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Theory of Intelligent Design, the best explanation of Origins » Intelligent Design » Irreducible complexity » The cell is irreducibly complex

The cell is irreducibly complex

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1 The cell is irreducibly complex on Thu Nov 14, 2013 8:58 am

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The cell is irreducibly complex

http://reasonandscience.heavenforum.org/t1299-the-cell-is-irreducibly-complex

Let's suppose an immensely unlikely random accident would produce a self-replicating RNA molecule in a prebiotic world. That molecule would have no function on its own, in the same manner as a piston has no function by its own unless fully mounted with the right fit in the cylinder. In the same manner, as a water turbine has no function on its own unless mounted at the river with the energy gradient, and all other parts to make energy, there would be no function for it. In the same manner, the energy turbine of life, ATP synthase, would have no function on its own, unless a proton gradient is established in the cell, and for that, a membrane to establish the gradient is required. Had the cell membrane, the energy gradient, and ATP synthase not to be fully setup together right from the beginning, otherwise, one could not bear any function on its own, together with the other parts?  Let's suppose you have a car. You enter the car, turn the key, but the cable that connects the signal to the battery, the car's engine will not turn on. Intelligence is required to find out, which cable has to connect, to solve the problem. But in cells, even if one protein, as tiny as it might seem, is missing, cells cannot become alive either. A cell without any of the key enzymes to make energy, will not function. But all enzymes and proteins are intricately complex and must be interconnected in a metabolic network, to bear function.

Mainstream scientific papers confirm indirectly that cells are irreducible complex. The paper: Determination of the Core of a Minimal Bacterial Gene Set says: Based on the conjoint analysis of several computational and experimental strategies designed to define the minimal set of protein-coding genes that are necessary to maintain a functional bacterial cell, we propose a minimal gene set composed of 206 genes. Such a gene set will be able to sustain the main vital functions of a hypothetical simplest bacterial cell.

How Many Genes Can Make a Cell: The Minimal-Gene-Set Concept 
https://www.ncbi.nlm.nih.gov/books/NBK2227/
Several theoretical and experimental studies have endeavored to derive the minimal set of genes that are necessary and sufficient to sustain a functioning cell under ideal conditions, that is, in the presence of unlimited amounts of all essential nutrients and in the absence of any adverse factors, including competition. A comparison of the first two completed bacterial genomes, those of the parasites Haemophilus influenzae and Mycoplasma genitalium, produced a version of the minimal gene set consisting of ~250 genes. 

Compartmentalization is a necessary prerequisite for maintaining the integrity of such interdependent molecular systems and for permitting the variations required for speciation (Tawfik and Griffiths, 1998). 3

chemist Wilhelm Huck, professor at Radboud University Nijmegen
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity

Protocells formed in salt solution - closer to synthetic life than anyone


To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. — Lynn Margulis

http://news.illinois.edu/news/11/1005LUCA_ManfredoSeufferheld_JamesWhitfield_Caetano_Anolles.html
New evidence suggests that LUCA was a sophisticated organism after all, with a complex structure recognizable as a cell, researchers report. Their study appears in the journal Biology Direct. The study lends support to a hypothesis that LUCA may have been more complex even than the simplest organisms alive today, said James Whitfield, a professor of entomology at Illinois and a co-author on the study.


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 fulfill its task? Ok. You could use it as an 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 employed ?
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?

http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.171&rep=rep1&type=pdf
Functional parts are only meaningful within a whole, in other words, it is the whole that gives meaning to its parts. 1
Parts require a blueprint in order to be made upon specified complex instructional information. The information is based on a language system wich must be pre-established.
In order to define a sign or a code (which can be a symbol, an index, or an icon) a whole cluster of self-referring concepts is presupposed, that is, the definition cannot be given on a priori grounds, without implicitly referring to this cluster of conceptual agents. In other words, to define a specific subpart of a machine that requires a specific shape, size, material etc. the initial requirement is a 1. language or code system, and 2. the information based on that language to specify the part in question.
Intelligent agents think with an "end goal" in mind, allowing them to solve complex problems by taking many parts and arranging them in intricate patterns that perform a specific function 2  They need to be able to organize parts availability, synchronization, manufacturing and assembly coordination and interface compatibility of the single parts and subunits. The individual parts must precisely fit together.

