Irreducible Complexity: The existence of irreducible interdependent structures in biology is an undeniable fact

Irreducible Complexity: The existence of irreducible interdependent structures in biology is an undeniable fact

https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact#2133

Functional parts are only meaningful within a whole, in other words, it is the whole that gives meaning to its parts. This recursive dependency really seals off the system from deterministic bottom-up causation. The top-down causation constitutes an irreducible structure.
https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.171&rep=rep1&type=pdf

The whole is more than the sum of the parts. Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.  Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overarching design goal.
A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution. 

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 as factories ( cells ) or machines ( cells host a big number of the most various molecular machines and equal to factory 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 their excitation energy by Förster resonance energy transfer 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? That's as if genetic mutations and natural selection had enough probability to generate interdependent individual parts being able to perform new functions while the individual would have no function unless interconnected.

A list of irreducibly complex systems
https://reasonandscience.catsboard.com/t2166-a-list-of-irreducible-complex-systems

Catch22, chicken and egg problems in biology and biochemistry
https://reasonandscience.catsboard.com/t2059-catch22-chicken-and-egg-problems-in-biology-and-biochemistry

Syllogisms about irreducible complexity
https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact#8349

Co-option: Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions
Scientific articles that argue directly or indirectly for intelligent design, and irreducible complexity
The cell is irreducibly complex
Does the Mullerian two step proposal refute irreducible complexity ?

Behe, Darwin's Black Box, page 39: 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 parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution.

An irreducibly complex system is characterized by five points:
1. a single system composed of several well-matched, interacting parts
2. that contribute to the basic function
3. the removal of any one of the parts causes the system to effectively cease functioning
4. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system
5. any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.

To No.3
The principle of evolutionary continuity, succinctly formulated by Albert Lehninger in his Biochemistry textbook. An adaptation that does not increase the fitness is no longer selected for and eventually gets lost in the evolution (in the current view, only those adaptations that effectively decrease the fitness end up getting lost). Hence, any evolutionary scenario has to invoke – at each and every step – only such intermediate states that are functionally useful (or at least not harmful).
https://onlinelibrary.wiley.com/doi/abs/10.1002/cbdv.200790167

A. G. CAIRNS-SMITH Seven clues to the origin of life, page 49:
We may make a machine by first designing it, then drawing up  a list of components that will be needed, then acquiring the components, and then building the machine. But that can never be the way that evolution works. It has no plan. It has no view of the finished system. It would not know in advance which pieces would be relevant. Even if amino acids (for example) had been in a 'probiotic soup', what use would they have been, long before their key use now (to make protein) had been hit on? It is the whole machine that makes sense of its components. Point two. Subsystems are highly INTERLOCKED within the universal system. For example, proteins are needed to make catalysts, yet catalysts are needed to make proteins. Nucleic acids are needed to make proteins, yet proteins are needed to make nucleic acids. Proteins and lipids are needed to make membranes, yet membranes are needed to provide protection for all the chemical processes going on in a cell. It goes on and on. The manufacturing procedures for key small molecules are highly interdependent: again and again this has to be made before that can be made - but that had to be there already. The whole is presupposed by all the parts. The interlocking is tight and critical. At the centre everything depends on everything. There are then four subsidiary points.
a)It is no surprise that our central biochemical machinery is now so conservative: when everything depends on everything it is difficult for anything to be changed.
b)Such a multiple interlocking of functions could only have been a product of evolution.
My comment: No!! Such a multiple interlocking of functions could only have been a product of intelligent design!!
c)This strong dependence of subsystems on each other is understandable as an evolutionary product in that it is typical of efficient pieces of machinery. A motor car, a clock, a television set, an oboe, a refrigerator, a tennis racquet . . . think of almost any sophisticated piece of engineering and you will find more or less diverse components, of little use by themselves, working in collaboration.
My comment:  Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. A piston has no use by its own. But only, when working inside a gasoline engine. A flagellar filament structural protein has no use by its own unless inserted and conjoined with all other proteins to form the flagella filament proteins In the same sense, as an engineer would not project, invent, create and make a blueprint of a piston with no use by its own, but only conjoined, and together with all other parts while projecting a whole engine, envisioning its end function and use, its evident that evolution without foresight would not come up with an intermediate biosynthesis products which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system. And evolution would also not produce the information for the assemblage of tiny molecular machines, enzymatic structures with unique contours, which also bear no function by their own, but only when inserted in cellular structures with higher ends, being essential for cells to self-replicate, and perpetuate life.
d) Less clear is how a gradual step-by-step evolution can lead to a system in which everything depends on everything.
My comment: Funny that Cairns-Smith proposes that such systems could only have been a product of evolution, to then, on the other hand, admit that is was less clear is how a gradual step-by-step evolution can lead to a system in which everything depends on everything. Well, it cannot. By experience, we know only of intelligence with forsesight that can instantiate such complex interlocked systems.

Behe et al provided a few examples, which have been popularized through ID literature. But it stretches through ALL natural systems, and on different system levels, to name :

Cosmology: Interdependence of the universe, with our milky way galaxy, solar system - sun - planets - sun - moon
Planet earth: Land - water - volcanoes - plate tectonics - earthquakes
Energy cycles on earth: water cycle, carbon cycle, nitrogen cycle, Phosphorus, Iron, and Trace Mineral cycles
Biology : Organism level - organ level - tissue level - cell level - molecular level

Imagine a production line in a factory. Many robots there are lined up, and raw materials are fed into the production line. The materials arrive at Robot one. It processes the first step. Then, when ready, the product moves on and is handed over to the next Robot. Next processing step. And that procedure repeats 17 times. In the end, there is a fully formed subpart, as the door of a car. That door is part of a larger object, like the finished car. That door by its own has no use unless mounted at the right place in the car.  Nobody would project a car door without visualizing the higher end upfront, in the project and development stage, and based on the requirement, specify the complex shape of the door which precisely will fit the whole of the chassis of the car where it will be mounted. And the whole production line and each robot the right placement and sequence where each robot will be placed must be planned and implemented as well. Everything has to be projected with a higher end goal in mind. And there is an interdependence. If one of the robots ceases to work for some reason, the whole fabrication ceases, and the completion of the finished car cannot be accomplished. That means, a tiny mal connection of one of the robots in the production line of the door might stop the production of the door, and the finished car cannot be produced.

- No glycine amino acids, no pyrimidines, no DNA - no life.
- No Watson Crick base pair fine-tuning, no DNA - no life.
- No topoisomerase II or helicase proteins, no DNA replication - no life perpetuation.
- No peripheral stalk, a subunit in ATP synthase nano turbines, no energy supply through ATP for biological cells, no advanced life.
- No cleavage of tRNA during its biosynthesis, tRNA's will not be useful for the cell, no life.
- No nitrogenase enzymes to fix nitrogen in an energy-demanding, triple bond-breaking process, no ammonia, required to make amino acids - no nitrogen cycle - no advanced life.
- No chlorophylls, no absorption of light to start photosynthesis, no starch and glucose - cells will have no food supply to sustain complex organisms - no advanced life on earth.
- No water evolving complex in photosynthesis, no oxygen, no advanced life.
- No carotenoids quenching heat in chlorophylls in the antenna complex, the surrounding membrane would be burned - no advanced life.  
- No rubisco, no fix of CO2, no hydrocarbons - no advanced life.
- No counterion in retinal, and rhodopsin could not receive visible light - and there would be no vision on earth by any organism.

This is just a small example - there are many others. The salient part is - in the same manner, as a robot has no function by itself and by its own, and outside of a factory, unless placed at the right production line, getting the right substrate from another robot, processing it in the right manner, and handing it over to the next processing step - which also has to have its right function and manufacturing proceeding pre-programmed- nothing done.

DNA is transcribed to RNA which is translated to Proteins.  But proteins are required to make DNA and RNA. This creates an endless loop, which is only solved when we posit that all three were created at the same time. ...

https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact




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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 parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution

If the basic function is not kept, or if parts of the proteins are used for other functions, that does not refute the argument. 

