A list of irreducible complex systems

A list of irreducible complex systems

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

Why do you never see in science articles asking questions like this ? What emerged first, Genes, or the gene regulatory network, and the information to pick or suppress the right genes at the right time? Simple. Because such simple questions make it evidently clear why naturalism fails. No Nobel price needed... btw.....

Interdependence of the DNA double helix, the genetic code, and the machinery to transcribe and translate the code to make proteins  3
Can an alphabet emerge without a conscious entity designing it? What purpose does an alphabet serve without a medium, such as ink and paper, to convey a message, without someone to craft the message, and without an audience to interpret it, based on a shared understanding of the language and its semantics?

Similarly, could the intricate structure of DNA materialize without a guiding intellect? What utility does DNA's coding system have without the double helix structure to store the necessary information for protein synthesis? What significance do the 'software' of the DNA code and the 'hardware' of the double helix hold without the cellular machinery required to decode, transcribe, and translate the DNA's instructions into proteins? Don't all these components need to coexist simultaneously for the system to function, given that the absence of any one element renders the others ineffective?

http://www.ncbi.nlm.nih.gov/pubmed/8335231
The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics. 

Must not only the alphabet, but also the storage medium be invented ? - That can be ink and paper, the hardware of a computer, or the morse code in various mediums ? 
Must not only the DNA code, but also the storage medium , the double helix, AND also the machinery to read and transcribe the message be invented, otherwise the first two have no function ? 

In the cell, things are however far more complex. There is a whole chain of subsequent events that must all be fully operational, and the machinery in place, in order to make the final product, that is proteins. That chain is constituted by INITIATION OF TRANSCRIPTION, CAPPING,  ELONGATION,  SPLICING, CLEAVAGE,POLYADENYLATION AND TERMINATION, EXPORT FROM THE NUCLEUS TO THE CYTOSOL, INITIATION OF PROTEIN SYNTHESIS (TRANSLATION), COMPLETION OF PROTEIN SYNTHESIS AND PROTEIN FOLDING. In order for evolution to work, the robot-like working machinery and assembly line  must be in place, fully operational. So the origin of the machines cannot be explained through evolution. All there is left, are random chemical reactions, or design. Chose which explanation seems more fitting the evidence.

Interdependence of the promoter region in DNA,  transcription factors, and RNA polymerase II  4
Transcription is the process of making RNA from a DNA template. Several key factors are involved in this process. Including, DNA, transcription factors, RNA polymerase, and ATP. This is a irreducible complex system. DNA, transcription factors, RNA polymerase, and ATP must be present, otherwise transcription cannot occur.  What came first, the TATA Box in the promoter region in DNA, or transcription factors, controlling the rate of transcription of genetic information from DNA to messenger RNA ? What use does one have without the other ? Both must have come into existence in the right exact time. And the RNA polymerase machine as well, since the other two without it have no function either. That is extremely sophisticated, interdependenet machinery that had to come into existence all at once. Thats best explained through a designer.  There are many more molecular machines involved in the process, namely additional proteins such as coactivators, chromatin remodelers, histone acetylases, deacetylases, kinases, and methylases etc..... this is a interdependent, highly coordinated complex machinery, where the single parts have no use, unless in conjunction with all other parts. This is one more prima facie example of intelligent design in micro biology.

In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. 1

For the transcription to take place, the enzyme that synthesizes RNA, known as RNA polymerase, must attach to the DNA near a gene. Promoters contain specific DNA sequences such as response elements that provide a secure initial binding site for RNA polymerase and for proteins called transcription factors that recruit RNA polymerase. These transcription factors have specific activator or repressor sequences of corresponding nucleotides that attach to specific promoters and regulate gene expression.