Biological function and sign systems, resemble the complexity of computer programs.  There cannot be information without an interpreter,  there is no message coming from the genes without the cell machinery in place that interprets the genes. Catch 22. On the other hand the cell machinery must be rooted causally ( or have their origin ) in the symbolic codes for at least two reasons. Firstly, the cell machinery consists of different parts that have to be produced in a number of copies depending on a memory ( instructions stored in dna ). Secondly, functionality of the cell machinery implies a three-dimensional folding, which is determined by the intrinsic properties of the building blocks e.g. amino acids. In addition there are control mechanisms for protein folding. The production of proteins presupposes a control mechanism involving the genes that secures ( and defines ) the entire sequence of amino acids before the folding takes place.  This leaves us with two mutually dependent categories of chemical structures or events (symbols and cell machinery), which does not fit with the axioms of probability that only considers one-way dependency. Thus, the structure of life has a probability to emerge randomly of zero.

Life express both function and sign systems, which indicates that it is not a subsystem of the universe, since chance and necessity cannot explain sign systems, meaning, purpose, and goals 

Now lets apply that to biology.

What good would DNA, mRNA, RNA polymerase, tRNA's, Ribosomes and chaperones be good for by their own, if not interconnected in a working cell ? Why would a prebiotic soup produce these molecular machines ? They would only become functional with the instructions encoded in DNA, defining and specifying how they would have to be interconnected The thing is, there's no driver for any of the pieces to emerge 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 a planning organizing creative intelligence.  

Biological systems are functionally organized , integrated into an interdependent network, and complex, like human-made machines and factories. The wiring of an 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 addressed adequately.

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 robot in a factory assembly line fails, employees are ready to detect the error and make the repair. In the cell, the malfunction 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.


The Irreducible Complexity of a Protein

http://coldcasechristianity.com/2012/christianity-promotes-rational-and-evidential-exploration/

   Now let’s take a look again at the simple protein and see how it is assembled out of amino acids. These acids have to come together in a specific way and if they do, then they begin to fold up onto themselves to form the specific shapes and clusters that we call proteins. But ask yourself the question: how do these amino acids know how to join to each other? Is there a natural attraction between the acids that acts like magnets coming together? No.. When scientists discovered DNA, they unlocked a powerful secret within the cell. They realized that the acids come together in response to INFORMATION and DIRECTION from the DNA molecule which exists alongside the acids and proteins! The DNA directs the assembly of the acids and provides a blueprint for the operation! And DNA is the most densely packed molecule in the known universe. It is a highly complex, highly ordered and extremely large assembly of information containing more data than the largest human library and posing a far greater problem for evolutionists to explain that the most complicated proteins!



   DNA poses a dilemma. Proteins cannot form without the DNA information and direction. But DNA is highly complex, ordered and informational. Where does it come from? As it turns out, the DNA molecule is filled with specific information that directs the assembly of the overall organism. And it is required for the protein to exist. The ‘irreducible complexity’ of the protein is not just a number of simple amino acid chemicals. The ‘irreducible complexity’ of the protein also includes the most complex known molecule in the universe: the DNA molecule. ‘Irreducible complexity’ of the protein demonstrates that the random forces of nature cannot explain the origin of life.

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

For a nonliving system, questions about irreducible complexity are even more challenging for a totally natural non-design scenario, because natural selection — which is the main mechanism of Darwinian evolution — cannot exist until a system can reproduce.  For an origin of life we can think about the minimal complexity that would be required for reproduction and other basic life-functions.  Most scientists think this would require hundreds of biomolecular parts, not just the five parts in a simple mousetrap or in my imaginary LMNOP system.  And current science has no plausible theories to explain how the minimal complexity required for life (and the beginning of biological natural selection) could have been produced by natural process before the beginning of biological natural selection.



http://evidencepress.com/articles/ultimate-irreducible-complexity/

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.


Another huge problem is that information is useless unless it can be read. But the decoding machinery is itself encoded on the DNA. The leading philosopher of science, Karl Popper (1902–1994), expressed the huge problem:

‘What makes the origin of life and of the genetic code a disturbing riddle is this: the genetic code is without any biological function unless it is translated; that is, unless it leads to the synthesis of the proteins whose structure is laid down by the code. But … the machinery by which the cell (at least the non-primitive cell, which is the only one we know) translates the code consists of at least fifty macromolecular components which are themselves coded in the DNA. Thus the code can not be translated except by using certain products of its translation. This constitutes a baffling circle; a really vicious circle, it seems, for any attempt to form a model or theory of the genesis of the genetic code.

A classic example of interdependence is that of DNA and proteins. Within each cell, proteins manufacture, repair, and access DNA. So, DNA depends on proteins. But DNA provides the blueprints for protein structure, so proteins also depend on DNA. These two system parts stand and function only when working together, and they fall apart when separated from each other.

http://evidencepress.com/articles/ultimate-irreducible-complexity/

“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.”