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/)

https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact

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Alone, and individually, each of the 17 enzymes that synthesize Chlorophyll can do nothing. But together, lined up like in a factory production line, they process the intermediate substrates, hand it over to the next, and the next, 17 manufacturing steps, one enzyme machine fine-tuned to produce the substrate, which the next enzyme can process, that in the end, makes the chlorophyll molecule, the most abundant organic compound found on earth, in bacteria, plants, algae, diatoms, plankton, corals and, oxygenating the oceans, make abundant marine life possible.

Chlorophyll by its own can do nothing. But together with many other Chlorophylls in the antenna complex, it can transfer, when energized to a higher energy state through photons, its resulting high-energy electron state to its adjacent Chlorophyll, and so down to the reaction center, and energize the P680 special Chlorophyll pair, and start the electron chain. But the lineup and order of these Chlorophylls cannot be just so. It must be just right. Each Chlorophyll must have the right distance, one from the other, to produce the energy transfer. And what an energy transfer that is - it's an engineering marvel !! It's almost 100% efficient, and done by quantum mechanical Förster resonance energy transfer principles !!! The stupendous ingeniosity cannot be enough outlined.... Human-made solar panels, in comparison, have just 20% efficiency...

The reaction center IMHO cannot operate and release an electron, if it does not find its replacement - which the oxygen-evolving complex provides.
If the oxygen-evolving complex would be not there, no oxygen would be released into the atmosphere and no respiration could occur, and no advanced life exist !!
Chlorophyll by its own in the antenna complex, will produce triplet states and burn the membrane where they are embedded. But Carotenoid chromophores do join them, and prevent triplet states to occur - they quench the solar energy when too strong, and release it as heath.

Yup, No Carotenoids, and you would probably not be here to read my lines. To make Carotenoids, it is another extremely complex biosynthesis process, but that's another story....

Not only does oxygenic photosynthesis provide the oxygen needed for life, but also Carbon, the basic building blocks of life. How ? Virtually all the organic carbon on earth derives ultimately from the carbon dioxide in the air that Rubisco, a protein working in the dark reactions of photosynthesis,  fixes from the atmosphere. Without it, advanced life would not be possible.  The unfinished subunits of Rubisco require co and post-translational modifications, specific proteins that help like assembly robots in the manufacturing process, sophisticated pathways, and mechanisms of protein import and targeting in chloroplasts through large multiprotein translocon complexes in the stroma, and advanced protein communication and information systems. All this is of bewildering complexity, where dozens of individual interconnected and finely tuned parts are required, a web of interlocked extremely complex advanced molecular machines where if one is missing, nothing goes. The right folding of proteins is just one of several other essential processes in order to get a functional protein. But a functional protein by its own has no function unless correctly embedded through the right assembly sequence and order at the right functional place." that's precisely the problem of evolution. there is no foresight. So why would evolution produce an assembly chaperone enzyme to make rubisco? You don't make a robot for an assembly line if the end product is not known.

Each of the over 27 protein complexes in photosynthesis cannot do anything on their own, but inserted in the whole pathway, it will produce carbohydrates, the food for all advanced life forms.

Gods truth: everything was created in a short period of time, fully developed and functional, physical reality able to begin to interact on all system levels right from the start: Like turning the key of a fully made car on, and the engine turns on, and starts to do its job.

The devils lie: everything began by no agency at all, step by step, slowly slowly, one step of complexity building over the other, information appearing by random unguided processes, like chemicals inventing a language, and write an instructional blueprint to make the most complex self-replicating factory in the universe, chemicals interacting randomly, and nature permitting what succeeds to pass through and build up slowly, to produce consciousness, beauty, intelligence, morality, and intrinsic values of life.

We can never underestimate how a subtle lie, repeated enough times, by enough people, specially propagated by authority, makes its way through to be popularized, accepted and believed as unquestionable truth, and hard to be eradicated.

Once a lie has settled in one's mind, that person becomes accustomed to rely on that lie in its whole thinking process, and questioning it requires mental energy. But mental energy and thinking is expensive and requires concentration and efforts -its required to get out of a comfort zone - and since a life without God pleases the flesh - let's keep the intruder out of the door - change not required - so they think. And so the self-delusion perpetuates, and many see the urgent need to come to FB and expose their ultracrepidarianism.

Interdependence and irreducible structures in nature are the most fundamental principles in life


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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 ready 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."


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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)


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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:

https://reasonandscience.catsboard.com/t2115-the-best-of-darwins-black-box#3760





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

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
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:



1. http://iose-gen.blogspot.com.br/20

The paradoxical urinary concentrating mechanism

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

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/

Koonin, the logic of chance, page 376
Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage, is extremely difficult even within a speculative scheme let alone experimentally.

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.



Man-made machines vs molecular machines 

A machine is organized, given that the operation of each part is dependent on it being properly arranged with respect to every other part, and to the system as a whole. Organisms, unlike machines, are not only organized but are also self-organizing and self-regenerating systems.  Organisms are intrinsically purposive because they have an autonomous self: the phenomena of self-formation, self-preservation, self-reproduction, and self-restitution are all characteristic of the internal organizational dynamics of living systems. 

Conversely, machines are extrinsically purposive because they lack an autonomous self: their causal means of production reside outside of themselves, demanding outside intervention not just for their construction and assembly but also for their maintenance. For the sustained operation of a machine, an external agent is required to determine when defective components need to be repaired or replaced, and to carry them out in a timely fashion. In an organism, all of these processes are carried out from within. Confronted with a machine, one is justified in inferring the existence of an external creator responsible for producing it in accordance with a preconceived plan or design. Confronted with an organism, one is not.

The distinction between intrinsic and extrinsic forms of purposiveness also helps explain another crucial dissimilarity between organisms and machines, namely that the attribution of functions has a different basis and a different significance in these two kinds of systems.  Machines have functions, organisms do not. It is only the parts (or traits) of organisms that have functions. In machines, both parts and wholes can be ascribed functions in the same sense. The reason for this is that the attribution of a function to a particular entity is enabled by the fact that the beneficiary of its operation is an external agent. A machine has a function because its operation is good for something; that is, it is designed to operate in ways that serve the ends of its maker or user. An organism does not have a function because its operation is not good for anything; it simply acts to ensure its continued existence.
http://sci-hub.ren/https://www.sciencedirect.com/science/article/pii/S1369848613000824?fbclid=IwAR1J9AeZa6Dr5hD3qDU8m4OUJfPzE4BENS_yuD-jeOgucAwhOBsGcXI_avA

My comment: An important distinction is that the implementation of self-replication, self-regulation, self-adaptation, homeostasis, is by a significant magnitude of higher complexity than machines that need continuous maintenance from an outside source, and has to be pre-programmed from the beginning.

But there IS a purpose of the living:
In Psalm 104:31, the psalmist declared, “Let the Lord be glad in his works.”

The highest degree of manufacturing  performance, excellence, precision, energy efficiency, adaptability to external change, economy, refinement and intelligence of production automatization ( at a scale from 1 -100,  = 100 )  we find in proceedings adopted by  each cell,  analogous to a factory , and biosynthesis pathways and processes in biology.  A cell uses a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. In this maze of pathways, there are many branch points where different enzymes compete for the same substrate. The system is so complex that elaborate controls are required to regulate when and how rapidly each reaction occurs. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme.
https://reasonandscience.catsboard.com/t1987-information-biosynthesis-analogy-with-human-programming-engeneering-and-factory-robotic-assembly-lines




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.




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.

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

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

https://reasonandscience.catsboard.com/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.

Dembski 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.

https://reasonandscience.catsboard.com/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.

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;

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

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.

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.

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?

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

Irreducible Complexity And The Evolutionary Literature

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

Darwins Black Box page 40:

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.

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).

1) http://www.evolutionnews.org/2015/01/problem_3_rando091121.html

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.

