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Theory of Intelligent Design, the best explanation of Origins » Molecular biology of the cell » Cell membrane and Membrane proteins » The Cell membrane, irreducible complexity

The Cell membrane, irreducible complexity

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1 The Cell membrane, irreducible complexity on Sun Nov 24, 2013 8:57 am

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The Cell membrane, irreducible complexity

Cell Membranes, origins through natural mechanisms, or design ? 1

http://reasonandscience.heavenforum.org/t2128-membrane-structure#3798

The Interdependency of Lipid Membranes and Membrane Proteins 2
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.

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.

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.




How Are Cell Membranes Synthesized?

http://www.nature.com/scitable/topicpage/endoplasmic-reticulum-golgi-apparatus-and-lysosomes-14053361

Membranes and their constituent proteins are assembled in the endoplasmic reticulum. This organelle contains the enzymes involved in lipid synthesis, and as lipids are manufactured in the endoplasmic reticulum, they are inserted into the organelle's own membranes. This happens in part because the lipids are too hydrophobic to dissolve into the cytoplasm.

The ER, Golgi apparatus, and lysosomes are all members of a network of membranes, but they are not continuous with one another. Therefore, the membrane lipids and proteins that are synthesized in the ER must be transported through the network to their final destination in membrane-bound vesicles. Cargo-bearing vesicles pinch off of one set of membranes and travel along microtubule tracks to the next set of membranes, where they fuse with these structures.


Enzymes for cell wall synthesis conserved across species barriers

http://www.mpg.de/4372173/cell_wall_synthesis

BIOCHEMICAL REACTIONS FOR PEPTIDOGLYCAN SYNTHESIS
The biosynthesis of PG can be divided into three different stages (reviewed in references 162, 190, and 191). The first stage occurs in the cytoplasm and leads to the synthesis of the nucleotide sugar-linked precursors UDP-N-acetylmuramyl-pentapeptide (UDP-MurNAc-pentapeptide) and UDP-N-acetylglucosamine (UDP-GlcNAc). In the second stage, which takes place at the cytoplasmic membrane, precursor lipid intermediates are synthesized. The phospho-MurNAc-pentapeptide moiety of UDP-MurNAc-pentapeptide is transferred to the membrane acceptor bactoprenol, yielding lipid I [MurNAc-(pentapeptide)-pyrophosphoryl-undecaprenol]. Then, GlcNAc from UDP-GlcNAc is added to lipid I, yielding lipid II [GlcNAc-β-(1,4)-MurNAc-(pentapeptide)-pyrophosphoryl-undecaprenol], which is the substrate for the polymerization reactions in bacteria that have directly cross-linked PG. The use of a lipophilic molecule such as bactoprenol enables the cell to transport hydrophilic precursors from the aqueous environment of the cytoplasm, through the hydrophobic membrane, and to the externally situated sites of incorporation into the growing PG.

http://boscoh.com/protein/looking-at-the-surface-of-a-membrane.html



A Cell Must Have a Membrane

A lipid membrane without its protein pumps and channels would let water enter the cell, but would keep nutrients out, starving the cell,{Essential Cell Biology, p. 347, 356-357} so proteins had to work together with the lipids from the first, another important evidence, of carefully planned irreducible complexity.

http://www.apologeticspress.org/APContent.aspx?category=9&article=1367&topic=328

Each cell is contained inside a two layer membrane made of lipids . Lipids are only formed by living cells. “Though a few organic substances–for instance, certain simple amino acids–can form relatively easily under prebiotic conditions, other biochemical building blocks, such as nucleotides and lipids, require for their synthesis a ‘real factory.’ … The synthesis of these substances involves a series of reactions, each reaction following the previous one in utmost accuracy.”{Iris Fry, The Emergence of Life on Earth, 2000, p. 126, 176-177} Contrary to the false claims of some textbooks that lipid coacervates evolved into cells, lipids are only produced by accurately controlled reactions in living cells. This is important evidence!