A specific example described in the book is the interdependence of DNA, RNA and protein. We summarize the issue, “DNA, RNA and proteins cannot do their jobs without the help of at least one of the other two. DNA is a library of detailed information for the various structures within the cell. It has the information for the manufacture of each protein. RNA is a copy of instructions from the DNA and is sent as a messenger to the ribosomes for making proteins. There are two types of proteins; functional proteins such as enzymes, and structural proteins, which compose the organelles. Living cells need all three molecules at the same time. The chance, simultaneous natural appearance of the three distinct, interdependent complex systems is just not possible.” Not only are these three needed for life, but an organism also needs a cell membrane, usable energy, reproduction and all left-handed amino acids. The cell itself is a tremendous and irrefutable example of irreducible complexity.

Considering the cell as being the ultimate irreducibly complex system, there is no conceivable way that life could arise by natural causes. Darwin’s theory of numerous, successive, slight modifications simply does not work when discussing the origin of life. The problem that irreducibly complexity brings to evolution is clearly daunting for evolutionists. Their way to deal with the problem is to dismiss it as nonscientific, pseudoscience or religion dressed in a tuxedo. However, when one looks at the issue of origin of life through the lens of irreducible complexity, it simply brings one with a reasonable mind to his or her knees, admitting life cannot begin by natural causes.


http://christianevidences.org/scientific-evidence/hematology/the-cell-and-irreducible-complexity/




http://www.rejectionofpascalswager.net/behe.html

Cellular transport systems:

Gated transport is called thus due to it's similarity to our everyday experience of passing through a guarded (electronically or otherwise) gate. This system require three basic components to work: an identification tag, a scanner (to verify identification) and a gate (that is activated by the scanner). The system needs all three components to work otherwise it will not work. Thus in a cell, when a protein is to be manufactured, one of the first steps is for the mRNA [c] to be transported out from the nucleus into the cytoplasm. This requires gated transport of the mRNA at the nuclear pore. Proteins in the pore reads a signal from the RNA (the scanner reads the identification tag) and opens the pore (gate is opened).


DNA and information

The structure of DNA polymerase is determined by information stored on DNA, but it takes DNA polymerase and other proteins to make DNA.  Furthermore, information to make DNA polymerase must be transferred to RNA before it can be used to make proteins from amino acids.  Making the RNA copy also requires proteins.
Can you see where the process has a beginning?  Could any of it function before the whole system was complete?
This system will not work unless all the components are present and functioning.  This means that in order to start life you must have proteins and RNA and DNA.

The cell is irreducibly complex
http://reasonandscience.heavenforum.org/t1299-the-cell-is-irreducibly-complex

The irreducible, code-instructed process to make cell factories and machines points to intelligent design
http://reasonandscience.heavenforum.org/t2364-the-irreducible-code-instructed-process-to-make-cell-factories-and-machines-points-to-intelligent-design

All cellular functions are  irreducibly complex
http://reasonandscience.heavenforum.org/t2179-the-cell-is-a-interdependent-irreducible-complex-system

The Cell membrane, irreducible complexity
http://reasonandscience.heavenforum.org/t2128-membrane-structure#3798

The Interdependency of Lipid Membranes and Membrane Proteins
http://reasonandscience.heavenforum.org/t2397-the-interdependency-of-lipid-membranes-and-membrane-proteins

Factory and machine planning and design, and what it tells us about cell factories and molecular machines
http://reasonandscience.heavenforum.org/t2245-factory-and-machine-planning-and-design-and-what-it-tells-us-about-cell-factories-and-molecular-machines

Genome information, protein synthesis,  the biosynthesis pathways in biologiy, and the analogy of human programming, engeneering, and factory robotic assembly lines
http://reasonandscience.heavenforum.org/t1987-information-biosynthesis-analogy-with-human-programming-engeneering-and-factory-robotic-assembly-lines

What might be a Cell’s minimal requirement of parts ?  
http://reasonandscience.heavenforum.org/t2110-what-might-be-a-protocells-minimal-requirement-of-parts

How Cellular Enzymatic and Metabolic networks  point to design
http://reasonandscience.heavenforum.org/t2371-how-cellular-enzymatic-and-metabolic-networks-point-to-design




1. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.171&rep=rep1&type=pdf
2. http://www.evolutionnews.org/2011/03/a_closer_look_at_one_scientist045311.html
3. http://complex.upf.es/~andreea/2006/Bib/MonnardDeamer.NutrientUptakeByProtocells.pdf



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2 Re: The cell is irreducibly complex on Sat Nov 16, 2013 11:01 am

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Essential parts and functions in the cell