A  life hosting universe is a gigantic irreducible  and interdependent structure

http://reasonandscience.heavenforum.org/t1468-irreducible-complexity-is-a-undeniable-fact#5767

1. There are many systems and parts in biology, that can be named, that require to be integrated to work. They work interdependently, only in a joint venture, and can be classified as irreducibly complex. A few examples are:
No glycine amino acids, no pyrimidines, no DNA - no life. No Watson Crick base pair fine-tuning, no DNA - no life. No Topoisomerase II or helicase proteins, no DNA replication - no life perpetuation. No peripheral stalk, a subunit in ATP synthase Nano turbines, no energy supply trough ATP for biological cells, no advanced life. No cleavage of tRNA during its biosynthesis, tRNA's will not be useful for the cell, no life. No Nitrogenase enzymes to fix nitrogen in an energy demanding, triple bond breaking process, no ammonia, required to make amino acids - no nitrogen cycle - no advanced life. No chlorophyll, no absorption of light to start photosynthesis, no starch and glucose - cells will have no food supply to sustain complex organisms - no advanced life on earth. No water evolving complex in photosynthesis, no oxygen, no advanced life. No carotenoids quenching heat in chlorophyll in the antenna complex, the surrounding membrane would be burned - no advanced life.   No Rubisco, no fix of CO2, no hydrocarbons - no advanced life. No counterion in retinal, and Rhodopsin could not receive visible light - and there would be no vision on earth by any organism.
2. It's like to have a gigantic jigsaw puzzle of millions of pieces that trigger a knob. If not ALL puzzle pieces are brought together to complete it, the knob does not switch, and light does not turn on. None of the above-mentioned proteins has any function if not interconnected and inserted at the right place like a sub-part in a machine or production line. In the same manner, as a robot has no function by itself and by its own, and outside a factory, unless placed at the right production line, getting the right substrate from another robot, processing it in the right manner, and handing it over to the next processing step - which also has to have its right function and manufacturing proceeding pre-programmed- nothing is done and achieved. Often, if in a production line, just one robot goes havoc, the entire production lines stop to function. If you have a fully working car, but lose the key, you cannot turn it on, and it will not start. Sometimes, a tiny cable goes oxidized, or breaks and the car stop to function.  
3. Life is an unimaginable balancing act, beginning with the setup of physical laws upon which the properties and operation of the physical universe depends, fine-tuning of the universe, the fundamental forces, our galaxy, the earth and its life-permitting conditions, but, if helicase, just ONE protein that unwinds DNA, is not here, our universe would be lifeless.
4. This is evidence of planned design by a powerful creator, that knows how, and not a lifeless magic trick blindly believed by so many atheists.

The Defining Concept of Biochemistry Is “Molecular Recognition Through Structural Complementarity”

http://reasonandscience.heavenforum.org/t2062-proteins-how-they-provide-striking-evidence-of-design#5818

Reginald H. Garrett, Biochemistry, 6th edition :
Structural complementarity is the means of recognition in biomolecular interactions. The complicated and highly organized patterns of life depend on the ability of biomolecules to recognize and interact with one another in very specific ways. Such interactions are fundamental to metabolism, growth, replication, and other vital processes. The interaction of one molecule with another, a protein with a metabolite, for example, can be most precise if the structure of one is complementary to the structure of the other, as in two connecting pieces of a puzzle or, in the more popular analogy for macromolecules and their b ligands, a lock and its key.

This principle of structural complementarity is the very essence of biomolecular recognition. Structural complementarity is the significant clue to understanding the functional properties of biological systems. Biological systems, from the macromolecular level to the cellular level, operate via specific molecular recognition mechanisms based on structural complementarity: A protein recognizes its specific metabolite, an antibody recognizes its antigen, a strand of DNA recognizes its complementary strand, sperm recognize an egg. All these interactions involve structural complementarity between molecules.

My comment:
It's remarkable how the author does not avoid teleology in his vocabulary. Recognizing something depends on volition, which biomolecules definitively lack.

The principle of structural complementation extends in ALL molecular biology and is a core reason why the origin of proteins based on non-intelligent causal mechanisms is far too unspecific, besides being the very core of Behe's argument of irreducible complexity: Most proteins depend on multiple interlocked and interdependent subunits, structurally and by form fine-tuned and adapted to each other, which work in a coordinated manner together, provoking conformational changes and a vast array of different reactions. One subunit has no function in absence of the other, in the same manner as a lock has no function without the key. Recognition of the other subunit(s) must be pre-visualized, thought of, invented, and implemented accordingly. And that all depends on intelligence......

When secular science papers confirm irreducible complexity, but don't know it.....

How Structure Arose in the Primordial Soup

Primitive organisms began to split into the different branches that make up the tree of life. In between those two seminal events, some of the greatest innovations in existence emerged: the cell, the genetic code and an energy system to fuel it all. ALL THREE of these are ESSENTIAL to life as we know it, yet scientists know disappointingly little about how any of these remarkable biological innovations came about.

https://www.scientificamerican.com/article/how-structure-arose-in-the-primordial-soup/

Scientific articles that argue directly or indirectly for intelligent design, and irreducible complexity

http://reasonandscience.heavenforum.org/t1498-scientific-articles-that-argue-directly-or-indirectly-for-intelligent-design-and-irreducible-complexity

“The process of photosynthesis is a very complex set of INTERDEPENDENT metabolic pathways “How it could have evolved is a bit mysterious.”
Robert Blankenship, professor of biochemistry at Arizona State University

Interdependency and phosphorylation of KIF4 and condensin I are essential for organization of chromosome scaffold
17 Aug 2017
Kinesin family member 4 (KIF4) and condensins I and II are essential chromosomal proteins for chromosome organization by locating primarily to the chromosome scaffold. However, the mechanism of how KIF4 and condensins localize to the chromosome scaffold is poorly understood. Here, we demonstrate a close relationship between the chromosome localization of KIF4 and condensin I, but not condensin II, and show that KIF4 and condensin I assist each other for stable scaffold formation by forming a stable complex. Moreover, phosphorylation of KIF4 and condensin I by Aurora B and polo-like kinase 1 (Plk1) is important for KIF4 and condensin I localization to the chromosome. Aurora B activity facilitates the targeting of KIF4 and condensin I to the chromosome, whereas Plk1 activity promotes the dissociation of these proteins from the chromosome. Thus, the interdependency between KIF4 and condensin I, and their phosphorylation states play important roles in chromosome scaffold organization during mitosis.

In this study, we further examined the interdependency of KIF4 and other scaffold proteins in chromosome organization. The results reveal that KIF4 localization to the chromosome scaffold is regulated interdependently with condensin I. The results indicate an interdependency of localization of KIF4 and condensin I on the chromosome scaffold.

It has been shown that condensin I loading to the chromosome is largely regulated by Aurora B [22–25]. This modification of condensin I is found to be conserved from yeast to humans [25]. Interdependency and physical interaction between KIF4 and condensin I for their chromosome localization raise the question whether KIF4 is regulated by Aurora B. In this study, interdependency and physical interaction between KIF4 and condensin I for localization to the chromosome were revealed. These results suggest that the interaction between KIF4 and condensin I may assist both proteins to bind and organize stably to the chromosome scaffold.

What might be a Cell’s minimal requirement of parts ?  
https://reasonandscience.catsboard.com/t2110-what-might-be-a-protocells-minimal-requirement-of-parts

Biological organisation demonstrates that low-level functions support top-level function

On the lowest level are compartments that produce the basic building blocks of life, RNA and DNA, carbohydrates, and fatty acids, which we can call subcomponents. These support the top-level function. This forms a
complete interdependent unity, where the overarching function depends on the production of the basic building blocks on the lowest end, which is assembled into proteins, co-factors, holo-enzymes, assembly lines, organelles, and last not least, functional cells.


Picture from Undeniable, Douglas Axe, page  78

The hierarchical structure characterizes the relationships between parts. In this scheme, the parts at intermediate levels (between the elementary constituents and the functional whole) are referred to as components. The number of intermediate levels and components depends both on the complexity of the whole.  Fact is that the subparts or elements must perform their functions in the correct manner, in order for the whole thing its large function. There is an interdependence between the lowest level and the top level. If one of the lower elements is missing or does not work properly, global mal-function is the consequence or no function at all. For example:

- No glycine amino acids, no pyrimidines, no DNA - no life.
- No Watson Crick base pair fine-tuning, no DNA - no life.
- No topoisomerase II or helicase proteins, no DNA replication - no life perpetuation.
- No peripheral stalk, a subunit in ATP synthase nano turbines, no energy supply trough ATP for biological cells, no advanced life.
- No cleavage of tRNA during its biosynthesis, tRNA's will not be useful for the cell, no life. 
- No nitrogenase enzymes to fix nitrogen in an energy demanding, triple bond breaking process, no ammonia, required to make amino acids - no nitrogen cycle - no advanced life.