“A living cell is a self-reproducing system of molecules held inside a container. The container is the plasma membrane - a fatty film so thin and transparent that it cannot be seen directly in the light microscope. It is simple in construction, being based on a sheet of lipid molecules…. Although it serves as a barrier to prevent the contents of the cell from escaping and mixing with the surrounding medium…the plasma membrane does much more than that. Nutrients have to pass inward across it if the cell is to survive and grow, and waste products have to pass outward. Thus the membrane is penetrated by highly selective channels and pumps, formed from protein molecules, that allow specific substances to be imported while others are exported. Still other protein molecules in the membrane act as sensors to enable the cell to respond to changes in its environment.”{Bruce Alberts, Essential Cell Biology, 1998, p. 347}


If cells had really formed spontaneously, we would expect their important parts to be made of materials that form easily under natural conditions. However, not one of the four: lipids, proteins, RNA, or DNA, can be made that way at all! Amazing! Not one is formed in nature except by a living cell, yet for a cell to live, all must be there at the same time, each one doing its job. If God had wanted to shout to you that He is here, and show you proof that He created, could you find a more convincing proof for Him to use? Run, don’t walk to the nearest Bible and get to know your awesome Creator personally - through His Son, Jesus Christ!

proteins that are coded by DNA are used by cells in the body to synthesise lipids and carbohydrates as well as most small molecules used in an organism.

http://www.ncbi.nlm.nih.gov/books/NBK9841/

The first cell is presumed to have arisen by the enclosure of self-replicating RNA in a membrane composed of phospholipids.

http://en.wikipedia.org/wiki/Phospholipid

Phospholipid synthesis occurs in the cytosol adjacent to ER membrane that is studded with proteins that act in synthesis (GPAT and LPAAT acyl transferases, phosphatase and choline phosphotransferase) and allocation (flippase and floppase). Eventually a vesicle will bud off from the ER containing phospholipids destined for the cytoplasmic cellular membrane on its exterior leaflet and phospholipids destined for the exoplasmic cellular membrane on its inner leaflet.

1) http://reasonandscience.heavenforum.org/t1331-the-cell-membrane-irreducible-complexity#1874
2) https://en.wikibooks.org/wiki/Structural_Biochemistry/The_Evolution_of_Membranes



Last edited by Admin on Sat Jan 30, 2016 8:04 am; edited 21 times in total

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2 Re: The Cell membrane, irreducible complexity on Sat Dec 14, 2013 7:22 pm

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The Design and Complexity of the Cell, Jeffrey Tomkins, Ph. D., 2012, pp. 24-25;http://www.icr.org/design-cell/

“… plasma membranes are … quite complex and … (function) as more than just a barrier … Some key functions of the membrane involve the import and export of chemical compounds through specialized transmembrane channels, sensory and signaling processes via specialized receptor proteins imbedded in the membrane, and osmotic (water) regulation … through special portals.” 8

“Within the … membrane is the internal cell matrix … called cytosol or cytoplasm, which is a semi-fluid substance. … Like the … membrane, the complexity of … cytoplasm seems to grow with every new discovery in cell biology.”

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3 Re: The Cell membrane, irreducible complexity on Sun Jun 29, 2014 12:25 pm

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http://scienceandscientist.org/biology/#_ftnCell

The origin of life theory should clarify the origin of the distinctive phenomena which maintains life, such as reproduction, metabolism, and their corollaries (cell division, information carriers, genetic code, growth, maintenance, response to external stimuli, etc.). Reproduction is undoubtedly crucial for the continuation of any form of life. For this reason, evolutionists believe some form of molecular replication must have been started spontaneously in the prebiotic environment as a simple, entirely physicochemical form of reproduction. On the other hand, cellular metabolism is understood as a set of chemical reactions that occur in biological systems to maintain life. This vital process helps organisms to grow and reproduce, maintain, and respond to their environments. The metabolism process is classified in two different classes, catabolism and anabolism. Catabolism process produces useful energy and the anabolism process uses that energy to build components of cells such as proteins and nucleic acids. Through metabolic pathways, in a number of steps one chemical converts itself into another chemical by a sequence of enzymes. Enzymes are essential for the metabolic processes, since enzymes permit biological systems to make necessary reactions that require energy. Hence, some researchers believe in the supremacy of metabolism[12],[13],[15]-[19] and others assume the supremacy of reproduction.[11],[21],[72],[92],[93] Once again, scientists confront the same difficulty, ‘‘which came first, the chicken (metabolism) or the egg (reproduction)?’’

The contest between proponents of ‘metabolism first’ and ‘replication first’ persists unabated with both speculations subject to criticism. The ‘metabolism first’ speculation has been criticized by some of the prominent researchers in the field based on the judgment that major steps in the construction of such a metabolic scheme are exceedingly doubtful.[21],[92],[94],[95] The ‘replication first’ notion is also challenged, considering the observation that the de novo manifestation of oligonucleotides is questionable, and that there is no apparent pathway from an RNA world to the existing dual world of proteins and nucleic acids.[77],[96]

How a primitive cell developed its skin?

