etc.) and the target functions (EQU) is not very big. In fact, they were able to create EQU using only 5 of the more primitive logic operation subsystems. This means that as far as logic is concerned, only 5 of the basic logic functions used in the programs are needed to evolve EQU. They created a simulation which they knew could evolve the target function through the subsystems. (This is why I have titled this critique "Evolution by Intelligent Design.")
2.Too Much Selective Advantage: Selective advantage was given to literally every single addition of logic functions in the organisms which evolved EQU. Additionally, every mutation which added code, always added functional line(s) of code, while in nature mutations are never guaranteed to have any meaning or functionality in the environment. This makes the evolution of EQU essentially inevitable, and it does not test irreducible complexity. In a true irreducibly complex system, there will be no selective advantage along an evolutionary pathway. In real world, there is no guarantee that the subsystems you need will necessarily give you a selective advantage along your evolutionary pathway.
3.Illustrating that Irreducible Complexity is Unevolvable: When the aforementioned "selective advantage" was taken away, and fitness only increased when the target function EQU appeared, EQU NEVER EVOLVED in their simulations! This is very significant because it shows that they modeled true irreducible complexity, and that when they did, irreducible complexity could not evolve!

Modeling Irreducible Complexity

The paper made one profound finding when it accurately modeled true irreducible complexity (first full paragraph, pg. 143). Michael Behe has defined irreducible complexity as:
"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway." (A Response to Critics of Darwin’s Black Box, by Michael Behe, PCID, Volume 1.1, January February March, 2002; iscid.org/)

When Lenski et al. created a simulation with high irreducible complexity, i.e. there was no selective advantage until the target function arose, EQU never evolved! Consider this quote from the Lenski paper:

"At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection would not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment (P ~= 4.3 x 10-9, Fisher's exact test)."

In other words, when there is no selective advantage until you get the final function, the final function doesn't evolve. In this case, their simulation probably DID model biological reality because irreducible complexity claims that there is no advantage until you get the final function. In fact in such a scenario, it found that the evolution of such a structure was impossible. In other words, they just proved that irreducible complexity is unevolvable.



The Lenski paper can only be seen as a scientific response to the claims of ID proponents, published in a high profile journal such as Nature. Despite the fact that the authors of the Lenski paper would likely deny this fact, there are many clues which show that the article is intended as a rebuttal to the claims of ID proponents. Not only does this validate the work of ID proponents as posing a legitimate challenge to Darwin's theory, but it also indicates that the claims of ID proponents are eminently testable, falsifiable (though as discussed above, not yet falsified), and therefore also scientific in nature.

The article even attempts to address irreducible complexity without using the term. "Thus, although more than two dozen mutations were used to build EQU, undoing any one of them destroyed this function." They are stating that EQU was irreducibly complex, but yet it evolved. Thus, Exhibit C is as follows: the article directly purports to test the evolution of irreducible complexity but yet never uses the phrase. (Note: It is arguable that their stated conclusions about the evolution of irreducible complexity do not match the findings of their simulations. When EQU evolved, the study did not truly model irreducible complexity because it employed a "reward-all" environment where some function could be gained by adding parts which could also contribute to the final function. When the article properly modeled irreducible complexity, where only EQU was rewarded, EQU never evolved!)

While the author Carl Zimmer quotes co-author Christopher Adami to sing an over-inflated victory song, one important point should not be lost: this study implicitly proves that the claims of ID proponents, such the claim that some biological features are irreducible complexity, are eminently testable via the methods of science. Apparently Nature saw the claim of irreducible complexity as such a threat to evolution that it saw fit to publish a study which attempted to model the evolution of irreducible complexity.

1. http://iose-gen.blogspot.com.br/2010/06/introduction-and-summary.html#methnat
2. http://www.ideacenter.org/contentmgr/showdetails.php/id/840
3. http://content.csbs.utah.edu/~rogers/evidevolcrs/ircomp/

Further readings:
http://www.harunyahya.com/en/Books/592/darwinism-refuted/chapter/51
http://creationwiki.org/Some_systems_are_irreducibly_complex_%28Talk.Origins%29
http://tccsa.tc/articles/irreducible_complexity_ed.pdf
http://myxo.css.msu.edu/papers/nature2003/Nature03_Complex.pdf



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http://www.uncommondescent.com/intelligent-design/id-foundations-3-irreducible-complexity-as-concept-as-fact-as-macro-evolution-obstacle-and-as-sign-of-design/

http://www.uncommondescent.com/intelligent-design/id-foundations-2-counterflow-open-systems-fscoi-and-self-moved-agents-in-action/

ID Foundations, 3: Irreducible Complexity as concept, as fact, as [macro-]evolution obstacle, and as a sign of design

Irreducible complexity is probably the most violently objected to foundation stone of Intelligent Design theory. So, let us first of all define it by slightly modifying Dr Michael Behe’s original statement in his 1996 Darwin’s Black Box [DBB]:

What type of biological system could not be formed by “numerous successive, slight modifications?” Well, for starters, a system that is irreducibly complex.

By irreducibly complex I mean a single system composed of several well-matched interacting parts that contribute to the basic function, wherein the removal of any one of the [core] parts causes the system to effectively cease functioning.


[DBB, p. 39, emphases and parenthesis added. Cf. expository remarks in comment 15 below.]

Behe proposed this definition in response to the following challenge by Darwin in Origin of Species:

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. But I can find out no such case . . . . We should be extremely cautious in concluding that an organ could not have been formed by transitional gradations of some kind. [Origin, 6th edn, 1872, Ch VI: "Difficulties of the Theory."]

In fact, there is a bit of question-begging by deck-stacking in Darwin’s statement: we are dealing with empirical matters, and one does not have a right to impose in effect outright logical/physical impossibility — “could not possibly have been formed” — as a criterion of test.

If, one is making a positive scientific assertion that complex organs exist and were credibly formed by gradualistic, undirected change through chance mutations and differential reproductive success through natural selection and similar mechanisms, one has a duty to provide decisive positive evidence of that capacity.


Behe’s onward claim is then quite relevant: for dozens of

key cases, no credible macro-evolutionary pathway (especially no detailed biochemical and genetic pathway) has been empirically demonstrated and published in the relevant professional literature.

That was true in 1996, and despite several attempts to dismiss key cases such as the bacterial flagellum  or the relevant part of the blood clotting cascade , it arguably still remains to today.

Now, we can immediately lay the issue of the fact of irreducible complexity as a real-world phenomenon to rest.