Life is organized in a hierarchical way of sub-elements and parts which contribute in an interlocked, interdependent manner to promote  a final function 
, and each part contributing in a coordinated way to the whole is essential and irreducible. 

Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.
In other words: Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system?  
A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.


The setup of hierarchical levels of organization, where the function and proper set up of the higher level depends on the lower level, has always been observed to be due to intelligent planning, setup, and design. The same is true for the setup of wiring diagrams in an electrical engineering blueprint or a schematic of an integrated circuit. The genomic program of development demonstrates a multilayered, hierarchical,network-like architecture based on nodes and modules, orchestrating a specific pattern of gene expression. The fundamental role of upper-level Gene regulatory networks is to set up in embryonic space a progressive series of regulatory states, which functionally define first the regions of the body with respect to its axes; then the location of the progenitor fields of the body parts; then the subparts of each body part. Each dGRN module is controlled to be expressed at the right time, and as such, little if no variation is possible. It constitutes an interlocked system. GRNs are logic maps that constrain, orient and direct in detail each module in the lower hierarchy level so that a given gene is expressed at a given time and place. The tight functional constraints under which these systems of dGRNs operate result in catastrophic consequences if altered by mutation and selection mechanisms.

The setup of distant specific goals is always something done by intelligence ( teleology ). Modern biological sciences try to avoid teleology at all cost ( Not an easy task - and often not successfully )

Molecules, basic building blocks of life, proteins, cell compartments, organelles, and organs have often ONLY and EXCLUSIVELY function when employed as a part and ingredient in a complex organizational biological system. But that functional complexity is only achieved by building up lower levels of complexity, which contributes to that higher overarching order and purpose. Therefore, their origin cannot be explained by gradual Darwinian evolution, which depends on slow improvement and positive functionality and fitness on each evolutionary step over a long period of time.

Some reasons why life is an all or nothing process

Availability of some of the basic building blocks for life
Each of the following global energy Cycles are essential for advanced life on earth: the Water Cycle, Carbon Cycle, Nitrogen Cycle, Global Carbon Cycle, Phosphorus, Iron, and Trace Mineral cycles. They are also interdependent with each other. Which came first?

Nitrogen is essential for the make of nucleic acids and proteins—the two most important building blocks of life. The availability of nitrogen in the form of ammonia which microorganisms can uptake,  to produce DNA and amino acids, depends on the nitrogen cycle. But the nitrogen cycle depends on cooperating microorganisms, operating in a coordinated manner, which promotes a fine ecological cycle balance. These microorganisms could not emerge without DNA and nucleic acids.
What emerged first: DNA and nucleic acids to make these microorganisms, essential for the nitrogen cycle, or the Nitrogen cycle, essential for the production of these building blocks, making the origin of micro-organisms possible?
 
The carbon dioxide level in the atmosphere must be just right: If greater: runaway greenhouse effect would develop.  If less: plants would be unable to maintain efficient photosynthesis

Carbon has unique properties that make it the backbone of all organic compounds. Carbon must be made bioavailable through carbon dioxide fixation which depends on specialized enzymes that perform the task. In all living organisms, the central metabolic pathways promote the sugar-phosphate reactions which provide the precursor building blocks required for the make of RNA, DNA, lipids, energy, and redox coenzymes and amino acids—key molecules required for life. No non-enzymatic pathways to fix Carbon dioxide were likely responsible on early earth ( they would likely have disintegrated with UV radiation ). It takes enzymes to make the precursor building blocks of life. But it requires the precursor building blocks of life to make the key molecules, required to make enzymes which fix carbon. What came first?

Adaptation of life to the environment - essential for life
The ability to change over time in response to the environment is fundamental and is determined by the organism's genetics, its gene regulatory network, and modulation of the signaling pathways at transcriptional, post-transcriptional and post-translational levels. At least five life-essential signaling networks dependent on preprogrammed intracellular information transmission systems respond to environmental stress. How could the first living Cell have survived without the mechanism implemented from day one?

Reproduction is essential for the survival of all living things.
Reproduction is essential for the survival of all living things and depends on DNA replication, which involves more than thirty specialized proteins. Each essential for the task. It takes proteins to make DNA replication happen. But it takes the DNA replication process to make proteins. What came first?

The gene regulatory network:
What emerged first: Gene repression, or activation? Life would not exist without both....

What emerged first, genetic, or epigenetic information? Genetic information could not be expressed at the right time in the right place without the epigenetic information, when and where to do so.

Proteins and Catch22
Which came first, proteins or protein synthesis? If proteins are needed to make proteins, how did the whole thing start?" The end result of protein synthesis is required before it can begin.

Protein machines are needed to read the DNA, but these protein machines are themselves made upon the instructional blueprint stored in DNA.

The transition from RNA to DNA depends on Ribonucleotide reductase proteins. The make of proteins depends on the instructions from the instructional blueprint, stored in DNA.
DNA is required to make Ribonucleotide reductase proteins. But these proteins are required to make DNA. What came first?

Lipid Membranes
The Lipid membrane would be useless without membrane proteins but how could membrane proteins have emerged in the absence of functional membranes?

A living cell requires a protective lipid membrane, and a huge number of various types of life-essential membrane proteins, like proton pumps, receptor proteins, anchor proteins, channel proteins, transmembrane proteins, carrier proteins etc.  Lipid membrane and Membrane protein synthesis occur inside living Cells, protected by the Cell membrane, and a homeostatic milieu. Membrane protein synthesis depends on the ordered organized import of the basic building blocks to make them.  What emerged first, Cell membranes and membrane proteins, or their synthesis, if its synthesis depends on both?

Metabolic pathways
The central metabolic pathways like glycolysis or the Citric Acid cycle are essential to make Adenine triphosphate ( ATP ),  the energy currency in the cell, and amino acids, the basic building blocks of proteins. These metabolic pathways use enzymes, which are made through ATP and amino acids. How did these pathways emerge?

Metabolism, or replicator, what came first?
Both metabolism and replication are complementary processes. RNA is claimed to be the information carrier prior to DNA on early earth, and a catalyst at the same time. How could it have been so, without energy supply depending on metabolism?

Error check and repair
There are elaborate surveillance mechanisms, DNA and RNA quality control, and repair systems. The DNA and protein error check and repair system would have needed to be there from the beginning. What came first, RNA or DNA replication, or quality control, error check and repair mechanisms?

What came first, the software, or the hardware in the Cell ?
DNA is an information storage system like a hard disk of a computer and stores algorithmic (instructional) information.  What emerged first, the DNA molecule which equals to the hardware, or the blueprint stored through DNA, which equals a software? There is no reason for information processing machinery to exist without the software and vice versa.

RNA nor DNA outside of a living cell has no function, no purpose. To exercise its task, DNA must be part of a large factory-like production line, with each compartment exercising its specific purpose alongside the others in a cooperative manner, where one compartment depends on the product of another. That raises an insurmountable hurdle for unguided processes in early earth. If biochemical processes inside living cells only result in purposeful outcomes, if interconnected and interdependent like in a factory assembly line, how did the individual specific parts emerge, if they have no function by their own ?