In eukariotic cells, the response elements in promoter regions are Pribnow box, TATA box, BRE, CAAT box 

The cell is irreducibly complex  7
The cell is an interdependent functional city. We state, “The cell is the most detailed and concentrated organizational structure known to humanity. It is a lively microcosmic city, with factories for making building supplies, packaging centers for transporting the supplies, trucks that move the materials along highways, communication devices, hospitals for repairing injuries, a massive library of information, power stations providing usable energy, garbage removal, walls for protection and city gates for allowing certain materials to come and go from the cell.” The notion of the theoretical first cell arising by natural causes is a perfect example of irreducibly complexity. Life cannot exist without many numerous interdependent complex systems, each irreducibly complex on their own, working together to bring about a grand pageant for life to exist.

Cell Membranes, origins through natural mechanisms, or design ?  6
According to this website : The Interdependency of Lipid Membranes and Membrane Proteins
The cell membrane contains various types of proteins, including ion channel proteins, proton pumps, G proteins, and enzymes. These membrane proteins function cooperatively to allow ions to penetrate the lipid bilayer. The interdependency of lipid membranes and membrane proteins suggests that lipid bilayers and membrane proteins co-evolved together with membrane bioenergetics.

My comment: The nonsense of this assertion is evident. How could the membrane proteins co-evolve, if they had to be manufactured in the machinery , protected by the cell membrane ? 
The cell membrane contains various types of proteins, including ion channel proteins, proton pumps, G proteins, and enzymes. These membrane proteins function cooperatively to allow ions to penetrate the lipid bilayer. 
The ER and Golgi apparatus together constitute the endomembrane compartment in the cytoplasm of eukaryotic cells. The endomembrane compartment is a major site of lipid synthesis, and the ER is where not only lipids are synthesized, but membrane-bound proteins and secretory proteins are also made. 

My comment: So in order to make cell membranes, the Endoplasmic Recticulum is required. But also the Golgi Apparatus, the peroxysome, and the mitochondria. But these only function, if protected and encapsulated in the cell membrane.  What came first, the cell membrane, or the endoplasmic recticulum ? This is one of many other catch22 situations in the cell, which indicate that the cell could not emerge in a stepwise gradual manner, as proponents of natural mechanisms want to make us believe.

Not only is the cell membrane intricate and complex (and certainly not random), but it has tuning parameters such as the degree to which the phospholipid tails are saturated. It is another example of a sophisticated biological design about which evolutionists can only speculate. Random mutations must have luckily assembled molecular mechanisms which sense environmental challenges and respond to them by altering the phospholipid population in the membrane in just the right way. Such designs are tremendously helpful so of course they would have been preserved by natural selection. It is yet another example of how silly evolutionary theory is in light of scientific facts.

Nucleosomes and irreducible complexity 8
A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight  histone protein cores. This structure is often compared to thread wrapped around a spool. The basic level of DNA compaction is the nucleosome, where the double helix is wrapped around the histone octamer containing two copies of each histone H2A, H2B, H3 and H4. Linker histone H1 binds the DNA between nucleosomes and facilitates packaging of the 10 nm "beads on the string" nucleosomal chain into a more condensed 30 nm fiber.
Histones are among the most highly conserved eucaryotic proteins. For example, the amino acid sequence of histone H4 from a pea and from a cow differ at only 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids, so that a change in any position is deleterious to the cell. This suggestion has been tested directly in yeast cells, in which it is possible to mutate a given histone gene in uitro andintroduce it into the yeast genome in place of the
normal gene. As might be expected, most changes in histone sequences are lethal; the few that are not lethal cause changes in the normal pattern of gene expression, as well as other abnormalities.
If a change in histone sequences are lethal, how could it probably come to be in gradual steps, or trial and error ? As long as the correct sequence is not reached, no function.....
Nucleosome assembly following DNA replication, DNA repair and gene transcription is critical for the maintenance of genome stability and epigenetic information.
In assembling a nucleosome, the histone folds first bind to each other to form H3-H4 and H2A-H2B dimers, and the H3-H4 dimers combine to form tetramers. An H3-H4 tetramer then further combines with two HZA-H2B dimers to form the compact octamer core, around which the DNA is wound.
The  assembly is a sequential  multistep process, requiring several  folds and steps in a highly organized, regulated and precise manner, and must have been programmed and functional right from the beginning. Histone chaperones play important roles in regulating the intricate steps involved in folding of histones together with DNA to form correctly assembled nucleosomes, furthermore  assembly, disassembly and histone exchange to facilitate DNA replication, repair and transcription. There is a need for histone chaperones to guide the process and each step along the assembly pathway is carefully controlled and regulated by these histone chaperones. It is evident that a stepwise evolutionary fashion of development of histone chaperones to guide the process would result in a disaster. They had to be there fully working and programmed to do their job right from the start.  
Furthermore, to add to the already amazing machine like performance,  (linker histones) have to participate at each step in the processes of nucleosome assembly, disassembly and histone exchange during different genomic processes.   Linker histone H1 is an essential component of chromatin structure ( so its irreducible ).  H1 links nucleosomes into higher order structures.
Nucleosome formation is dependent on the positive charges of the H4 histones and the negative charge on the surface of H2A histone fold domains. Acetylation of the histone tails disrupts this association, leading to weaker binding of the nucleosomal components. Histone acetyltransferases (HATs) and Histone deacetylase ( HDAC ) are also essential enzymes, that  remove through acetylation the  positive charge on the histones, and as a consequence, the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription. This relaxation can be reversed by HDAC activity.
So we can conclude that all these parts, DNA,  Linker histone H1, histones H2A, H2B, H3 and H4,and acetyltransferases (HATs) and Histone deacetylase ( HDAC ) form 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, while Histone chaperones are also essential to build the since they guide the process and each step along the assembly pathway.