For, a situation where core, well-matched, and co-ordinated parts of a system are each necessary for and jointly sufficient to effect the relevant function is a commonplace fact of life. One that is familiar from all manner of engineered systems; such as, the classic double-acting steam engine:


Such a steam engine is made up of rather commonly available components: cylinders, tubes, rods, pipes, crankshafts, disks, fasteners, pins, wheels, drive-belts, valves etc. But, because a core set of well-matched parts has to be carefully organised according to a complex “wiring diagram,” the specific function of the double-acting  steam engine is not explained by the mere existence of the parts.

Nor, can simply choosing and re-arranging similar parts from say a bicycle or an old-fashioned car or the like create a viable steam engine.  Specific mutually matching parts [matched to thousandths of an inch usually], in a very specific pattern of organisation, made of specific materials, have to be in place, and they have to be integrated into the right context [e.g. a boiler or other source providing steam at the right temperature and pressure], for it to work.

If one core part breaks down or is removed — e.g. piston, cylinder, valve, crank shaft, etc., core function obviously ceases.

Irreducible complexity is not only a concept but a fact.

But, why is it said that irreducible complexity is a barrier to Darwinian-style [macro-]evolution and a credible sign of design in biological systems?

First, once we are past a reasonable threshold of complexity, irreducible complexity [IC] is a form of functionally specific complex organisation and implied information [FSCO/I], i.e. it is a case of the specified complexity that is already immediately a strong sign of design on which the design inference rests. (NB: Cf. the first two articles in the ID foundations series — here and here.)

Fig. B, on the exploded, and nodes and arcs “wiring diagram” views of how a complex, functionally specific entity is assembled, will help us see this:

Fig. B (i): An exploded view of a gear pump. (Courtesy, Wikipedia)

Fig. B(ii): A Piping  and Instrumentation Diagram, illustrating how nodes, interfaces and arcs are “wired” together in a functional mesh network (Source: Wikimedia, HT: Citizendia; also cf. here, on polygon mesh drawings.)

We may easily see from Fig. B (i) and (ii) how specific components — which may themselves be complex — sit at nodes in a network, and are wired together in a mesh that specifies interfaces and linkages. From this, a set of parts and wiring instructions can be created, and reduced to a chain of contextual yes/no decisions. On the simple functionally specific bits metric, once that chain exceeds 1,000 decisions, we have an object that is so complex that it is not credible that the whole universe serving as a search engine, could credibly produce this spontaneously without intelligent guidance. And so, once we have to have several well-matched parts arranged in a specific “wiring diagram” pattern to achieve a function, it is almost trivial to run past 125 bytes [= 1,000 bits] of implied function-specifying information.

Of the significance of such a view, J. S Wicken observed in 1979:
‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems.  Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65. (Emphases and notes added. Nb: “originally” is added to highlight that for self-replicating systems, the blue print can be built-in.)]

Indeed, the implication of that complex, information-rich functionally specific organisation is the source of Sir Fred Hoyle’s metaphor of comparing the idea of spontaneous assembly of such an entity to a tornado in a junkyard assembling a flyable 747 out of parts that are just lying around.

Similarly, it is not expected that if one were to do a Humpty Dumpty experiment — setting up a cluster of vials with sterile saline solution with nutrients and putting in each a bacterium then pricking it so the contents of the cell leak out — it is not expected that in any case, the parts would spontaneously re-assemble to yield a viable bacterial colony.

But also, IC is a barrier to the usual suggested counter-argument, co-option or exaptation based on a conveniently available cluster of existing or duplicated parts. For instance, Angus Menuge has noted that:

For a working [bacterial] flagellum to be built by exaptation, the five following conditions would all have to be met:

   C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.

   C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

   C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

   C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

   C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly.

( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

In short, the co-ordinated and functional organisation of a complex system  is itself a factor that needs credible explanation.

However, as Luskin notes for the iconic flagellum, “Those who purport to explain flagellar evolution almost always only address C1 and ignore C2-C5.” [ENV.]

And yet, unless all five factors are properly addressed, the matter has plainly not been adequately explained. Worse, the classic attempted rebuttal, the Type Three Secretory System [T3SS] is not only based on a subset of the genes for the flagellum [as part of the self-assembly the flagellum must push components out of the cell], but functionally, it works to help certain bacteria prey on eukaryote organisms. Thus, if anything the T3SS is not only a component part that has to be integrated under C1 – 5, but it is credibly derivative of the flagellum and an adaptation that is subsequent to the origin of Eukaryotes. Also, it is just one of several components, and is arguably itself an IC system. (Cf Dembski here.)

Going beyond all of this, in the well known Dover 2005 trial, and citing ENV, ID lab researcher Scott Minnich has testified to a direct confirmation of the IC status of the flagellum:

Scott Minnich has properly tested for irreducible complexity through genetic knock-out experiments he performed in his own laboratory at the University of Idaho. He presented this evidence during the Dover trial, which showed that the bacterial flagellum is irreducibly complex with respect to its complement of thirty-five genes. As Minnich testified: “One mutation, one part knock out, it can’t swim. Put that single gene back in we restore motility. Same thing over here. We put, knock out one part, put a good copy of the gene back in, and they can swim. By definition the system is irreducibly complex. We’ve done that with all 35 components of the flagellum, and we get the same effect.” [Dover Trial, Day 20 PM Testimony, pp. 107-108. Unfortunately, Judge Jones simply ignored this fact reported by the researcher who did the work, in the open court room.]

That is, using “knockout” techniques, the 35 relevant flagellar proteins in a target bacterium were knocked out then restored one by one.

The pattern for each DNA-sequence: OUT — no function, BACK IN — function restored.

Thus, the flagellum is credibly empirically confirmed as irreducibly complex.

The “Knockout Studies” concept — a research technique that rests directly on the IC property of many organism features –needs some explanation.



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What natural selection lacks, intelligent design—purposive, goal-directed selection—provides

What natural selection lacks, intelligent design—purposive, goal-directed selection—provides

http://reasonandscience.heavenforum.org/t1468-irreducible-complexity-is-a-undeniable-fact#2534

Behe has provided the strongest smackdown of Darwins theory with his proposal of irreducible complexity. One of the things that illustrate the concept best and most clear is the fact that biological systems find their equivalence in human made factories, machines and production lines. Nobody produces a machine part or a factory without a goal in mind. Undirected occurrances will never lead to the origin and production of a distant specific goal, of a machine part with its intrincate form, size, match with other parts, and right materials, nor the instructions where, how, and when to mount the subpart in the machine. But thats precisely what is needed in the world of cells, molecules and proteins. Cells are factories, containing thousands of proteins that interact in intricate manners like machines, and are interlinked through the metabolic network, like a electric board.