As it has become EVIDENTLY CLEAR, no slow step by step process can lead to the complexity observed in biological systems, but ALL THROUGH biology and chemistry evidence points to INTERDEPENDENCE and the lack of function of MOST intermediate substrates in biosynthesis pathways, which means, natural selection would not have how to select them. In most cases, it is as follows: Step a + step b + step c are essential to produce X. But step a and step b produces non-functional intermediates unless they are handed over to step c resulting in X, which HAS function. All steps to produce intermediate compounds usually require COMPLEX ENZYMES AND PROTEINS, which also have to be genetically expressed. And to make them, another complex machinery is required for uptake of the basic compounds, import into the cell, and metabolic and catabolic processings to make the substrates for these molecular machines, as metal cofactors used in reaction centers. Then these proteins must be assembled and shuttled to the right place, where the manufacturing and biosynthesis pathways take place, the interconnection of each enzyme must be right, as for example enzyme c + enzyme a + enzyme b would confer no useful product. The synthesis sequence must be right, protein a first produces product a, handed over to enzyme b which makes substrate b, then handed over to protein c which makes c, to get the right final product. Non-mental, unguided mechanisms are not capable to produce such factory like systems and proceedings."

A piston used in a car engine requires a complex fabrication process to be manufactured with the right shape, size, and materials. On its own, it bears no function. But in a car engine, it is fundamental. Without it, the engine will not work. Nobody would produce a piston without foreseeing the end destination and use, the place to be mounted, and its function.

A protein requires a complex fabrication process to be synthesized with the right shape, size, and materials. On its own, it bears no function. But in a living cell, it is fundamental. Without it, the cell will not operate. Often, proteins work interdependently with other proteins in a production line like process, producing goods used in the cell. Random molecules laying around on prebiotic earth do not have the "urge" to start chemical reactions, complexify and employ natural selection to select components of a future system with specific purposes of a higher order and complexity, that would only have use and work in an interdependent manner in the system after the completion of that much larger system.

A few answers to Dan Cardinale in regards of his video: Creation Myth: Irreducible Complexity

https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact#8332

Creation Conversation with Otangelo Grasso on Irreducible Complexity
https://www.youtube.com/watch?v=DTkyFbu_kEI&fbclid=IwAR0jsmVDUQJfOhd_eMaJy9iVRZH_5_E0GrL7_sPShWd3fF0GdiI6ETuwWA8

Creation Myth: Irreducible Complexity
https://www.youtube.com/watch?v=JSdsgd1gF-A
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 parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution.

An irreducibly complex system is characterized by five points:
1. a single system composed of several well-matched, interacting parts
2. that contribute to the basic function
3. the removal of any one of the parts causes the system to effectively cease functioning
4. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system
5. any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.

Dan: an irreducibly complex system cannot be produced directly that is by continuously improving the initial function
Reply:  That is not what Behe wrote. The initial function is what has to be explained. And in order for that initial function to be, it depends on several well-matched, interacting parts. We see that all over in biology, where a specific purposeful function is only achieved when several well-matched parts interact with each other.

Translation:
Irreducible parts:
mRNA
genetic code
45 tRNAs
20 amino acids
20 aminoacyl-tRNA-synthetases
proofreading function
prokaryotic ribosomes
small subunit (designated 30S): 16S rRNA and 21 proteins
The large subunit (50S): 23S and 5S rRNAs and 34 proteins
eukaryotic ribosomes
small subunit (40S):18S rRNA and 30 proteins
large subunit (60S): 28S, 5.8S, and 5S rRNAs and about 45 proteins
AUG codon to start translation  ( GUG codon in some bacteria)
The trans-translation mechanism which is a key component of multiple quality control pathways in bacteria that ensure proteins are synthesized with high fidelity in spite of challenges such as transcription errors.

Irreducible stages:
Initiation, elongation, and termination

Initiation: the first step of the initiation stage is the binding of a specific initiator methionyl tRNA and the mRNA to the small ribosomal subunit. The large ribosomal subunit then joins the complex, forming a functional 1.ribosome on which elongation of the polypeptide chain proceeds.
2.A number of specific non-ribosomal proteins are also required for the various stages of the translation process:
Prokaryotes: IF-1, IF-2, IF-3
Eukaryotes: eIF-1, eIF-1A, eIF-2, eIF-2B, eIF-3, eIF-4A, eIF-4B, eIF-4E, eIF-4G, eIF-5
Elongation
Prokaryotes:  EF-Tu, EF-Ts, EF-G
Eukaryotes:   eEF-1α, eEF-1βγ, eEF-2
Elongation factor (EF-Tu in prokaryotes, eEF-1α in eukaryotes)
release factors (RF-1, RF-2 and RF-3 in prokaryotes, in eukaryotic cells release factors (eRF-1,and eRF-3)
Termination
Prokaryotes: RF-1, RF-2, RF-3
Eukaryotes: eRF-1, eRF-3

Biogenesis of the ribosome: 
The Ribosome requires over 200 scaffold proteins, chaperones, and 75 cofactors for its assembly.
maturation of tRNA's:
Proteins:
CCA tRNA nucleotidyltransferase 1 ,
Zinc phosphodiesterase ELAC protein 2
and  Enzymatic  complexes:
Ribonuclease P: Human nuclear RNase P consists of 10 Protein subunits and one RNA subunit.
tRNA ligase complex
tRNA-splicing endonuclease



Dan: or in a different place this right here in this sentence we're also excluding exception because he's saying we have to continuously improve the initial function well we know there are biological systems that can appear via exception which is where it does one thing and then it is co-opted to do a different thing.
Reply: Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions
https://reasonandscience.catsboard.com/t1572-irreducible-complexity-is-an-obstacle-to-darwinism-even-if-parts-of-a-system-have-other-functions

In order to catch a mouse, a mousetrap needs a platform, spring, hammer, holding bar, and catch. Now, suppose you wanted to make a mousetrap. In your garage you might have a piece of wood from an old Popsicle stick (for the platform), a spring from an old wind-up clock, a piece of metal (for the hammer) in the form of a crowbar, a darning needle for the holding bar, and a bottle cap that you fancy to use as a catch. But these pieces, even though they have some vague similarity to the pieces of a working mousetrap, in fact are not matched to each other and couldn't form a functioning mousetrap without extensive modification. All the while the modification was going on, they would be unable to work as a mousetrap. The fact that they were used in other roles (as a crowbar, in a clock, etc.) does not help them to be part of a mousetrap. As a matter of fact, their previous functions make them ill-suited for virtually any new role as part of a complex system.

The argument of co-option
1. Co-option in microbiology means borrowing parts of systems from different places to form a new system. When in this way a new system is generated it has a new function. This proves evolution.
2a. But in the evolutionary scheme not all the systems were available by co-option.
2b. In the simple example of E-coli only 10 out of 40 components can be traced back as having been developed by co-option.
2c. The rest of the 30 components are unique and new. There are simply no known homologues to them. These 30 components were not available for co-option in hypothetic ancestral lines leading from e.g. a bacterium with no flagellum.
3. This again proves the existence of a designer who is no one else then God.

Dan: what good is half an eye argument but it turns out that half an eye is pretty darn good uh sure you might not be able to see write images or perceive images but if you can detect light and dark as many organisms can that's useful if you can detect degrees of light and dark that's useful if you can detect the source of light that's useful so you can have functional intermediates that aren't the full trait but they're
still beneficial they're still more helpful than having nothing related 
Reply: Main topics on the origin of eyes
https://reasonandscience.catsboard.com/t2695-main-topics-on-the-origin-of-eyes

Otangelo Grasso
February 24, 2020, 4:08 AM
The Evolution of the Eye, Demystified
https://evolutionnews.org/2020/02/the-evolution-of-the-eye-demystified/?fbclid=IwAR3fgWoc02Xy0jgggCKa2TLLofsQkuSh3vUWf2xSNk73jU1iMJGzwiTJk2Y

Rhodopsin:
1. Rhodopsin proteins, the main players in vision, the visual cycle, the signal transduction pathway, the eye, eye-nerve, and visual cortex in the brain, and visual data processing are  irreducible, integrated, systems, which each by themselves are irreducibly complex, but on a higher structural level, are interdependent, and work together in a joint venture to create vision.
2. If each of the mentioned precursor systems would evolve through a gradual emergence by slight, gradual modifications, these would result in nonfunctional subsystems. Since natural selection requires a function to select, these subsystems are irreconcilable with the gradualism Darwin envisioned.
3. But lets suppose that even if in a freaky evolutionary accident the individual subsystems would be generated, they would still have to be assembled into an integrated functional system of higher order, requiring meta-information directing the assembly process to produce the final functional system, that is genetic information to regulate parts availability, synchronization, and manage interface compatibility. The individual parts must precisely fit together.
4. 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 4. 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 minds having the capabilities to produce cameras, telescopes, and information processing systems.