The mechanism by which chromosomal DNA molecules are held together: entrapment within cohesin rings?

mysterious has been the trigger for what is arguably the most dramatic and one of the most highly regulated events in the life of a eukaryotic cell, the sudden disjunction of sister chromatids at the metaphase to anaphase transition. 1

Work in our lab has shown that sister chromatids are held together by a multi-subunit complex called cohesin whose Smc1 and Smc3 subunits are rod shaped proteins with ABC-like ATPases at one end of 50nm long intra-molecular anti-parallel coiled coils. At the other ends are pseudo-symmetrical hinge domains that interact to create V shaped Smc1/Smc3 heterodimers. N- and C-terminal domains within cohesin’s third subunit, known as α kleisin, bind to Smc3 and Smc1 ATPase heads respectively, thereby creating a huge tripartite ring whose integrity is essential for holding sister DNAs together. A thiol protease called separase opens the cohesin ring by cleaving its α kleisin subunit, which causes cohesin’s dissociation from chromosomes and triggers sister chromatid disjunction.


Regulation of chromosome condensation and segregation. 2

Regulated and controlled chromosome condensation and segregation is essential for the transmission of genetic information from one generation to the next. A myriad of techniques has been utilized over the last few decades to identify proteins required for the organized compaction of the massive length of a cell's DNA. A full understanding of the components and processes involved relies on further work, exploiting biochemical, genetic, cytological, and proteomics approaches to complete the picture of how a cell packages and partitions its genome during the cell cycle.

Condensins: universal organizers of chromosomes with diverse functions 3

Condensins are multisubunit protein complexes that play a fundamental role in the structural and functional organization of chromosomes in the three domains of life. Most eukaryotic species have two different types of condensin complexes, known as condensins I and II, that fulfill nonoverlapping functions and are subjected to differential regulation during mitosis and meiosis.

The multisubunit condensin complex is essential for the structural organization of eukaryotic chromosomes during their segregation by the mitotic spindle 4


Recruitment of the conserved centromeric protein shugoshin is essential for biorientation, but its exact role has been enigmatic. 5


A mystery surrounding tubulin, the protein that plays a crucial role in the passing of genetic material from a parent cell to daughter cells, has been at least partially solved. 6 Nogales and her colleagues also identified a region in Dam1 essential for the regulation of the complex, by spindle-checkpoint kinase enzymes. "These kinases are signaling proteins that, based on tension in the spindles, tell the ring when the time is right for it to let go of the microtubules," Nogales says. "We have found that without this region, the ability of the Dam1 to form a ring is reduced."

All eukaryotic cells must segregate their chromosomes equally between two daughter cells at each division. This process needs to be robust, as errors in the form of loss or gain of genetic material have catastrophic effects on viability. Chromosomes are captured, aligned, and segregated to daughter cells via interaction with spindle microtubules mediated by the kinetochore. 7


Topoisomerase II enzymes are essential in the separation of entangled daughter strands during replication. This function is believed to be performed by topoisomerase II in eukaryotes and by topoisomerase IV in prokaryotes. Failure to separate these strands leads to cell death.

Controlled transport of macromolecules between the cytoplasm and nucleus is essential for homeostatic regulation of cellular functions. For instance, gene expression entails coordinated nuclear import of transcriptional regulators to activate transcription and nuclear export of the resulting messenger RNAs for cytoplasmic translation. Thus, Ddx19 participates in mRNA export, translation and nuclear import of a key transcriptional regulator. 9

Cell membranes are crucial to the life of the cell. 10

Nucleo-cytoplasmic transport of RNAs and proteins is essential for eukaryotic gene expression. 11


The field of mitochondrial ion channels has recently seen substantial progress, including the molecular identification of some of the channels. An integrative approach using genetics, electrophysiology, pharmacology, and cell biology to clarify the roles of these channels has thus become possible. It is by now clear that many of these channels are important for energy supply by the mitochondria and have a major impact on the fate of the entire cell as well. 12


Mammalian mtDNA only encodes 13 proteins, but these are nevertheless essential for cell viability as they are crucial components of the oxidative phosphorylation system, located in the inner mitochondrial membrane 13

In eukaryotes, lipid metabolism requires the function of peroxisomes. These multitasking organelles are also part of species-specific pathways such as the glyoxylate cycle in yeast and plants or the synthesis of ether lipid in mammals.Peroxisomal function is essential for life. 14

Fatty acids are aliphatic acids fundamental to energy production and storage, cellular structure and as intermediates in the biosynthesis of hormones and other biologically important molecules. 15

Coenzyme A (CoA) is an essential cofactor in numerous metabolic and energy-yielding reactions and is involved in the regulation of key metabolic enzymes 16