Dembsky puts it very eloquently :

The problem is that nature has too many options and without design couldn’t sort them all out. Natural mechanisms are too unspecific to determine any particular outcome. Mutation and natural selection or luck/chance/probablity could theoretically form a new complex morphological feature like a leg or a limb with the right size and form , and arrange to find out the right body location to grow them , but it could also produce all kinds of other new body forms, and grow and attach them anywhere on the body, most of which have no biological advantage or are most probably deleterious to the organism. Natural mechanisms have no constraints, they could produce any kind of novelty. Its however that kind of freedom that makes it extremely unlikely that mere natural developments provide new specific evolutionary arrangements that are advantageous to the organism. Nature would have to arrange almost a infinite number of trials and errors until getting a new positive arrangement. Since that would become a highly unlikely event, design is a better explanation. This situation becomes even more acentuated when natural selection is not a possible constrainer, since evolution depends on replication, which did not exist prior dna replication

Stephen Meyer: What natural selection lacks, intelligent design—purposive, goal-directed selection—provides. Rational agents can arrange both matter and symbols with distant goals in mind. In using language, the human mind routinely "finds" or generates highly improbable linguistic sequences to convey an intended or preconceived idea. In the process of thought, functional objectives precede and constrain the selection of words, sounds, and symbols to generate functional (and meaningful) sequences from a vast ensemble of meaningless alternative possible combinations of sound or symbol. Similarly, the construction of complex technological objects and products, such as bridges, circuit boards, engines, and software, results from the application of goal-directed constraints. Indeed, in all functionally integrated complex systems where the cause is known by experience or observation, designing engineers or other intelligent agents applied constraints on the possible arrangements of matter to limit possibilities in order to produce improbable forms, sequences, or structures. Rational agents have repeatedly demonstrated the capacity to constrain possible outcomes to actualize improbable but initially unrealized future functions. Repeated experience affirms that intelligent agents (minds) uniquely possess such causal powers. Analysis of the problem of the origin of biological information, therefore, exposes a deficiency in the causal powers of natural selection and other undirected evolutionary mechanisms that corresponds precisely to powers that agents are uniquely known to possess. Intelligent agents have foresight. Such agents can determine or select functional goals before they are physically instantiated. They can devise or select material means to accomplish those ends from among an array of possibilities. They can then actualize those goals in accord with a preconceived design plan or set of functional requirements. Rational agents can constrain combinatorial space with distant information-rich outcomes in mind. The causal powers that natural selection lacks—by definition—are associated with the attributes of consciousness and rationality—with purposive intelligence. Thus, by invoking intelligent design to overcome a vast combinatorial search problem and to explain the origin of new specified information, contemporary advocates of intelligent design are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence.



http://reasonandscience.heavenforum.org/t1468-irreducible-complexity

There are many parts, subunits of enzymes and proteins, co-factos etc. that have no apparent multiple functions and could not be co-opted or be available through horizontal gene transfer, or whatever. I mention this because its a frequent argument brought forward by the skeptics. It is irrelevant if subparts of a molecular machine can serve a different function. The moment anyone discusses some different function, they are no longer talking about irreducible complexity, they are talking about something else. Behe already directly responded to this nonsense, stated himself that mentioning other functions is a strawman, and went on to comment that never once did he ever suggest that subparts could not have secondary functions. He never discussed them because those questions are irrelevant. One example of irreducible complexity are the last 8 enzymes used in the biosynthesis pathway of chlorophyll http://reasonandscience.heavenforum.org/t1546-chlorophyll-biosynthesis-pathway  for what reason would these enzymes emerge naturally , if by their own , and not duly embedded in the whole biosynthesis process, they have no use at all ? and even lets say chlorophyll : why would nature invent such extremely complex pathways to produce such a complex molecule, if, even if ready to go, it is not embedded in the whole process of photosynthesis ? and how could they be embedded in the system, if the light harvesting complex were not present ? please explain. Furthermore, i wonder how nature came up with the information to make the individual parts, the subunits, and providing the right assembly instructions for the individual parts, and the whole thing. As its known, body plans and 3d cell shape does not depend only on genetic information, but also epigenetic information and other unknown factors.

What natural selection lacks, intelligent design—purposive, goal-directed selection—provides. Rational agents can arrange both matter and symbols with distant goals in mind. In using language, the human mind routinely "finds" or generates highly improbable linguistic sequences to convey an intended or preconceived idea. In the process of thought, functional objectives precede and constrain the selection of words, sounds, and symbols to generate functional (and meaningful) sequences from a vast ensemble of meaningless alternative possible combinations of sound or symbol. Similarly, the construction of complex technological objects and products, such as bridges, circuit boards, engines, and software, results from the application of goal-directed constraints. Indeed, in all functionally integrated complex systems where the cause is known by experience or observation, designing engineers or other intelligent agents applied constraints on the possible arrangements of matter to limit possibilities in order to produce improbable forms, sequences, or structures. Rational agents have repeatedly demonstrated the capacity to constrain possible outcomes to actualize improbable but initially unrealized future functions. Repeated experience affirms that intelligent agents (minds) uniquely possess such causal powers.  Analysis of the problem of the origin of biological information, therefore, exposes a deficiency in the causal powers of natural selection and other undirected evolutionary mechanisms that corresponds precisely to powers that agents are uniquely known to possess. Intelligent agents have foresight. Such agents can determine or select functional goals before they are physically instantiated. They can devise or select material means to accomplish those ends from among an array of possibilities. They can then actualize those goals in accord with a preconceived design plan or set of functional requirements. Rational agents can constrain combinatorial space with distant information-rich outcomes in mind. The causal powers that natural selection lacks—by definition—are associated with the attributes of consciousness and rationality—with purposive intelligence. Thus, by invoking intelligent design to overcome a vast combinatorial search problem and to explain the origin of new specified information, contemporary advocates of intelligent design are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence.








http://www.designinference.com/documents/2004.01.Irred_Compl_Revisited.pdf

The articles included in this issue demonstrate some striking parallels between artifactual and biological/molecular machines. In the first place, molecular machines, like man-made machines, perform highly specific functions. Second, the macromolecular machine complexes feature multiple parts that interact in distinct and precise ways, with defined inputs and outputs. Third, many of these machines have parts that can be used in other molecular machines (at least, with slight modification), comparable to the interchangeable parts of artificial machines. Finally, and not least, they have the cardinal attribute of machines: they all convert energy into some form of ‘work’.