Eye / brain is a interdependent and irreducible complex system 9
The visual system is made of three major parts: the eyeballs with retina, the optic nerve, and the visual cortex. The eye ball has at least individual 16 parts, while the visual system, consisting in the optic nerve and visual cortex, en-globes total at least another individual 14 parts. These items are minimal requirements for vision of humans. The question is, which evolved first: the retina (eyeball), the optic nerve, or the visual cortex ? Since all of these are interdependent, they would have had to arise and evolve at the same time, either interconnect since the beginning, or at the right time all togheter, once fully evolved. Not one of the three items could have preceded the others, as they would be useless. It is unimaginable to think of a different use that could be assigned to each part individually, and how each could individually have function and advantage of survival. If any one to three of these items were partially evolved, no vision would be achieved. There would be no possible advantage, and evolution could not continue.

The thalamus relies on electrochemical codes to the visual cortex. The visual cortex then interprets the signals and converts the signals into light, color, and visual images. Light, color, and visual images do not exist at all outside of a receptive brain. In fact they don’t exist at all inside of our visual cortex. Our visual images are pure perception. Tehy don’t exist in reality. The brain “manufactures” the light that we see, as well as the odors that we smell, sound we hear, taste, and texture. Without a brain’s visual cortex to interpret the signals it gets from the retina, the electromagnetic waves from the sun would only be useful in warming and energizing the planet earth. How would evolution “know” that if it evolved this incredibly complex vision system, light, color, and incredible images would be at the finish line.

http://www.detectingdesign.com/humaneye.html

If a change in selective pressures favored a dimpled eyespot with a slight increase in visual acuity, pretty soon the majority of the population would have dimpled eyespots.  The problem with this notion is that no population of creatures with flat eyespots shows any sort of intra-population range like this were even a small portion of the population has dimpled eyespots to any selectable degree.  This is a common assertion, but it just isn't true.

the first step in vision is the detection of photons.  In order to detect a photon, specialized cells use a molecule called 11-cis-retinal.  When a photon of light interacts with this molecule, it changes its shape almost instantly.  It is now called trans-retinal.  This change in shape causes a change in shape of another molecule called rhodopsin.  The new shape of rhodopsin is called metarhodopsin II.  Metarhodopsin II now sticks to another protein called transducin forcing it to drop an attached molecule called GDP and pick up another molecule called GTP.  The GTP-transducin-metarhodopsin II molecule now attaches to another protein called phosphodiesterase.  When this happens, phosphodiesterase cleaves molecules called cGMPs.  This cleavage of cGMPs reduces their relative numbers in the cell.  This reduction in cGMP is sensed by an ion channel.  This ion channel shuts off the ability of the sodium ion to enter the cell.  This blockage of sodium entrance into the cell causes an imbalance of charge across the cell's membrane.  This imbalance of charge sends an electrical current to the brain.  The brain then interprets this signal and the result is called vision.