γ-tubulin is essential for normal microtubule organization in every organism in which it has been studied, and it is nearly ubiquitous throughout the eukaryotes 17

Su48 represents a previously unrecognized centrosome protein that is essential for cell division18

The ab tubulin heterodimer is the structural subunit of microtubules, which are cytoskeletal elements that are essential for intracellular transport and cell division in all eukaryotes. 19

Presently, the best studied are the mitotic Kinesin-13 proteins. Studies in both D. melanogaster and human cells suggest a division of labor between Kinesin-13 family members, such that different proteins contribute microtubule depolymerizing activity to the centrosome and centromere  during mitosis. These activities have been shown to be essential for spindle morphogenesis and chromosome segregation.  20

During cell division, mitotic spindles are assembled by microtubule-based motor proteins1, 2. The bipolar organization of spindles is essential for proper segregation of chromosomes, and requires plus-end-directed homotetrameric motor proteins of the widely conserved kinesin-5 (BimC) family  21

The various functions of the Endoplasmic Reticulum are essential to every cell, their relative importance varies greatly between individual cell types.

Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. 22

Telomeres, the specialized nucleoprotein structures that cap the ends of linear chromosomes, are essential for genome integrity and hence cell viability because they protect chromosome ends from fusions and degradation.  23

Initiation of cellular DNA replication is tightly controlled to sustain genomic integrity. In eukaryotes, the heterohexameric origin recognition complex (ORC) is essential for coordinating replication onset.


DNA helicases are essential during DNA replication because they separate double-stranded DNA into single strands allowing each strand to be copied. 


1) http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=591
2) http://www.ncbi.nlm.nih.gov/pubmed/12672496
3) http://genesdev.cshlp.org/content/26/15/1659.full
4) http://www.nature.com/nsmb/journal/v18/n8/full/nsmb.2087.html?WT.ec_id=NSMB-201108
5) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4063673/
6) http://www2.lbl.gov/Science-Articles/Archive/sabl/2007/Oct/onering.html
7) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216659/
8 ) https://en.wikipedia.org/wiki/Type_II_topoisomerase
9) http://www.nature.com/ncomms/2015/150114/ncomms6978/full/ncomms6978.html
10) http://reasonandscience.heavenforum.org/t2128-membrane-structure#3789
11) file:///E:/Downloads/genes-06-00163.pdf
12) http://physrev.physiology.org/content/94/2/519
13) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105550/
14) http://www.springer.com/us/book/9783709117873
15) http://reasonandscience.heavenforum.org/t2168-lipids-fatty-acids-and-the-origin-of-life?highlight=fatty+acids
16) http://mbe.oxfordjournals.org/content/21/7/1242.full
17) http://www.nature.com/nrm/journal/v12/n11/full/nrm3209.html#B10
18) http://creationsafaris.com/crev200604.htm
19) http://www2.lbl.gov/tt/publications/1706pub.pdf
20) http://labs.cellbio.duke.edu/kinesin/MTdisassembly.html
21) http://www.nature.com/nature/journal/v435/n7038/full/nature03503.html
22) http://www.ncbi.nlm.nih.gov/pubmed/14985753
23) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251085/
24) http://www.nature.com/nature/journal/v519/n7543/full/nature14239.html       Nature 519, 321–326 (19 March 2015) doi:10.1038/nature14239

25) http://www.nature.com/scitable/definition/helicase-307




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3 Re: The cell is irreducibly complex on Mon Dec 02, 2013 4:41 pm

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The DNA - Enzyme System is Irreducibly Complex

http://www.ideacenter.org/contentmgr/showdetails.php/id/845

Which came first? DNA needs enzymes to replicate, but the enzymes are encoded by DNA. DNA needs protection provided by the cell wall, but the cell wall is also encoded by the DNA. The answer is that none came “first” for all are required in DNA-based life. These fundamental components form an irreducibly complex system in which all components must have been present from the start. This presents a challenge to the step-by-step evolution required by Darwin’s theory.

Hitching, p. 66.

The amino acids must link together to form proteins, and the other chemicals must join up to make nucleic acids, including the vital DNA. The seemingly insurmountable obstacle is the way the two reactions are inseparably linked—one can’t happen without the other. Proteins depend on DNA for their formation. But DNA cannot form without pre-existing protein.

John C. Walton, (Lecturer in Chemistry, University of St. Andrews, Fife, Scotland,Organization and the Origin of Life,” Origins, Vol. 4, No. 1, 1977, pp. 30–31.