A functional system is irreducibly complex if it contains a multipart subsystem (i.e., a set of two or more interrelated parts) that cannot be simplified without destroying the system’s basic function.


I refer to this multipart subsystem as the system’s irreducible core.

We can therefore define the core of a functionally integrated system as those parts that are indispensable to the system’s basic function: remove parts of the core, and you can’t recover the system’s basic function from the other remaining parts. To say that a core is irreducible is then to say that no other systems with substantially simpler cores can perform the system’s basic function.

As another example of an irreducibly complex system, consider an old-fashioned pocket watch. The basic function of the watch is to tell time by means of a winding mechanism. Several parts of the watch are indispensable to that basic function, for instance, the spring, the face, and the hour hand. These belong to the irreducible core. But note that other parts of the watch are dispensable, for instance, the crystal, the metal case, and the chain. Because these parts are unnecessary or redundant to the system’s basic function, they do not belong to the irreducible core.



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Examples of Irreducibly Complex systems:

1.      Behe’s flagellum.  Some bacteria have on-board propulsion systems consisting of a rotary motor, a free turning shaft, a bushing around the shaft as it emerges to the outside, and a propeller.  The motor can reverse directions and go to 100,000 rpm. All components are required in order to function.

2.      Bombardier Beetle. The beetle contains two sacs, one which contains a volatile substance and another containing an oxidizing substance; it also has a mixing chamber, an expulsion mechanism, and a movable nozzle for aiming the ejection of the explosive mixture at a foe.

3.      DNA / RNA Interactions.  DNA supplies the blueprint of the required protein to the RNA, which uses the blueprint to manufacture the protein.  One can’t do anything without the other.

4.      Stomach.  Digests, yet doesn’t digest itself.

5.      Coagulation of blood.  If blood coagulated inside the vein, the entire arterial/venous system would clog shut.  If blood did not coagulate when it needs to, excessive bleeding to the point of death would occur.  A number of clotting factors are needed in order for blood clotting to perform correctly.

6.      First Life.  Requires 9 essential features, all present simultaneously.

7.      Feathers.  Extremely complex mechanisms that are not direct off-shoots of hair or scales.

8.      Toxic snakes. 3 necessary systems: They generate toxin in a fashion that keeps them immune, they hypodermically inject the toxin without injecting themselves, they consume their own toxin by eating the prey, yet are unaffected.

9.      Giraffe’s neck. Must have extra vascular valves to make the length work.

10. DNA / protein dependency: DNA requires proteins, but proteins require DNA.



This is an interesting example of an irreducibly complex system. This channel regulates the flow of ions into the cell is called; mechanical channel.

Ingredients:

1) Kanał acts as a of the door on spring, Which closes the door.

2) Twine (filament) that extends and opens the door to the channel.

3) The cord is attached to the cell, Which bends and pulls the string and opens the door to channel.

Everything is driven by sound waves;

http://www.youtube.com/watch?v=1VmwHiRTdVc

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5 A 12 hole Golf course on Sat Apr 26, 2014 6:10 pm

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http://www.angelfire.com/pro/kairosfocus/resources/Info_design_and_science.htm

  One point is clear: granted that there are indeed many systems and/or correlated subsystems in biology, which have to be classified as irreducibly complex and that such systems are essentially involved in the formation of morphological characters of organisms, this would explain both, the regular abrupt appearance of new forms in the fossil record as well as their constancy over enormous periods of time. For, if "several well-matched, interacting parts that contribute to the basic function" are necessary for biochemical and/or anatomical systems to exist as functioning systems at all (because "the removal of any one of the parts causes the system to effectively cease functioning") such systems have to (1) originate in a non-gradual manner and (2) must remain constant as long as they are reproduced and exist. And this could mean no less than the enormous time periods mentioned for all the living fossils hinted at above. Moreover, an additional phenomenon would also be explained: (3) the equally abrupt disappearance of so many life forms in earth history . . . The reason why irreducibly complex systems would also behave in accord with point (3) is also nearly self-evident: if environmental conditions deteriorate so much for certain life forms (defined and specified by systems and/or subsystems of irreducible complexity), so that their very existence be in question, they could only adapt by integrating further correspondingly specified and useful parts into their overall organization, which prima facie could be an improbable process -- or perish . . . .

   According to Behe and several other authors [5-7, 21-23, 53-60, 68, 86] the only adequate hypothesis so far known for the origin of irreducibly complex systems is intelligent design (ID) . . . in connection with Dembski's criterion of specified complexity . . . . "For something to exhibit specified complexity therefore means that it matches a conditionally independent pattern (i.e., specification) of low specificational complexity, but where the event corresponding to that pattern has a probability less than the universal probability bound and therefore high probabilistic complexity" [23]. For instance, regarding the origin of the bacterial flagellum, Dembski calculated a probability of 10^-234[22].

Now, first, we must observe that Darwin's proposed test, on at least one major interpretation, is less generous than it first appears: "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." For, as Shapiro acidly but aptly noted, on the defects in such an appeal to bare possibility in defense of the RNA world hypothesis -- making a remark that, we observe, inadvertently also applies to his preferred metabolism first scenario -- that:

On the one side you have a intelligent agency based system of irreducible complexity of tight integrated , information rich functional systems which have ready on hand energy directed  for such, that routinely generate the sort of phenomenon being observed.  And on the other side imagine a golfer, who has played a golf ball through an 12 hole course. Can you imagine that  the ball could also play itself around the course in his absence ? Of course, we could not discard, that natural forces, like wind , tornadoes or rains or storms  could produce the same result, given enough time.  the chances against it however are so immense, that the suggestion implies that the non-living world had an innate desire to get through the 12 hole course.



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https://apologeticspress.org/APContent.aspx?category=12&article=980

Consider that the production of red blood cells, one of the major constituents within the vascular system, is regulated by erythropoietin—a hormone produced in the kidney. Yet that kidney requires red blood cells to deliver oxygenated blood. So which evolved first? Did the red blood cells produce in lethal quantities until a kidney had evolved the ability to produce erythropoietin, or did the hormone exist before the production of these red blood cells? The human circulatory system is far more than a series of evolutionary steps that evolved to increase gas and nutrient transport efficiency. A close examination of this complex network reveals architectural planning and design that can only be comprehended in light of an intelligent Designer.