Visual data processing
1. Sight is the result of complex data processing. Data input requires a common understanding between sender and receiver/retrieval of the data coding and transmission protocols.
2. The rules of any communication system are always defined in advance by a process of deliberate choices. There must be a prearranged agreement between the sender and receiver, otherwise, communication is impossible.
3. Light can be considered an encoded data stream that is decoded and re-encoded by the eye for transmission via the optic nerve and decoded by the visual cortex. The sophisticated control systems in the human eye processes images and controls the eye muscles with speed and precision. 2 Synchronized 576MP cameras.  Data is multiplexed, that is multiple signals are combined into  one signal to 1MP to enter the optic nerve. Then de-multiplexed in the brain. Chromatic aberration is corrected by software. 2 pictures processed together to generate a 3D model. The Brain processes that model, extracts data from millions of coordinates and then sends very precise control data back to the muscles, the iris, lens and so on.
4. Only a Master Designer could have imagined/conceptualized and implemented these four things—language, the transmitter of language, multiplexing and de-multiplexing the message, and receiver of language since all have to be precisely defined in advance before any form of communication can be possible at all.

Dan: a single instance of a system that has irreducible complexity evolving is sufficient to falsify the hypothesis
Reply: Either a system is  irreducibly complex, and must therefore be designed, or the product of evolution. Either one or the other. It can't be both.

In the same sense, as an engineer would not project, invent, create and make a blueprint of a piston with no use by its own, but only conjoined, and together with all other parts while projecting a whole engine, envisioning its end function and use, its evident that unguided random natural events without foresight would not come up with assemblage of tiny molecular machines, enzymatic structures with unique contours, which bear no function by their own, but only when inserted in cellular structures with higher ends, being essential for cells to self-replicate, and perpetuate life.

Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.
In other words: Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overarching design goal.
A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution. 

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 as factories ( cells ) or machines ( cells host a big number of the most various molecular machines and equal to factory 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 their excitation energy by Förster resonance energy transfer 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? That's as if genetic mutations and natural selection had enough probability to generate interdependent individual parts being able to perform new functions while the individual would have no function unless interconnected.

The extraordinary cellular propulsion system of Mycoplasma mobile - faster than Usain Bolt
https://reasonandscience.catsboard.com/t2765-the-extraordinary-cellular-propulsion-system-of-mycoplasma-mobile-faster-than-usain-bolt

1. Behe used, as an illustration, a moustrap, where all the components are required for its function, and as such, it is irreducibly complex. Mycoplasma mobile is a bacteria which uses flexible legs, that literally walk on the surface. Its biomotility mechanism is unique. Mycoplasma mobile is propelled by Gli349 protein “legs” which repeatedly catch and release on the surface where they walk, and are driven by the force exerted by a so-called P42 protein through Gli521 molecules, supported by surface structure on which they walk, based on the consumption of energy in the form of ATP. Each of the four proteins used for walking are essential. Mutation experiments in the last decade have demonstrated that these proteins, each, must be precisely and correctly sequenced, otherwise, the function ceases, and motility is not possible.
2. Four component proteins are directly involved in the mechanism, and at least 10 proteins are involved in the cytoskeleton. None of the four proteins has significant sequence similarities with proteins of any other bacterias. So there could not be co-option. 
3. Since none of these components can be dismissed without harming the motility function, this system is irreducible, interdependent, working as an integrated system, and on top, none of the components could be co-opted from other organisms.  


1. Gli349 protein is the "leg" responsible for  binding on the surface during gliding and is required to convey movement.
2. Gli521 is the motor or the gear-transmitting force from the motor to the leg. 
3. Gli123 protein is necessary to stabilize  Gli349 and Gli521 proteins. 
4. P42 has ATPase activity. The energy for M. mobile gliding is supplied by ATP hydrolysis and that detachment from the solid surface is an energy-dependent process.

https://www.youtube.com/watch?v=Jz_5BXIOrHw

Co-option: Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions

https://reasonandscience.catsboard.com/t1572-irreducible-complexity-is-an-obstacle-to-darwinism-even-if-parts-of-a-system-have-other-functions

Behe's answer to that objection:

That's what often happens when people who are adamantly opposed to an idea publicize their own definitions of its key terms—the terms are manipulated to wage a PR battle. The evident purpose of Miller and others is to make the concept of IC so brittle that it easily crumbles. However, they are building a straw man.

I never wrote that individual parts of an IC system couldn't be used for any other purpose. (That would be silly—who would ever claim that a part of a mousetrap couldn't be used as a paperweight, or a decoration, or a blunt weapon?) Quite the opposite, I clearly wrote in Darwin's Black Box that even if the individual parts had their own functions, that still does not account for the irreducible complexity of the system. In fact, it would most likely exacerbate the problem, as I stated when considering whether parts lying around a garage could be used to make a mousetrap without intelligent intervention.

In order to catch a mouse, a mousetrap needs a platform, spring, hammer, holding bar, and catch. Now, suppose you wanted to make a mousetrap. In your garage you might have a piece of wood from an old Popsicle stick (for the platform), a spring from an old wind-up clock, a piece of metal (for the hammer) in the form of a crowbar, a darning needle for the holding bar, and a bottle cap that you fancy to use as a catch. But these pieces, even though they have some vague similarity to the pieces of a working mousetrap, in fact are not matched to each other and couldn't form a functioning mousetrap without extensive modification. All the while the modification was going on, they would be unable to work as a mousetrap. The fact that they were used in other roles (as a crowbar, in a clock, etc.) does not help them to be part of a mousetrap. As a matter of fact, their previous functions make them ill-suited for virtually any new role as part of a complex system.


The argument of co-option
1. Co-option in microbiology means borrowing parts of systems from different places to form a new system. When in this way a new system is generated it has a new function. This proves evolution.
2a. But in the evolutionary scheme not all the systems were available by co-option.
2b. In the simple example of the flagellum of E-coli, only 10 out of 40 components can be traced back as having been developed by co-option.
2c. The rest of the 30 components are unique and new. There are simply no known homologues to them.
     These 30 components were not available for co-option in hypothetic ancestral lines leading from e.g. a bacterium with no flagellum.
3. This again proves the existence of a designer who is no one else then God.

A Response to Sharon Begley's Wall Street Journal Column
Michael J. Behe
Discovery Institute

In order for co-option to produce a bacterial flagellum (for example) all of the component parts must have been present at the same time and in roughly the same place, and all of them must have had other naturally-selectable, useful functions. There is no evidence whatsoever that this ever was the case, or that it ever even could have been the case.

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.

Syllogisms about irreducible complexity

https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact#8349

1. In biology, there are many complex elementary components necessary to build large integrated macromolecular systems like multi-protein complexes (RNA polymerase), 3D printers (the ribosome), organelles (mitochondria), etc., where their making requires complex multistep enzyme-catalyzed biosynthesis pathways. These elementary components are only useful in the completion of that much larger system. Not rarely, these biosynthetic pathways produce intermediate products, that left without further processing, are either a) nonfunctional, or b) harmful and kill the cell (for example, Reactive Oxygen Species (ROS), in the biosynthesis pathway of Chlorophyll b.
2. A minimal amount of prescribed, pre-programmed, instructional complex information stored in genes is required to instruct the making of a) functional elementary components and b) the assembly instructions to integrate them into complex macromolecular systems. Natural selection would not fix an allele variant that would instruct the making of an intermediate, nonfunctional, or harmful elementary component, and play no role in guiding its evolution. Foreknowledge is required to get a complex biological system through implementing a biosemiotic information system (which is irreducibly complex), directing the making of functional elementary components, and assembly into the entire complex integrated system.
3. Therefore, the origin of biological systems based on biosemiotic instructions are best explained by a brilliant, super-powerful mind with foresight and intent, and not undirected evolutionary pressures.