Many other proteins are now needed to convert the proteins and other molecules just mentioned back to their original forms so that they can detect another photon of light and signal the brain.  If any one of these proteins or molecules is missing, even in the simplest eye system, vision will not occur

The question now of course is, how could such a system evolve gradually?  All the pieces must be in place simultaneously.  For example, what good would it be for an earthworm that has no eyes to suddenly evolve the protein 11-cis-retinal in a small group or "spot" of cells on its head?  These cells now have the ability to detect photons, but so what?  What benefit is that to the earthworm?  Now, lets say that somehow these cells develop all the needed proteins to activate an electrical charge across their membranes in response to a photon of light striking them.  So what?!  What good is it for them to be able to establish an electrical gradient across their membranes if there is no nervous pathway to the worm's minute brain?   Now, what if this pathway did happen to suddenly evolve and such a signal could be sent to the worm's brain.  So what?!  How is the worm going to know what to do with this signal?  It will have to learn what this signal means.  Learning and interpretation are very complicated processes involving a great many other proteins in other unique systems.  Now the earthworm, in one lifetime, must evolve the ability to pass on this ability to interpret vision to its offspring.  If it does not pass on this ability, the offspring must learn as well or vision offers no advantage to them.  All of these wonderful processes need regulation.  No function is beneficial unless it can be regulated (turned off and on).  If the light sensitive cells cannot be turned off once they are turned on, vision does not occur.  This regulatory ability is also very complicated involving a great many proteins and other molecules - all of which must be in place initially for vision to be beneficial.

The complexity of transcription through RNA polymerase enzymes and general transcription factors in eukaryotes 10
Transcription is the process of making RNA from a DNA template. Several key factors are involved in this process. Including, DNA, transcription factors, RNA polymerase, and ATP.
Many proteins (well over 100 individual subunits) must assemble at the start point of transcription to initiate transcription in a eucaryotic cell.
This is a irreducible complex system. DNA, transcription factors, RNA polymerase, and ATP must be present, otherwise transcription cannot occur.
Transcription begins with a strand of DNA. It is divided into several important regions. The largest of these is the transcription unit. This portion of the DNA will be used to produce RNA. Upstream of the transcription unit is the TATA box. An enhancer region may also be involved.
Several complexes, known as transcription factors, are required for successful transcription. The first is TFIID, the largest of the general factors. A component of this factor, TBP, binds to the DNA using the TATA box to position TFIID near the transcription initiation site. Other transcription factors, including TFIIA and TFIIB, then attach.
These complexes prepare the DNA for the successful binding of RNA polymerase. One RNA polymerase is bound, other transcription factors complete the mature transcription complex.
Now, energy must be added to the system for transcription to begin. This energy is provided by the reduction of ATP into ADP and Pi.
RNA polymerase then synthesizes an RNA template from the strand of DNA. Most factors are released after transcription begins. When the end of the transcription unit is reached, the RNA polymerase dissociates, and the newly formed strand of RNA is released.
All the parts must come into existence at the same time, one has no function without the others. Also the whole sequence of events must be coordinated, and all parts must fit precisely together. There is no feasable mechanism producing this complex system randomly and in a stepwise fashion. Evolution is not a option, since transcription is required to make proteins, which are required to make replication work, which is essential upon which evolution works.