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http://www.detectingdesign.com/irreduciblemousetrap.html#Another%20Problem

The problem, of course, is that nature cannot always produce novel beneficial functions by comparing genetic sequences to a pre-established sequence.  For example, how would a bacterium evolve a function like a single protein enzyme? - like a lactase enzyme?  A lactase enzyme is a protein that is able to dramatically improve the break down of the sugar lactose into glucose and galactose - each of which is then able to enter the glycolytic pathway to be used for energy.

http://thesweetscientists.blogspot.com.br/


 But, how would a bacterium evolve the lactose function?  It is a simple matter of getting a random protein sequence to bind to a lactose molecule more and more firmly?  Not really.  Simple binding is not enough.  The lactase enzyme has to bind in a fairly specific way to the lactose sugar in order to hydrolyze it to a useful degree.  Until this threshold is reached, there simply is no improved reproductive advantage gained by the bacterium.  It seems that this threshold requirement is about 380 fairly specified residues at minimum.  A useful lactase simply cannot be made with significantly lower minimum size and specificity requirements.  

These minimum requirements create a kind of threshold beyond which the lactase function simply cannot be built up gradually where very small one or two residues changes at a time result in a useful change in the degree of the lactase function.  Therefore, such functions cannot be evolved with Dawkins's or McDonald's proposed model.  There simply is no template or gradual step by step pathway from just any starting point to the minimum threshold requirement.  Only after this threshold has been reached can evolution take over and make further refinements - but not until.

Now, there are in fact examples of computer evolution that attempt to address the above problem, but how would someone like McDonald deal with this problem when it comes to evolving real biosystems?

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Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information

http://link.springer.com/article/10.1007/s00018-013-1394-1

Self-referential organisation, as we put it here, implies inter-conversion of information between logically distinct coding systems specifying each other reciprocally. Thus, the holistic approach assumes selfreferentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organisational complexity of the genetic regulation system of any cell. Put another way, this implies that the structural dynamics of the chromosome must be fully convertible into its genetic expression and vice versa. Since the DNA is an essential carrier of genetic information, the fundamental question is how this self-referential organisation is encoded in the sequence of the DNA polymer.

The article even specifies that there are "Three basic components underlying the irreducible organisational complexity of any living cell" where "the organisation is essentially circular with all three basic components standing in relationship to reciprocal determination."

1) the authors are “serious” scientists, not fringe people
2) They are using “irreducible complexity” in the same sense as Behe. This is not a case of accidental use of the same phrase to mean something different. Their term “holistic” is another way of saying the same thing, that the system requires all of its parts to work.
3) This “holistic” approach is one that is becoming common in systems biology.

Researchers Suggest Molecular Machine Is Irreducibly Complex

http://www.sciencedaily.com/releases/2014/08/140807154143.htm

"The structure of this biological machine is conceptually similar to an engineer's blueprint, and it explains how each of the parts in this complex assemble into a functional complex that efficiently identifies viral DNA when it enters the cell," Wiedenheft said. "This surveillance machine consists of 12 different parts and each part of the machine has a distinct job. If we're missing one part of the machine, it doesn't work."

That's basically the definition of irreducible complexity right there: all parts are required for it to function.

http://www.evolutionnews.org/2014/08/researchers_sug088761.html



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Irreducible Complexity And The Evolutionary Literature

http://www.trueorigin.org/behe04.php

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10 Darwins Black Box on Fri Jul 24, 2015 6:08 pm

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Darwins Black Box page 40:

So let us attempt to evolve a bicycle into a motorcycle by the gradual accumulation of mutations. Suppose that a factory produced bicycles, but that occasionally there was a mistake in manufacture. Let us further suppose that if the mistake led to an improvement in the bicycle, then the friends and neighbors of the lucky buyer would demand similar bikes, and the factory would retool to make the mutation a permanent feature.
So, like biological mutations, successful mechanical mutations would reproduce and spread. If we are to keep our analogy relevant to biology, however, each change can only be a slight modification, duplication, or rearrangement of a preexisting component, and the change must improve the function of the bicycle. So if the factory mistakenly increased the size of a nut or decreased the diameter of a bolt, or added an extra wheel onto the front axle or left off the rear tire, or put a pedal on the handlebars or added extra spokes, and if any of these slight changes improved the bike ride, then the improvement would immediately be noticed by the buying public and the mutated bikes would, in true Darwinian fashion, dominate the market. Given these conditions, can we evolve a bicycle into a motorcycle? We can move in the right direction by making the seat more comfortable in small steps, the wheels bigger, and even (assuming our customers prefer the «biker» look) imitating the overall shape in various ways. But a motorcycle depends on a source of fuel, and a bicycle has nothing that can be slightly modified to become a gasoline tank. And what part of the bicycle could be duplicated to begin building a motor? Even if a lucky accident brought a lawnmower engine from a neighboring factory into the bicycle factory, the motor would have to be mounted on the bike and be connected in the right way to the drive chain. How could this be done step-by-step from bicycle parts? A factory that made bicycles simply could not produce a motorcycle by natural selection acting on variation—by «numerous, successive, slight modifications»—and in fact there is no example in history of a complex change in a product occurring in this manner.
So far we have examined the question of irreducible complexity as a challenge to step-by-step evolution. But there is another difficulty for Darwin. My previous list of factors that render a mousetrap irreducibly complex was actually much too generous, because almost any device with the five components of a standard mousetrap will nonetheless fail to function. If the base were made out of paper, for example, the trap would fall apart. If the hammer were too heavy, it would break the spring. If the spring were too loose, it would not move the hammer. If the holding bar were too short, it would not reach the catch. If the catch were too large, it would not release at the proper time. A simple list of components of a mousetrap is necessary, but not sufficient, to make a functioning mousetrap.

In order to be a candidate for natural selection a system must have minimal function: the ability to accomplish a task in physically realistic circumstances. A mousetrap made of unsuitable materials would not meet the criterion of minimal function, but even complex machines that do what they are supposed to do may not be of much use. To illustrate, suppose that the world's first outboard motor had been designed and was being marketed. The motor functioned smoothly— burning gasoline at a controlled rate, transmitting the force along an axle, and turning the propeller—but the propeller rotated at only one revolution per hour. This is an impressive technological feat; after all, burning gasoline in a can next to a propeller doesn't turn it at all. Nonetheless, few people would purchase such a machine, because it fails to perform at a level suitable for its purpose.

Performance can be unsuitable for either of two reasons. The first reason is that the machine does not get the job done. A couple fishing in the middle of a lake in a boat with a slow-tuming propeller would not get to the dock: random currents of the water and wind would knock their boat off course. The second reason that performance might be unsuitable is if it is less efficient than can be achieved with simpler means. No one would use an inefficient, outboard motor if they could do just as well or better with a sail.