Many systems in biology are irreducibly complex
1. There are many systems and parts in biology, that can be named, that require to be integrated to work. They work interdependently, only in a joint venture, and can be classified as irreducibly complex. A few examples are:
No glycine amino acids, no pyrimidines, no DNA - no life. No Watson Crick base pair fine-tuning, no DNA - no life. No Topoisomerase II or helicase proteins, no DNA replication - no life perpetuation. No peripheral stalk, a subunit in ATP synthase Nano turbines, no energy supply trough ATP for biological cells, no advanced life. No cleavage of tRNA during its biosynthesis, tRNA's will not be useful for the cell, no life. No Nitrogenase enzymes to fix nitrogen in an energy-demanding, triple bond-breaking process, no ammonia, required to make amino acids - no nitrogen cycle - no advanced life. No chlorophyll, no absorption of light to start photosynthesis, no starch and glucose - cells will have no food supply to sustain complex organisms - no advanced life on earth. No water evolving complex in photosynthesis, no oxygen, no advanced life. No carotenoids quenching heat in chlorophyll in the antenna complex, the surrounding membrane would be burned - no advanced life.   No Rubisco, no fix of CO2, no hydrocarbons - no advanced life. No counterion in retinal, and Rhodopsin could not receive visible light - and there would be no vision on earth by any organism.
2. It's like having a gigantic jigsaw puzzle of millions of pieces that trigger a knob. If not ALL puzzle pieces are brought together to complete it, the knob does not switch, and light does not turn on. None of the above-mentioned proteins has any function if not interconnected and inserted at the right place like a sub-part in a machine or production line. In the same manner, as a robot has no function by itself and by its own, and outside a factory unless placed at the right production line, getting the right substrate from another robot, processing it in the right manner, and handing it over to the next processing step - which also has to have its right function and manufacturing proceeding pre-programmed- nothing is done and achieved. Often, if in a production line, just one robot goes havoc, the entire production lines stop functioning. If you have a fully working car, but lose the key, you cannot turn it on, and it will not start. Sometimes, a tiny cable goes oxidized, or breaks and the car stop functioning.  
3. Life is an unimaginable balancing act, beginning with the setup of physical laws upon which the properties and operation of the physical universe depend, fine-tuning of the universe, the fundamental forces, our galaxy, the earth, and its life-permitting conditions, but, if helicase, just ONE protein that unwinds DNA, is not here, our universe would be lifeless.
4. This is evidence of planned design by a powerful creator, that knows how, and not a lifeless magic trick blindly believed by so many atheists.

The cell is irreducibly complex
1. A strand of RNA can make one simple chemical reaction occur, but that’s not all that is needed. Even a most primitive cell needs essential molecules of life to replicate and thus to continue to exist. If there is no quality control, no inspections, no checks and balances, no feedback, no networks in the system of the cell, what will happen? Only entropy.
2. In order for life to begin there is need of an irreducible complex system even within the simplest cell.
3. Therefore, a supreme intelligent designer of irreducible complex cell factories system most likely exists. 

The irreducible complexity of the cell
1. On the one side, we have the putative prebiotic soup with the random chaotic floating around of the basic building blocks of life, and on the other side,  the first living self-replicating cell ( LUCA ), a supposed fully operational minimal self-replicating cell, using the highly specific and sophisticated molecular milieu with a large team of enzymes which catalyze the reactions to produce the four basic building blocks of life in a cooperative manner, and furthermore, able to maintain intracellular homeostasis, reproduce, obtaining energy and converting it into a usable form, getting rid of toxic waste, protecting itself from dangers of the environment, doing the cellular repair, and communicate.  
2. The science paper: Structural analyses of a hypothetical minimal metabolism proposes a minimal number of 50 enzymatic steps catalyzed by the associated encoded proteins. They don't, however, include the steps to synthesize the 20 amino acids required in life. Including those, the minimal metabolome would consist of 221 enzymes & proteins. A large number of molecular machines, co-factors, scaffold proteins, and chaperones are not included, required to build this highly sophisticated chemical factory.
3. There is simply no feasible viable prebiotic route to go from a random prebiotic soup to this minimal proteome to kick-start metabolism by unguided means. This is not a conclusion by ignorance & incredulity, but it is reasonable to be skeptical, that this irreducibly complex biological system, entire factory complexes composed of myriads of interconnected highly optimized production lines, full of computers and robots could emerge naturally defying known and reasonable principles of the limited range of random unguided events and physical necessity. Comparing the two competing hypotheses, chance vs intelligent design, the second is simply by far the more case-adequate & reasonable explanation.

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 explanation for the origin of information and irreducible complexity in biological systems.

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.  

The argument by the impossibility of gradual development
1. Proponents of neo-Darwinism try to prove 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 have 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.

1. 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.
2. The pathway must go all the way through, otherwise, chlorophyll is not synthesized.
3. Therefore, the Chlorophyll biosynthesis pathway is irreducibly complex.


The blood clotting system
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 Robinson 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


The irreducible interdependence of information generation and transmission systems
1. Codified information transmission system depends on: 
a) A language where a symbol, letters, words, waves or frequency variations, sounds, pulses, or a combination of those are assigned to something else. Assigning meaning of characters through a code system requires a common agreement of meaning. Statistics, Semantics, Synthax, and Pragmatics are used according to combinatorial, context-dependent, and content-coherent rules. 
b) Information encoded through that code,
c) An information storage system, 
d) An information transmission system, that is encoding, transmitting, and decoding.
e) Eventually translation ( the assignment of the meaning of one language to another )
f)  Eventually conversion ( digital-analog conversion, modulators, amplifiers)
g) Eventually transduction converting the nonelectrical signals into electrical signals
2. In living cells, information is encoded through at least 30 genetic, and almost 30 epigenetic codes that form various sets of rules and languages. They are transmitted through a variety of means, that is the cell cilia as the center of communication, microRNA's influencing cell function, the nervous system, the system synaptic transmission, neuromuscular transmission, transmission b/w nerves & body cells, axons as wires, the transmission of electrical impulses by nerves between brain & receptor/target cells, vesicles, exosomes, platelets, hormones, biophotons, biomagnetism, cytokines and chemokines, elaborate communication channels related to the defense of microbe attacks, nuclei as modulators-amplifiers. These information transmission systems are essential for keeping all biological functions, that is organismal growth and development, metabolism, regulating nutrition demands, controlling reproduction, homeostasis, constructing biological architecture, complexity, form, controlling organismal adaptation, change,  regeneration/repair, and promoting survival. 
3. The origin of such complex communication systems is best explained by an intelligent designer. Since no humans were involved in creating these complex computing systems, a suprahuman super-intelligent agency must have been the creator of the communication systems used in life. 

The software and hardware of the cell are irreducibly complex
1. The cell contains a complex information storage medium through DNA.
2. The cell has a complex information processing system ( through  RNA polymerase, transcription factors, a spliceosome, a  ribosome,  chaperone enzymes, specialized transport proteins, and ATP
3. The cell contains a genetic code that is at or very close to a global optimum for error minimization across plausible parameter space
4. The cell stores complex, specified, coded information ( the software )
5. The cell has a complex translation system through a universal cipher, which assigns 61 codons (4x4x4=64-3 stop and start=64) to 20 amino acids and permits the translation of the genetic code into functional proteins
6. This constitutes a logical structure of information processing: DNA>>RNA>>>Protein, based on software and hardware. Both aspects must be explained.
7. There is no reason for information processing machinery to exist without the software, and vice versa.
8. Systems of interconnected software and hardware are irreducibly complex.
9. A irreducible complex system can not arise in a stepwise, evolutionary manner.
10. Only minds are capable to conceptualise and implement  instructional information control systems transformed into molecular dynamics
11. Therefore, an intelligent designer exists.