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

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

1) https://reasonandscience.catsboard.com/t1585-nitrogenase
2) https://reasonandscience.catsboard.com/t2093-dna-is-irreducible-complex#3665
3) https://reasonandscience.catsboard.com/t2039-interdependence-of-the-dna-double-helix-the-genetic-code-and-the-machinery-to-transcribe-and-translate-the-code-to-make-proteins#3464
4) https://reasonandscience.catsboard.com/t2038-interdependence-of-the-promoter-region-in-dna-transcription-factors-and-rna-polymerase-ii#3462
5) https://reasonandscience.catsboard.com/t1299-the-cell-is-irreducibly-complex
6) https://reasonandscience.catsboard.com/t2128-membrane-structure#3798
7) https://reasonandscience.catsboard.com/t1299-the-cell-is-irreducibly-complex
8 ) https://reasonandscience.catsboard.com/t2051-nucleosomes-function-and-design?highlight=nucleosomes
9) https://reasonandscience.catsboard.com/t1638-eye-brain-is-a-interdependent-and-irreducible-complex-system
10) https://reasonandscience.catsboard.com/t2036-the-complexity-of-transcription-through-rna-polymerase-enzymes-and-general-transcription-factors-in-eukaryotes#3451

The chlorophyll biosynthesis pathway is irreducible complex 1

https://reasonandscience.catsboard.com/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. 

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 by its own, if not fully embedded in the fotosyntesis process ? none.
What good would there be for fotosynthesis without chlorophyill in place, capturing light, and transmitting it to the photosystem ? none, since capturing 
light is essential for the whole process. 

‘Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved?’

Five following conditions would all have to be met:

the issue about the observed origin of irreducible complexity, similarly, is not to be dismissed by saying that’s Behe’s argument. Have you had an empirically warranted answer to Menuge’s  C1 – 5 criteria for exaptation  (  a shift in the function of a trait during evolution. For example, a trait can evolve because it served one particular function, but subsequently it may come to serve another.). . . the usual attempted counter? If not, then the issue of irreducible complexity is very definitely still on the table. The criteria:

For a working biological system 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 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 sub systems 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.)

Blankenship: Molecular mechanisms of photosynthesis pg.208:

It is not conceivable that highly complex molecules such as chlorophylls were synthesized by prebiotic chemistry, given their very specific functional groups and multiple chiral centers. Instead, they are the end product of a progressive evolutionary development, in which simple molecules are the start of the biosynthesis chain and are then progressively elaborated in later steps. In this view, each intermediate in the modern pathway was at some point the end point in the pathway. This requires that each intermediate in the modern pathway be usable in the past as an end product. In the case of chlorophyll biosynthesis, Granick proposed that simple porphyrins or porphyrin precursors were the starting points, and that successive steps were added to improve the efficiency of the pigments or to extend light absorption into new spectral ranges. This is an appealing
idea and is probably at least partially true. The Granick hypothesis in the context of photosynthesis has been championed by Mauzerall (1992), as well as embraced by others (Olson and Pierson, 1987; Olson, 1999, 2006).

This is about the best explanation that proponents of naturalistic origins can come up with. All it exemplifies is baseless just so assertions in a superficial manner. Pseudo science at its best. It should be clear to any honest thinker that there is a hudge gap of explanatory power between proponents of naturalism, and design. 

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. Photosynthesis missing one piece (like chlorophylls) 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!

The heme biosynthesis pathway is irreducible complex. 2

Heme biosynthesis is a complex pathway with 8 highly specific steps, of which 6 steps are used by specific enzymes uniquely in this pathway.
The pathway must go all the way through, otherwise heme is not synthesized.
Therefore, the heme biosynthesis pathway is irreducible complex.

Questions:
What good would there be, if the pathway would go only up to the 7th step ? none
What good would there be, if the pathway would go all the way through the 8th step ? Heme would be produced , BUT :
What good for survival would there be for Heme by its own, if not fully embedded in the globin proteins? none.
What good would there be for red bloodcells without hemoglobin, transporting oxygen to the cells in the body ? none, transporting oxygen is essential for the whole process. I conclude therefore that the heme biosynthesis pathway is irreducible complex, and could not have evolved upon mutation and natural selection.