The «simplest» self-sufficient, replicating cell has the capacity to produce thousands of different proteins and other molecules, at different times and under variable conditions. Synthesis, degradation, energy generation, replication, maintenance of cell architecture, mobility, regulation, repair, communication—all of these functions take place in virtually every cell, and each function itself requires the interaction of numerous parts. Because each cell is such an interwoven meshwork of systems, we would be repeating the mistake of Francis Hitching by asking if multicellular structures could have evolved in step-by-step Darwinian fashion. That would be like asking not whether a bicycle could evolve into a motorcycle, but whether a bicycle factory could evolve into a motorcycle factory!
Evolution does not take place on the factory level; it takes place on the nut-and-bolt level.

The arguments of Dawkins and Hitching fail because they never discuss what is contained in the systems over which they are arguing. Not only is the eye exceedingly complex, but the «light-sensitive spot» with which Dawkins begins his case is itself a multicelled organ, each of whose cells makes the complexity of a motorcycle or television set NUTS AND BOLTS

Mechanical objects can't reproduce and mutate like biological systems, but hypothesizing comparable events at an imaginary factory shows that mutation and reproduction are not the main barriers to evolution of mechanical objects. It is the requirements of the structure-function relationship itself that block Darwinian-style evolution.

if it is the job of one protein to bind specifically to a second protein, then their two shapes must fit each other like a hand in a glove. If there is a positively charged amino acid on the first protein, then the second protein better have a negatively charged amino acid; otherwise, the two will not stick together. If it is the job of a protein to catalyze a chemical reaction, then the shape of the enzyme generally matches the shape of the chemical that is its target. When it binds, the enzyme has amino acids precisely positioned to cause a chemical reaction. If the shape of a wrench or a jigsaw is significantly warped, then the tool doesn't work.

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11 Re: Irreducible complexity is a undeniable fact on Wed Nov 04, 2015 11:16 am

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Problem 3: Step-by-Step Random Mutations Cannot Generate the Genetic Information Needed for Irreducible Complexity 1

Editor's note: This is Part 3 of a 10-part series based upon Casey Luskin's chapter, "The Top Ten Scientific Problems with Biological and Chemical Evolution," in the volume More than Myth, edited by Paul Brown and Robert Stackpole (Chartwell Press, 2014). The full chapter can be found online here. Other individual installments can be found here: Problem 1, Problem 2, Problem 4, Problem 5, Problem 6, Problem 7, Problem 8, Problem 9, Problem 10.
According to evolutionary biologists, once life got started, Darwinian evolution took over and eventually produced the grand diversity we observe today. Under the standard view, a process of random mutation and natural selection built life's vast complexity one small mutational step at a time. All of life's complex features, of course, are thought to be encoded in the DNA of living organisms. Building new features thus requires generating new information in the genetic code of DNA. Can the necessary information be generated in the undirected, step-by-step manner required by Darwin's theory?
Most everyone agrees that Darwinian evolution tends to work well when each small step along an evolutionary pathway provides some survival advantage. Darwin-critic Michael Behe notes that "if only one mutation is needed to confer some ability then Darwinian evolution has little problem finding it."24 However, when multiple mutations must be present simultaneously to gain a functional advantage, Darwinian evolution gets stuck. As Behe explains, "If more than one [mutation] is needed, the probability of getting all the right ones grows exponentially worse."25
Behe, a professor of biochemistry at Lehigh University, coined the term "irreducible complexity" to describe systems which require many parts -- and thus many mutations -- to be present -- all at once -- before providing any survival advantage to the organism. According to Behe, such systems cannot evolve in the step-by-step fashion required by Darwinian evolution. As a result, he maintains that random mutation and unguided natural selection cannot generate the genetic information required to produce irreducibly complex structures. Too many simultaneous mutations would be required -- an event which is highly unlikely to occur.
Observation of this problem is not limited to Darwin-critics. A paper by a prominent evolutionary biologist in the prestigious journal Proceedings of the U.S. National Academy of Science. acknowledges that "simultaneous emergence of all components of a system is implausible."26 Likewise, University of Chicago evolutionary biologist Jerry Coyne -- a staunch defender of Darwinism -- admits that "natural selection cannot build any feature in which intermediate steps do not confer a net benefit on the organism."27 Even Darwin intuitively recognized this problem, as he wrote in Origin of Species:


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.28


Evolutionary scientists like Darwin and Coyne claim they know of no real-world case where Darwinian selection gets blocked in this manner. But they would agree, at least in principle, that there are theoretical limits to what Darwinian evolution can accomplish: If a feature cannot be built by "numerous, successive, slight modifications," and if "intermediate steps do not confer a net benefit on the organism," then Darwinian evolution will "absolutely break down."
The problems are real. Modern biology continues to uncover more and more examples where biological complexity seems to outstrip the information-generative capacity of Darwinian evolution.


Molecular Machines
In his book Darwin's Black Box, Michael Behe discusses molecular machines which require multiple parts to be present before they could function and confer any advantage on the organism. Behe's most famous example is the bacterial flagellum -- a micromolecular rotary-engine, functioning like an outboard motor on bacteria to propel it through liquid medium to find food. In this regard, flagella have a basic design that is highly similar to some motors made by humans containing many parts that are familiar to engineers, including a rotor, a stator, a u-joint, a propeller, a brake, and a clutch. As one molecular biologist writes in the journal Cell, "[m]ore so than other motors, the flagellum resembles a machine designed by a human."29 However the energetic efficiency of these machines outperforms anything produced by humans: the same paper found that the efficiency of the bacterial flagellum "could be ~100%."30
There are various types of flagella, but all use certain basic components. As one paper in Nature Reviews Microbiology acknowledges, "all (bacterial) flagella share a conserved core set of proteins" since "Three modular molecular devices are at the heart of the bacterial flagellum: the rotor-stator that powers flagellar rotation, the chemotaxis apparatus that mediates changes in the direction of motion and the T3SS that mediates export of the axial components of the flagellum."31 As this might suggest, the flagellum is irreducibly complex. Genetic knockout experiments have shown that it fails to assemble or function properly if any one of its approximately 35 genes are missing.32 In this all-or-nothing game, mutations cannot produce the complexity needed to provide a functional flagellar rotary engine one incremental step at a time, and the odds are too daunting for it to assemble in one great leap. Indeed, the aforementionedNature Reviews Microbiology paper admitted that "the flagellar research community has scarcely begun to consider how these systems have evolved."33
Yet the flagellum is just one example of thousands of known molecular machines in biology. One individual research project reported the discovery of over 250 new molecular machines in yeast alone.34 The former president of the U.S. National Academy of Sciences, Bruce Alberts, wrote an article in the journalCell praising the "speed," "elegance," "sophistication," and "highly organized activity" of these "remarkable" and "marvelous" molecular machines. He explained what inspired those words: "Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts."35Biochemists like Behe and others believe that with all of their coordinated interacting parts, many of these machines could not have evolved in a step-by-step Darwinian fashion.
But it's not just multi-part machines which are beyond reach of Darwinian evolution. The protein-parts themselves which build these machines would also require multiple simultaneous mutations in order to arise.