The origin of the genetic code presents formidable unsolved problems. The coded information in the nucleotide sequence is meaningless without the translation machinery, but the specification for this machinery is itself coded in the DNA. Thus without the machinery the information is meaningless, but without the coded information the machinery cannot be produced! This presents a paradox of the ‘chicken and egg’ variety, and attempts to solve it have so far been sterile.

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4 Re: The cell is irreducibly complex on Fri Dec 27, 2013 11:13 am

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http://www.arn.org/docs/odesign/od201/peeringdbb201.htm

There is good evidence to suggest that the process of cell division is indeed irreducibly complex, for the steps involved are interdependent and highly coordinated. For example, crucial steps such as DNA transcription require proteins (see Figure 1)—while protein synthesis in turn is dependent upon transcription. Moreover, evidence suggests that the processes involved in cell division are highly regulated and coordinated in a sequential fashion. For instance, in bacteria, cytokinesis does not proceed until DNA replication is complete, so that the DNA is precisely partitioned into the developing daughter cells. Each process itself is complex and if any one of the processes is inhibited, cell division ceases. This interdependence fits the criteria of an irreducibly complex system.


http://xwalk.ca/origin2.html

The chicken-egg dilemma has confounded scientists for decades. Chemist John Walton noted the dilemma in 1977 when he stated:

   "The origin of the genetic code presents formidable unsolved problems. The coded information in he nucleotide sequence is meaningless without the translation machinery, but the specification for his machinery is itself coded in the DNA. Thus without the machinery the information is meaningless, but without the coded information, the machinery cannot be produced. This presents a paradox of the 'chicken and egg' variety, and attempts to solve it have so far been sterile."


http://xwalk.ca/origin.html#fn20

The Chicken or the Egg?

Any discussion of the origin of life would not be complete without a look at the greatest paradox of all: What came first, DNA or the proteins essential for the production of DNA?
Since the structure of DNA was deciphered in 1953, biologists have discovered that the process of duplicating DNA requires as many as twenty specific protein enzymes. These enzymes function to unwind, un-zip, copy, and rewind the DNA molecule. There are even enzymes that screen and correct for copying errors!
The instructions for the production of all proteins, including these enzymes, are in turn stored on the DNA molecule. So which came first: The DNA molecule or the proteins necessary to make DNA? You can't make DNA without highly specific proteins. But you can't make proteins unless you have a system in place to code for and build those proteins in the first place. And that means DNA.

Harold Blum recognized this  when he stated:

 "...The riddle seems to be: How, when no life existed, did substances come into being which, today, are absolutely essential to living systems, yet which can only be formed by




those systems?...A number of major properties are essential to living systems as we see them today, the origin of any of which from a 'random' system is difficult enough to conceive, let alone the simultaneous origin of all."


http://creationevolutiondesign.blogspot.com.br/2007/01/mullers-theory-and-nucleic-acid-theory.html

Shapiro, R., "Origins: A Skeptic's Guide to the Creation of Life on Earth," Summit Books: New York NY, 1986, p.135)

"Genes and enzymes are linked together in a living cell two interlocked systems, each supporting the other. It is difficult to see how either could manage alone. Yet if we are to avoid invoking either a Creator or a very large improbability, we must accept that one occurred before the other in the origin of life. But which one was it? We are left with the ancient riddle: Which came first, the chicken or the egg? In its biochemical form, protein versus nucleic acid, the question is a new one, dating back no further than Watson and Crick and our knowledge of the structure and function of the gene. In its essence, however, the question is much older, and has provoked passion and acrimony that extend beyond the boundaries of science. In an earlier, broader form, the question asked whether the gene or protoplasm had primacy, not only in the origin but also in the development of life."

(Frank B. Salisbury, "Doubts about the Modern Synthetic Theory of Evolution," American Biology Teacher, 33: 335-338 (September, 1971).)

It's nice to talk about replicating DNA molecules arising in a soupy sea, but in modern cells this replication requires the presence of suitable enzymes. ... [T]he link between DNA and the enzyme is a highly complex one, involving RNA and an enzyme for its synthesis on a DNA template; ribosomes; enzymes to activate the amino acids; and transfer-RNA molecules. ... How, in the absence of the final enzyme, could selection act upon DNA and all the mechanisms for replicating it? It's as though everything must happen at once: the entire system must come into being as one unit, or it is worthless. There may well be ways out of this dilemma, but I don't see them at the moment.



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5 Re: The cell is irreducibly complex on Thu Jan 16, 2014 7:26 pm

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http://www.c4id.org.uk/index.php?option=com_content&view=article&id=239:new-research-on-protein-folding-demonstrates-intelligent-design&catid=52:frontpage&Itemid=1

Indeed it would seem that for any cell to function there needs to be not just proteins but, at the same time, these chaperone systems, which are absolutely essential for proper folding and maintenance of proteins. Without such systems, in place already, the cell will not function.