I mentioned that some enzymes have to be imported into the mitochondrion. These enzymes contain special protein sequences called targeting signals that direct them to the right place. So the next question: is globin targeted to the mitochondrion? No - it is synthesised on ribosomes, attached to the Golgi apparatus in the cytoplasm and it stays there. Some of the haem made in the mitochondrion is used by mitochondrial proteins called cytochromes, but the rest is exported back outside where it can attach to the globin protein. Have a look at these Wikipedia pages: heme and porphyrin, for some more details. Porphyrins, by the way, are intermediates in haem synthesis that also have the tetrapyrrole structure.

Researchers have done experiments in which they synthesised globin protein chains to see at what point the haem attached. It can attach when about 80-90 amino acids have emerged from the ribosome - in other words, it attaches to the "nascent chain" as the protein is being synthesised. One of the mysteries that we don't fully understand is how the haemoglobin assembles itself properly - so as it has 2 alpha chains and 2 beta chains each with a haemoglobin attached.

Question : for what reason would evolution try to assemble the heme to the globin ? what survival advantage would there be provided by a globin without the heme ? and what advantage of the heme without the globin ?

Photosynthesis is irreducible complex 3

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. 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. So it seems that photosynthesis falsifies the theory of evolution, where all small steps need to provide a survival advantage.

ATP synthase is an irreducibly complex motor  4


1.The nucleotide binding stator subunits (“cylinders”) :  The electrostatic interaction of these rotor and stator charges is essential for torque generation
2.The central stalk (“crankshaft”) : The torsional elasticity of the central stalk and the bending and stretching elasticity of the peripheral stalk create an elastic coupling between Fo and F1. Is is essential.
3, The A/V rotor subunit (“adapter”) ; It is not used in all ATP synthase motors, and can therefore be reduced.
4. The Rotor ring (“turbine”) ;  A ring of 8–15 identical c-subunits is essential for ion-translocation by the rotary electromotor of the ubiquitous FOF1-
ATPase.
5.The Jon channel forming subunit ; Subunit a harbors the ion channel that provides access to the binding site on the c11 ring in the middle of the membrane from the periplasmic surface . The channel is essential for the operation of the enzyme, because mutants in which the channel is blocked are completely inactive in both the ATP synthesis and/or coupled ATP hydrolysis mode
6. The peripheral stalk (“pushrod”) ; The peripheral stalk of F-ATPases is an essential component of these enzymes. It extends from the membrane distal point of the F1 catalytic domain along the surface of the F1 domain with subunit a in the membrane domain.
7 - 11 do not exist in all atp synthase motors, and can therefore be reduced. 

There are at least 5 subunit parts essential to mantain the basice function of the ATP synthase motor. 

ATP synthase is an irreducibly complex motor—a proton-driven motor divided into rotor and stator portions as described and illustrated earlier in this paper. Protons can flow freely through the CF0 complex without the CF1 complex, so that if it evolved first, a pH gradient could not have been established within the thylakoids. The δ and critical χ protein subunits of the CF1 complex are synthesized in the cytosol and imported into the chloroplast in everything from Chlorella to Eugenia in the plant kingdom.49 All of the parts must be shipped to the right location, and all must be the right size and shape, down to the very tiniest detail. Using a factory assembly line as an analogy, after all the otherwise useless and meaningless parts have been manufactured in different locations and shipped in to a central location, they are then assembled, and, if all goes as intended, they fit together perfectly to produce something useful. But the whole process has been carefully designed to function in that way. The whole complex must be manufactured and assembled in just one certain way, or nothing works at all. Since nothing works until everything works, there is no series of intermediates that natural selection could have followed gently up the back slope of mount impossible. The little proton-driven motor known as ATP synthase consists of eight different subunits, totalling more than 20 polypeptide* chains, and is an order of magnitude smaller than the bacterial flagellar motor,50 which is equally impossible for evolutionists to explain.