Research Challenges the Darwinian Mechanism
In 2000 and 2004, protein scientist Douglas Axe published experimental research in the Journal of Molecular Biology on mutational sensitivity tests he performed on enzymes in bacteria.36 Enzymes are long chains of amino acids which fold into a specific, stable, three-dimensional shape in order to function. Mutational sensitivity experiments begin by mutating the amino acid sequences of those proteins, and then testing the mutant proteins to determine whether they can still fold into a stable shape, and function properly. Axe's research found that amino acid sequences which yield stable, functional protein folds may be as rare as 1 in 1074 sequences, suggesting that the vast majority of amino acid sequences will not produce stable proteins, and thus could not function in living organisms.
Because of this extreme rarity of functional protein sequences, it would be very difficult for random mutations to take a protein with one type of fold, and evolve it into another, without going through some non-functional stage. Rather than evolving by "numerous, successive, slight modifications," many changes would need to occur simultaneously to "find" the rare and unlikely amino acid sequences that yield functional proteins. To put the matter in perspective, Axe's results suggest that the odds of blind and unguided Darwinian processes producing a functional protein fold are less than the odds of someone closing his eyes and firing an arrow into the Milky Way galaxy, and hitting one pre-selected atom.37
Proteins commonly interact with other molecules through a "hand-in-glove" fit, but these interactions often require multiple amino acids to be 'just right' before they occur. In 2004, Behe, along with University of Pittsburgh physicist David Snoke, simulated the Darwinian evolution of such protein-protein interactions. Behe and Snoke's calculations found that for multicellular organisms, evolving a simple protein-protein interaction which required two or more mutations in order to function would probably require more organisms and generations than would be available over the entire history of the Earth. They concluded that "the mechanism of gene duplication and point mutation alone would be ineffective...because few multicellular species reach the required population sizes."38
Four years later during an attempt to refute Behe's arguments, Cornell biologists Rick Durrett and Deena Schmidt ended up begrudgingly confirming he was basically correct. After calculating the likelihood of two simultaneous mutations arising via Darwinian evolution in a population of humans, they found that such an event "would take > 100 million years." Given that humans diverged from their supposed common ancestor with chimpanzees only 6 million years ago, they granted that such mutational events are "very unlikely to occur on a reasonable timescale."39
Now a defender of Darwinism might reply that these calculations measured the power of the Darwinian mechanism only within multicellular organisms where it is less efficient because these more complex organisms have smaller population sizes and longer generation times than single-celled prokaryotic organisms like bacteria. Darwinian evolution, the Darwinian notes, might have a better shot when operating in organisms like bacteria, which reproduce more rapidly and have much larger population sizes. Scientists skeptical of Darwinian evolution are aware of this objection, and have found that even within more-quickly evolving organisms like bacteria, Darwinian evolution faces great limits.
In 2010, Douglas Axe published evidence indicating that despite high mutation rates and generous assumptions favoring a Darwinian process, molecular adaptations requiring more than six mutations before yielding any advantage would be extremely unlikely to arise in the history of the Earth.
The following year, Axe published research with developmental biologist Ann Gauger regarding experiments to convert one bacterial enzyme into another closely related enzyme -- the kind of conversion that evolutionists claim can easily happen. For this case they found that the conversion would require a minimum of at least seven simultaneous changes,40 exceeding the six-mutation-limit which Axe had previously established as a boundary of what Darwinian evolution is likely to accomplish in bacteria. Because this conversion is thought to be relatively simple, it suggests that more complex biological features would require more than six simultaneous mutations to give some new functional advantage.
In other experiments led by Gauger and biologist Ralph Seelke of the University of Wisconsin, Superior, their research team broke a gene in the bacterium E. colirequired for synthesizing the amino acid tryptophan. When the bacteria's genome was broken in just one place, random mutations were capable of "fixing" the gene. But even when only two mutations were required to restore function, Darwinian evolutionseemed to get stuck, with an inability to regain full function.41
These kind of results consistently suggest that the information required for proteins and enzymes to function is too great to be generated by Darwinian processes on any reasonable evolutionary timescale.


Darwin Skeptics Abound
Drs. Axe, Gauger, and Seelke are by no means the only scientists to observe the rarity of amino acid sequences that yield functional proteins. A leading college-level biology textbook states that "even a slight change in primary structure can affect a protein's conformation and ability to function."42 Likewise, evolutionary biologist David S. Goodsell writes:


[O]nly a small fraction of the possible combinations of amino acids will fold spontaneously into a stable structure. If you make a protein with a random sequence of amino acids, chances are that it will only form a gooey tangle when placed in water.43


Goodsell goes on to assert that "cells have perfected the sequences of amino acids over many years of evolutionary selection." But if functional protein sequences are rare, then it is likely that natural selection will be unable to take proteins from one functional genetic sequence to another without getting stuck in some maladaptive or non-beneficial intermediate stage.
The late biologist Lynn Margulis, a well-respected member of the National Academy of Sciences until her death in 2011, once said "new mutations don't create new species; they create offspring that are impaired."44 She further explained in a 2011 interview:


[N]eo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change-led to new species. I believed it until I looked for evidence.45


Similarly, past president of the French Academy of Sciences, Pierre-Paul Grasse, contended that "[m]utations have a very limited 'constructive capacity'" because "[n]o matter how numerous they may be, mutations do not produce any kind of evolution."46
Many other scientists feel this way. Over 800 Ph.D. scientists have signed a statement agreeing they "are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life."47 Indeed, two biologists wrote in Annual Review of Genomics and Human Genetics: "it remains a mystery how the undirected process of mutation, combined with natural selection, has resulted in the creation of thousands of new proteins with extraordinarily diverse and well optimized functions. This problem is particularly acute for tightly integrated molecular systems that consist of many interacting parts..."48 Perhaps it would be less mysterious if the theoretical conceptions could be expanded beyond unguided evolutionary mechanisms like random mutation and natural selection to explain the origin of complex biological features.