Now, as explained, these chaperone systems are themselves made of proteins which also require the assistance of chaperones to correctly fold and to maintain integrity once folded. Chaperones for chaperones in fact. The very simplest of cells that we know of have these systems in place.

Darwinian evolution requires step by step changes in molecular systems, with one step leading to another in a manner that is statistically reasonable to expect from selection of mutant strains. There is no Darwinian explanation however for the evolution of proteins which already have chaperone systems in place to ensure proper function.

This points very strongly to an intelligent origin of these ‘ingenious’ systems found in all of life.

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6 Re: The cell is irreducibly complex on Mon Jan 20, 2014 9:39 am

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http://telicthoughts.com/the-irreducible-complexity-of-dna-replication/

Replication must begin somewhere. Why not at the origin of replication with the formation of a replication fork. A prepriming complex of proteins forms. Included are DnaA proteins and single stranded binding proteins. Also involved are DNA helicases to separate the strands, DNA topoisomerases to respond to supercoils, DNA polymerase and DNA ligase.

Don't bother making semantic arguments about how to define irreducible complexity. There are multiple parts needed for function. The challenge lies in demonstrating the incremental evolution of these components.

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7 Re: The cell is irreducibly complex on Mon Jan 20, 2014 9:43 am

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http://www.uncommondescent.com/intelligent-design/yet-another-irreducible-complexity-no-brainer-twisted-ropes/

I find the phenomenon of the DNA supercoiling problem and its biochemical solution even more compelling than examples like protein synthesis and the bacterial flagellum, since twisted ropes are familiar to everyone. This might make for another highly persuasive ID mascot.

How could random variation and natural selection come up with a pair of biochemical scissors and a repair mechanism that cuts and splices the twisted DNA molecule in order to relieve torsional tension? What would be the functional, naturally-selectable intermediate steps in a hypothetical stochastically generated evolutionary process? It is clear that there could not possibly be any.

I’m suffering from a state of extreme cognitive dissonance. How can educated, intelligent scientists continue to defend the obviously indefensible, in light of what is now known about the nature of living systems (at all levels, not just the biochemical)? Richard Dawkins has remarked that biology was once a mystery, but “Darwin solved that.” Really?

http://www.creationscience.com/onlinebook/LifeSciences39.html

DNA cannot function without hundreds of preexisting proteins,but proteins are produced only at the direction of DNA. Because each needs the other, a satisfactory explanation for the origin of one must also explain the origin of the other. Therefore, the components of these manufacturing systems must have come into existence simultaneously. This implies creation.



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8 Re: The cell is irreducibly complex on Mon Jan 20, 2014 10:05 am

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http://www.evolutionnews.org/2013/09/more_irreducibl077051.html

[Minnich] Even if you concede you had all the parts necessary to build one of these machines, that's only part of the problem. Maybe even more complex -- I think more complex -- is the assembly instructions. That is never addressed by opponents of the irreducible complexity argument.

[Narrator] Studies of the bacterial motor have, indeed, an even deeper level of complexity. For its construction not only requires specific parts, but also a precise sequence of instructions for assembly.

[Minnich] You've got to make things at the right time. You've got to make the right number of components. You've got to assemble them in a sequential manner. You've got to be able to tell if you've assembled it properly so that you don't waste energy building a structure that's not going to be functional....

You build this structure from the inside out. You're counting the number of components in a ring structure or the stator, and once that's assembled, there's feedback that says, "OK, no more of that"; now, a rod is added; a ring is added; another rod is added; the U-joint [hook] is added. Once the U-joint is add a certain size, and a certain degree of bend, about a quarter turn, that's shut off, and then you start adding components for the propeller. These are all made in a precise sequence, just like you would build a building.


Paul Nelson then elaborates that the construction of one irreducibly complex machine (like the flagellum) requires the work of other machines; and those machines require other machines for their assembly. The whole assembly apparatus is itself irreducibly complex. In a memorable line, Jonathan Wells says, "what we have here is irreducible complexity all the way down."


Scott A. Minnich is an associate professor of microbiology at the University of Idaho :

“Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role in the origin of the system... We find such systems within living organisms.”