The velvet worms slime cannon mechanism is irreducibly complex  5


The Velvet Worm is armed with a pair of slime-guns, which are actually their front limbs. The slime squirts off the guns as gooey streams of liquid, normally directed at prey to ensnare them. Quite magically, this biological glue is supposed to harden into a gel almost immediately upon contact with the prey. Apparently, it would eat back the slime after the squirt. No wastage there! Such tactics reminds me of... the Spitting Spider (Scytodiidae) which also spits venom at their prey. 


it needs 5 different systems

1) weapon: slime pistol/gland which stores an adhesive which is what this slime is
2) ammunition: paralysing slime which only dries and hardens when ejected
3) targeting mechanism/ability
4) highly sensitive tentacles that carry the worm to the prey
5) poisonous saliva that begins the digestion process

Each of these traits would not provide any survival advantage by their own , and have to appear fully functional, otherwise the mechanism does not work.

Question: evolution is blind and would have to randomly generate each part, which in turn would need to provide a selection advantage to be passed to the next generation. It is very unlikely and there currently is no evidence that this happened. We can accept it on faith. how would you falsify this.?

How could the Velvet Worms molecules somehow forsee and KNOW the laws of fluidity and willingly respond to them? Which school they attended and what aspect of their interpretation of these laws did they apply in their molecular engineering project? Unless the fluid is fully ready and empowered to exercise its function, it has no function....... 

The nitrogen cicle, irreducible interdependence, and the origin of life 6

Nitrogen is a part of vital organic compounds in microrganisms, such as amino acids, proteins and DNA. During the conversion of nitrogen, cyanobacterias will first convert nitrogen from the atmosphere into ammonia and ammonium through nitrogenase, during the nitrogen fixation process. After ammonium fixation, the ammonia and ammonium that is formed convert it through further reduction to nitrite and nitrage into their cellular material, and on dying, decompose and make nitrogen available to the soil,  which serves plants for nutrition, after which they are converted into nitrogen-containing organic molecules, such as amino acids and DNA. Animals cannot absorb nitrates directly. They receive their nutrient supplies by consuming plants or plant-consuming animals.

So, resuming :  Without cyanobacteria - no fixed nitrogen is available. Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesised. Without DNA, no amino-acids,protein, or cyanobacteria are possible. So there you have a interdependent cycle, with no beginning. But, wait : there is more : cyanobacteria are facultative anaerobes - meaning that they can respire either aerobically or anaerobically. The complexity of two respiratory cycles is very high: the Krebs cycle alone requiring about 12 enzymes, and the anaerobic requiring somewhat fewer, say 8.  So in order for the cyanobacteria to survive, about 40 enzymes are already involved - none of which can be made without fixed nitrogen. So here we have a chicken-egg problem par excellence , which came first..... ??

Lighting is another source, but since its supposed that Photosynthesis had not evolved at the stage of a common ancestor, there was a reduced atmosphere without oxygen. If there was a reduced atmosphere ( which btw. there is no scientific evidence for, rather the oposit is the case ) then there would be no ozone layer, and  the ultraviolet radiation would penetrate the atmosphere and would destroy the amino acids as soon as they were formed. If the Cyanobacterias however would overcome that problem ( its supposed the bacterias in the early earth lived in the water, but that would draw other unsurmountable problems ), and evolve photosynthesis, they would have to evolve at the same time protective enzymes that prevented them oxygen to damage their DNA through hydroxyl radicals. So what evolutionary advantage would there be they to do this ?

To avoid their DNA getting wrecked by a hydroxyl radical that naturally occurs in the production of oxygen, the cyanobacteria would have had to evolve protective enzymes. But how could natural selection have led the cyanobacteria to evolve these enzymes if the need for them didn’t even exist yet?  The explanations are fantasious at best.  But even if lets say that enough nitrogen would be available at the primordial earth , that far from explains the information encoded in Fifteen nitrogen fixation or nitrogen fixation-related genes, including the structural genes for nitrogenase,nifHDK, which are clustered together as follows:nifB-fdxN-nifS-nifU-nifH-nifD- nifK-nifE-nifN-nifX-orf2-nifW-hesA-hesB-fdxH.Thesegenes are organized in at least six transcriptional units:nifB-fdxN-nifS-nifU, nifHDK, nifEN,nifX-orf2, nifW-hesA-hesB, and fdxH.......  