References Cited:
[24.] See Michael Behe, "Is There an 'Edge' to Evolution?" athttp://www.faithandevolution.org/debates/is-there-an-edge-to-evolution.php
[25.] Ibid.
[26.] Michael Lynch, "Evolutionary layering and the limits to cellular perfection,"Proceedings of the U.S. National Academy of Sciences,www.pnas.org/cgi/doi/10.1073/pnas.1216130109 (2012).
[27.] Jerry Coyne, "The Great Mutator (Review of The Edge of Evolution, by Michael J. Behe)," The New Republic, pp. 38-44, 39 (June 18, 2007).
[28.] Charles Darwin, Origin of Species (1859), Chapter 6, available athttp://www.literature.org/authors/darwin-charles/the-origin-of-species/chapter-06.html
[29.] David J. DeRosier, "The turn of the screw: The bacterial flagellar motor,"Cell, 93: 17-20 (1998).
[30.] Ibid.
[31.] Mark Pallen and Nicholas Matzke, "From The Origin of Species to the Origin of Bacterial Flagella," Nature Reviews Microbiology, 4:788 (2006).
[32.] These experiments have been done on flagella in E. coli and S. typhimurium. See Transcript of Testimony of Scott Minnich, pp. 103-112, Kitzmiller et al. v. Dover Area School Board, No. 4:04-CV-2688 (M.D. Pa., Nov. 3, 2005). Other experimental studies have identified over 30 proteins necessary to form flagella. See Table 1. in Robert M. Macnab, "Flagella," in Escheria Coli and Salmonella Typhimurium: Cellular and Molecular Biology Vol 1, pp. 73-74, Frederick C. Neidhart, John L. Ingraham, K. Brooks Low, Boris Magasanik, Moselio Schaechter, and H. Edwin Umbarger, eds., (Washington D.C.: American Society for Microbiology, 1987).
[33.] Mark Pallen and Nicholas Matzke, "From The Origin of Species to the Origin of Bacterial Flagella," Nature Reviews Microbiology, 4:788 (2006).
[34.] See "The Closest Look Ever at the Cell's Machines," ScienceDaily.com (January 24, 2006), athttp://www.sciencedaily.com/releases/2006/01/060123121832.htm
[35.] Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, 92:291 (February 6, 1998).
[36.] Douglas D. Axe, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds," Journal of Molecular Biology, 341: 1295-1315 (2004); Douglas D. Axe, "Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors," Journal of Molecular Biology, 301: 585-595 (2000).
[37.] See Stephen C. Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design, p. 211 (Harper One, 2009).
[38.] Michael Behe and David Snoke, "Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues," Protein Science, 13: 2651-2664 (2004).
[39.] Rick Durrett and Deena Schmidt, "Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution," Genetics, 180:1501-1509 (2008). For a more detailed discussion of this argument, see Ann Gauger, Douglas Axe, Casey Luskin, Science and Human Origins (Discovery Institute Press, 2012).
[40.] Ann Gauger and Douglas Axe, "The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway," BIO-Complexity, 2011 (1): 1-17.
[41.] Ann Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke, "Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness," BIO-Complexity, 2010 (2): 1-9.
[42.] Neil A. Campbell and Jane B. Reece, Biology, p. 84 (7th ed., 2005).
[43.] David S. Goodsell, The Machinery of Life, pp. 17, 19 (2nd ed., Springer, 2009).
[44.] Lynn Margulis, quoted in Darry Madden, UMass Scientist to Lead Debate on Evolutionary Theory, Brattleboro (Vt.) Reformer (February 3, 2006).
[45.] Lynn Margulis quoted in "Lynn Margulis: Q + A," Discover Magazine, p. 68 (April, 2011).
[46.] Pierre-Paul Grassé, Evolution of Living Organisms: Evidence for a New Theory of Transformation (Academic Press: New York NY, 1977).
[47.] See "A Scientific Dissent from Darwinism" athttp://www.dissentfromdarwin.org/
[48.] Joseph W. Thornton and Rob DeSalle, "Gene Family Evolution and Homology: Genomics Meets Phylogenetics," Annual Review of Genomics and Human Genetics, 1:41-73 (2000).

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What good is a one cylinder motor for without a piston ?
What good is a piston for, if not used fully mounted in the cylinder with the right size to fit and interconnected, to fullfill its task ? Ok. You could use it as a Ashtray. But for that, you would not need to produce it highly specified with piston rings, connecting rod etc. 
What good is a production line of pistons for, if the end product, the piston, has no place to be employd ?
What good is a transport system for, if there is no place to deliver the goods , and a communication system to direct them to the right place ?

Now lets apply that to biology.  

Biological systems are  functionally organised , integrated in a interdependent network, and  complex,  like human made machines and factories. The wiring of a electrical device equals to metabolic pathways. A minimal metabolic network is required in every cell, and must have emerged prior life began. For the assembly of a biological system of multiple parts, not only  the origin of the genome information to produce all subunits and assembly cofactors must be explained, but also parts availability ( The right materials must be transported to the building site. Often these materials in their raw form are unusable. Other complex machines come into play to transform the raw materials into usable form.  All this requires specific information. )  synchronization, ( these parts must be read at hand at the building site )  manufacturing and assembly coordination ( which required the information of how to assemble each single part correctly, at the right place, at the right moment, and in the right position ) , and interface compatibility ( the parts must fit together correctly, like lock and key ) . Unless the origin of all these steps are properly explained, functional complexity as existing in biological systems has not been adressed adequatedely.

The immense challenge to unguided, random mechanisms becomes even more evidence, once you remove the delusional crutches of evolution, and look into the origin of the first self-replicating cell. The solutions to overcome problems like DNA replication errors or damage must all be pre-programmed, and the repair "working horses" to resolve the problem must be ready in place and "know" what to do how, and when, and able to compare between what is right, and what is in error.  If a roboter in a factory assembly line fails, employees are ready to detect the error and make the repair . In the cell, the mal function of any  part even as tiny and irrelevant as it might seem, can be fatal, and if the repair mechanisms are not functioning correctly and fully in place right from the start, the repair can't be done, and life ceases.  These repair enzymes which cleave, join, add, replace etc. must be programmed in order to function properly right from the start. Aberrantly processed pre-tRNAs for example are eliminated through a nuclear surveillance pathway by degradation of their 3′ ends, whereas mature tRNAs lacking modifications are degraded from their 5′ends in the cytosol.

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