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9 Re: The cell is irreducibly complex on Fri Jan 24, 2014 10:02 am

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http://www.arn.org/docs/odesign/od201/peeringdbb201.htm

Cell division and the protocell

One of the more popular theories of protocell evolution, presented in biology textbooks, involves the encapsulation of the basic processes of biopolymer synthesis in a membrane (Cooper, 1997). It is then postulated that the protocell began to divide by a simple mechanism. In other words, it is assumed that all the cell functions required for life, perhaps even those required for cell division, were pre-manufactured and pre-functioning processes sequestered together by a cell membrane. (One barrier to cell division that the early protocell would encounter is that in an aqueous environment there is a natural physical resistance to the membrane disruption needed for cell division. For the sake of discussion, we will assume that the dividing protocell was in a membrane-disrupting environment that promoted some type of membrane blebing or stressing so that new cells could bud or pinch off the protocell.)

There are several fundamental problems with the encapsulation theory. First, how does a cytokinesis process develop before the membrane forms the cell? Cytokinesis requires a membrane-enclosed cytoplasmic space and could only develop after encapsulation. Yet in that case—if cytokinesis evolved only after encapsulation—then it would have to evolve rapidly, otherwise the cell would not reproduce and its long-term survival would be questionable. One possible postulate is that the early cytokinesis process was a much simpler process compared with the complex cytokinesis mechanism observed in bacteria today. That would imply, however, that there was very little regulation or no coordination between DNA replication and cytokinesis and other cell systems, which in turn implies that the division of the membrane and successful transfer of genetic material was haphazard and inefficient. The protocell would partition its DNA into new daughter bacteria, and then divide, by random uncoordinated processes.

There is good evidence to suggest that the process of cell division is indeed irreducibly complex, for the steps involved are interdependent and highly coordinated. For example, crucial steps such as DNA transcription require proteins (see Figure 1)—while protein synthesis in turn is dependent upon transcription. Moreover, evidence suggests that the processes involved in cell division are highly regulated and coordinated in a sequential fashion. For instance, in bacteria, cytokinesis does not proceed until DNA replication is complete, so that the DNA is precisely partitioned into the developing daughter cells. Each process itself is complex and if any one of the processes is inhibited, cell division ceases. This interdependence fits the criteria of an irreducibly complex system.

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10 Re: The cell is irreducibly complex on Mon Feb 10, 2014 10:52 am

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https://releasingthetruth.wordpress.com/tag/irreducible-complexity/

How could ATP synthase “evolve” from something that needs ATP, manufactured by ATP synthase, to function? Absurd “chicken-egg” paradox! Also, consider that ATP synthase is made by processes that all need ATP—such as the unwinding of the DNA helix with helicase to allow transcription and then translation of the coded information into the proteins that make up ATP synthase. And manufacture of the 100 enzymes/machines needed to achieve this needs ATP! And making the membranes in which ATP synthase sits needs ATP, but without the membranes it would not work. This is a really vicious circle for evolutionists to explain.

http://www.youtube.com/watch?v=XI8m6o0gXDY

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11 Re: The cell is irreducibly complex on Sat May 16, 2015 3:28 pm

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http://dialogue.adventist.org/articles/15_2_ward_e.htm

The primordial cell, like any other, would depend on its energy-generating biochemistry in order to operate crucial metabolic processes and synthesize essential molecules. As mentioned, information for molecular synthesis is stored in DNA. Energy generated by the cell is required for DNA synthesis and cellular replication. DNA synthesis depends upon enzymes whose blueprint is contained in DNA. None of these systems could function if it were not for the cell membrane separating the cell's biochemical reactions from the external environment. Indeed, enzymes encoded by information in DNA direct synthesis of the membrane itself--irreducible complexity at its best.

In his book, Behe analyzes published scientific literature on mechanisms of molecular and biochemical evolution. He also examines papers published in the Journal of Molecular Evolution (JME) since its founding in 1971. His conclusion: None of the papers published in JME over the entire course of its life as a journal has ever proposed a detailed model by which a complex biochemical system might have been produced in a gradual, step-by-step Darwinian fashion

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12 Re: The cell is irreducibly complex on Mon Apr 10, 2017 7:33 pm

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Douglas Futuyma, a prominent American biologist admits as much:

“Organisms either appeared on the earth fully developed or they did not. If they did not, they must have developed from preexisting species by some process of modification. If they did appear in a fully developed state, they must indeed have been created by some omnipotent intelligence” (Futuyma, 1983, p. 197).

In fact, Futuyma’s words underline a very important truth. He writes that when we look at life on Earth, if we see that life emerges all of a sudden, in its complete and perfect forms, then we have to admit that life was created, and is not a result of chance. As soon as naturalistic explanations are proven to be invalid, then creation is the only explanation left.

chemist Wilhelm Huck, professor at Radboud University Nijmegen
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity

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