Human organ development, it can't happen through evolution 7

Byron Bledsoe :

There are many examples of irreducible complexity, that could be cited. Consider the circulatory system. It consists of blood, veins, arteries, and the heart. The blood in turn consists of plasma and red and white corpuscles, and more. The heart consists of chambers, muscles, valves, a timing mechanism, blood vessels to nourish the heart tissue, and nerves to control the heart muscles. To be useful, the arteries require the entire respiratory system to provide them with oxygen, and require the entire digestive system to provide them with food and water. Also, the heart nerves require a connection to the nervous system to control timing of the heart muscles. These required respiratory, digestive , and nervous systems are complex systems within themselves, having many components. With all these components in place and properly connected they perform a beautiful function. They keep us alive. But take away any component, and death is the result. What good would the incipient development or even the complete development  of any of these components be in the absence and proper connection of all the other components ? What good would the blood vessels be for without the heart, and the blood ? I consider this argument to be the most powerful argument the creationists have. More importantly, this argument alone is enough to convince me that God had to be involved in some way, even if evolution  was apart of the process. 

The Nitrogenase enzyme,  the molecular sledgehammer 1

http://www.ebi.ac.uk/interpro/entry/IPR000392

Nitrogen fixing bacteria possess a nitrogenase enzyme complex that catalyses the reduction of molecular nitrogen to ammonia [PMID: 2672439, PMID: 6327620, ]. The nitrogenase enzyme complex consists of two components:

 Component I is nitrogenase MoFe protein or dinitrogenase, which contains 2 molecules each of 2 non-identical subunits.

 Component II is nitrogenase Fe protein or dinitrogenase reductase, which is a homodimer. The monomer is encoded by the nifH gene [PMID: 6327620].

The subunits are unique , and cannot be used in other proteins. 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

DNA is irreducible complex 2

Individual bases : take away the sugar in the DNA backbone = no function
Take away the phosphate in the backbone = no function
Take away the nucleic acid bases = no function
Evolution is not a driving force at this stage, since replication of the cell depends on DNA.
So the individual DNA molecules are irreducible complex
DNA in general ( the double helix )
Unless the two types, purines, and pyrimidines are present, and so the individual four bases = no function, and no hability of information storage
The enzymes and proteins for assembly and synthesis of the DNA structure must also be present, otherwise, no DNA double helix......

Self-organizing biochemical cycles

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC18793/

How were ribonucleotides first formed on the primitive earth? This is a very difficult problem. Stanley Miller's synthesis of the amino acids by sparking a reducing atmosphere (2) was the paradigm for prebiotic synthesis for many years, so at first, it was natural to suppose that similar methods would meet with equal success in the nucleotide field. However, nucleotides are intrinsically more complicated than amino acids, and it is by no means obvious that they can be obtained in a few simple steps under prebiotic conditions. A remarkable synthesis of adenine (3) and more or less plausible syntheses of the pyrimidine nucleoside bases (4) have been reported, but the synthesis of ribose and the regiospecific combination of the bases, ribose, and phosphate to give β-nucleotides remain problematical.



1) http://reasonandscience.heavenforum.org/t1546-chlorophyll-biosynthesis-pathway
2) http://reasonandscience.heavenforum.org/t1322-the-amazing-hemoglobin-molecule
3) http://reasonandscience.heavenforum.org/t1555-photosynthesis?highlight=photosynthesis
4) http://reasonandscience.heavenforum.org/t1439-atp-synthase
5) http://reasonandscience.heavenforum.org/t1729-the-superpowers-of-the-velvet-worm
6) http://reasonandscience.heavenforum.org/t1562-the-nitrogen-cicle-irreducible-interdependence-and-the-origin-of-life?highlight=irreducible
7) http://reasonandscience.heavenforum.org/t1743-human-organ-development-it-can-t-happen-through-evolution