Translation through the ribosome is an irreducible, integrated complex process
1. A bacterial cell depends upon a translation and coding system consisting of 106 distinct but functionally integrated proteins as well several distinct types of RNA molecules (tRNAs, mRNAs, and rRNAs). This system includes the ribosome (consisting of fifty distinct protein parts), the twenty distinct tRNA synthetases, twenty distinct tRNA molecules with their specific anticodons, about 200 ribosome assembly proteins and 75 co-factors, chaperones, free-floating amino acids, ATP molecules (for energy), and—last, but not least—information-rich mRNA transcripts for directing protein synthesis. Many of the proteins in the translation system perform multiple functions and catalyze coordinated multistep chemical transformations.
2. The ribosome is the 3D printer of proteins. A human-made 3D printer is made of several functional parts, like the nozzle, the extruder, cooling fan, heated be, the painter's tape, etc. The 3D extruder has no use on its own. But only, when working inside the 3D printer in the right place. In the same sense, as an engineer would not project, invent, create and make a blueprint of a 3D printer extruder with no use by its own, but only conjoined, and together with all other parts while projecting a whole printer, envisioning its end function and use, its evident that unguided random natural events without foresight would not come up with an assemblage of tiny molecular machines, enzymatic structures with unique contours, which bear no function by their own, but only when inserted as part of the ribosome with higher ends, being essential for cells to translate DNA information into proteins, and being a key part participating to perpetuate life. Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. In other words: Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overarching design goal. A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (instructed complex information), irreducible complexity, and the setup of complex machines with little tolerance of change.   Therefore, intelligent design constitutes the best explanations for the origin of the information guiding the making of the irreducible and integrated complex ribosome protein factory.

1. High information content (or specified complexity), irreducible complexity, and the setup of exquisitely integrated circuits, which by significant alterations are inevitably damaged or destroys the function,   constitute strong indicators or hallmarks of (past) intelligent design.
2.The high information content and biological irreducible metabolic pathways which also require regulation and structured in a cascade manner, similar to electronic circuit boards, utilizing proteins and enzymes that manifest by themself irreducible complexity, constitute strong indicators or hallmarks of (past) creation through intelligent intervention,  and design.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (instructed complex information), irreducible complexity, and the setup of complex circuits with little tolerance of change. 
4. Therefore, intelligent design constitutes the best explanation for the origin of information and irreducible complexity in metabolic biological circuits.


The oxygen-evolving complex (OEC) of photosystem II is irreducibly complex.
1. One of the most important and fundamental biochemical reactions on which all advanced life-forms depend is performed by the oxygen-evolving complex (OEC) in oxygenic photosynthesis, responsible for catalyzing the light-driven oxidation of water to molecular oxygen in plants, algae, and cyanobacteria. It is also described as "undoubtedly one of the most remarkable inventions in all of biology." OEC is surrounded by 4 core proteins of photosystem II at the membrane-lumen interface.  It remains a fundamental mystery of how this complicated, four-electron transfer process originated. Enigmatic is how the precise geometry and unique mechanism of the OEC came about. Key differences exist between oxygenic and anoxygenic photosynthetic machinery with no apparent homologs or transitional forms that would provide clues to their development. Foremost among these differences is the presence and key role of manganese at the site of water oxidation in photosystem II. This is distinct from bacterial anoxygenic reaction centers, which rely on redox-active periplasmic proteins as electron donors.
2. According to peer-reviewed scientific papers, each of the four extrinsic proteins, (PsbO, PsbP, PsbQ, and PsbR)  of plants are ESSENTIAL, and each was tested upon mutated form, and the mechanism was found inefficient and compromising the OEC function. Furthermore, a water network around the Mn4CaO5 cluster and D1 protein subunit of PSII is also indispensable, and irreducible.  Site-directed mutants show severe impairment of the water oxidation cycle and fail to grow photoautotrophically.
3. That means evolutionary intermediates are non-functional. There is a precise fit and size matching of the residues with the individual atoms of the clusters. This is evidence, that this most fundamental biochemical reaction could not have emerged by evolutionary, step-wise mechanisms, and therefore, Darwin's theory has been falsified and refuted. The only plausible alternative to Darwinian evolution is intelligent design.


The argument of the zip-codes within the cell
1.  Michael Denton compared the cell to a city.  He writes: “To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometers in diameter and resembles a giant airship large enough to cover a great city like London or New York.  What we would then see would be an object of unparalleled complexity and adaptive design.... a world of supreme technology and bewildering complexity.”
2. This has become more than true by discovering new details in the mind-boggling complex life of the cell. Proteins are the workhorses of the cell, but to get the most work out of them, they need to be in the right place.  In neurons, for example, proteins needed at axons differ from those needed at dendrites, while in budding yeast cells, the daughter cell needs proteins the mother cell does not.  In each case, one strategy for making sure a protein gets where it belongs is to shuttle its messenger RNA to the right spot before translating it. The destination for such an mRNA is encoded in a set of so-called “zipcode” elements, which loop out of the RNA string to link up with RNA-binding proteins.  In yeast, these proteins join up with a myosin motor that taxis the complex to the encoded location.
3. All the above speaks about the amazing, irreducible complexity and intelligent design of one of the simplest cells, the yeast. How this complex system evolved was not explained. This complexity found in the simple cell of yeast is one more example out of innumerable complex systems that are necessary for the existence of the cell. 
4. The irreducibly complex systems are evidence of an intelligent design that could have been made only by a super-intelligent person all men call God.


Proteasomes
1. The disposal of protein “trash” in the cell is the job of a complex machine called the proteasome.  What could be lower than trash collection?  Here also, sophisticated mechanisms work together. 
2. PhysOrg described a new finding that shows that “two different mechanisms are required to determine which targets to destroy.” The “recognition tag” and “initiator tag.”
3. Both mechanisms have to be aligned properly to enter the machine’s disposal barrel.  “The proteasome can recognize different plugs1, but each one has to have the correct specific arrangement of prongs1,” said a researcher at Northwestern University.
4. This is another example of interdependent irreducible complex systems. One can’t argue for evolution; that first only one system existed.
5. The work of a designer is again obvious and all men call him God.

The argument of increasing knowledge about the complexity of the cell 
1. Almost 30 years ago, in 1985 Michael Denton in his book Evolution: A Theory in Crisis, p. 328 compared a cell to a large city, filled with “supreme technology and bewildering complexity.”  Nowadays we have not only much more detailed information about the complexity of the cell and how life works but also every week in the reports/writings of science, new findings are made about regulators, teams, quality controls, checkpoints, conductors, players with starring roles. Let’s see a few examples:
a. Bricks that build:  “Researchers have found in mice that supporting cells in the inner ear, once thought to serve only a structural role, can actively help repair damaged sensory hair cells, the functional cells that turn vibrations into the electrical signals that the brain recognizes as sound.”
b. Master regulator: Whether or not a cell grows is decided by a remarkable protein kinase enzyme called mTOR. As part of two complexes, mTORC1 and mTORC2, mTOR integrates and interprets all sorts of factors that influence cell growth — including nutrients, stressors (=agents that causes stress to an organism), and the outputs of signal-transduction networks (=biological circuits that pass along information) — by targeting a multitude of substrates that drive processes such as protein translation, metabolism, and cell division. Research into mTOR-mediated signaling has taken on added urgency since it was discovered that most cancers contain mutations that inappropriately activate this protein.
The newly-uncovered structure of mTOR, made up of 1,500 amino acids, shows that it has a “gatekeeper mechanism that controls substrate access to the active site.”
c. Checkpoint charlies:  “MTBP acts with Treslin/TICRR to integrate signals from cell cycle and DNA damage response pathways to control the initiation of DNA replication in human cells.”
d. Damage repair: One latest study, performed on yeast cells, describes cooperation between translesion DNA synthesis (TLS), single-stranded DNA repair (ssDNA), and homologous recombination, which rebuilds a damaged strand from the intact strand.  “These findings suggest that ssDNA that might originate during the repair of closely opposed lesions or of ssDNA-containing lesions or from uncoupled replication may drive recombination directly in various species, including humans.”
2. All these examples indicate the irreducibly complex system of the cell’s life and structure. If not assembled all together at the same time even the simplest cell could not survive. There would be no life on this earth.
3. Intelligent design and creation by a brilliantly intelligent person all men call God is most likely true.

Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.
In other words: Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overarching design goal.
A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.