Abiogenesis hypothesis must also supply the means and pathways for primitive cell growth and division, as well as the mechanism by which cells could take up nutrients from their environment. All existing biological cells are membrane enclosed workspaces. The cell membrane is the container which holds a cell together. It manages to retain an internal milieu different from its environment within which genetic materials can reside and metabolic activities can take place without being lost to the environment. Existing cell membranes on earth are made of composite mixtures of amphiphilic molecules like phospholipids, sterols, and several other lipids, plus miscellaneous proteins that carry out transport and enzymatic works. Modern biological membranes are pretty secure under different environments and can tolerate a wide range of temperatures, pH, and salt concentrations. These biological membranes are exceptionally fine permeability barriers, so that present cells have comprehensive power over the intake of nutrients and the evacuation of wastes all the way through the dedicated channel, pump and pore proteins implanted in their membranes. Besides, immensely intricate biochemical machinery is mandatory for the growth and division of the cell membrane in a cell cycle. How a structurally simple primitive cell could accomplish all these essential membrane functions in primordial earth is a difficult problem to address. As compared to the research efforts on replications and metabolism, the starting point of primitive membranes is one of the most neglected fields in origin of life investigations. While the unrelenting disagreements in abiogenesis have been around the ‘metabolism first’ versus ‘replication first’ issue, there have also been competing thoughts for the origin of the cell membrane. We will ascertain below that the attempts to produce biological membranes under primordial earth are also suffering from multifaceted unsolved problems.

The experiments of Oparin’s[16],[97] and Fox[98] on coacervates and proteinoid respectively were accepted as a significant historical step in the field of prebiotic synthesis of cell membranes. However, neither coacervates nor proteinoid microspheres have a factual boundary membrane that can perform as a selective permeability barrier. Coacervates and proteinoid are prominently detailed in present high school biology textbooks, even though they are essentially unstable, lacking the capacity to supply a permeability barrier, and incapable of carrying metabolism. Consequently, the present concentration of research has transferred from colloid phenomena and protein chemistry to nucleic acids.[99],[100] Researchers proclaim that amphiphilic boundary structures contributed to the appearance of life on earth in primordial conditions.[101]-[103] As an expansion of this view, some scientists suggest a ‘Lipid World’ situation as an early evolutionary step in the appearance of cellular life on Earth. Moreover, some researchers have proposed that lipid membranes may have a hereditary potential because the majority membranes are produced from other membranes but not created de novo.[104],[105] However, these approaches have not received much attention, most likely due to the comparative scarcity of experimental evidence. Studies also claim that, in the middle of the abundance of the molecular variety anticipated to be originated in prebiotic Earth, lipid-like molecules have a discrete property. That is: a capability to carry out spontaneous aggregation to form droplets, micelles, bilayers and vesicles contained by an aqueous phase through entropy-driven hydrophobic exchanges.[106],[107] However, the concentration of biomolecules in the aqueous primordial Earth has been expected to be roughly 1 micromolar,[108] essentially insufficient for typical covalent chemical reactions indispensable for formation of hydrophobic and amphiphilic molecules.
Even if one ignores the difficulties in connection with the production of amphiphilic molecules in primordial earth, still we are left with several technical problems on the path of prebiotic synthesis of membranes. The physical and chemical properties of aqueous surroundings can considerably slow down self-assembly of amphiphilic molecules, perhaps significantly restricting the environments in which cellular life first emerged. For example, temperature significantly controls the stability of vesicle membranes. It has been suggested that the primitive life forms were hyperthermophiles that originated in geothermal regions such as hydrothermal vents[109] or deep subterranean hot aquifers.[110] However, under these conditions, the intermolecular forces that stabilize self-assembled molecular systems are relatively weak. Hence, such locations are not suitable for lipid bilayer membranes to assemble. There are also several similar restrictions attached with the ionic composition and pH of the environment proposed for the origin of life.[111],[112]
To escape similar impractical situations, many researchers are speculating that amphiphilic compounds existed in carbonaceous meteorites. These compounds might have self-assembled into membranous vesicles under suitable circumstances and were latter delivered to the early Earth from outer space by meteoritic and cometary infall.[113],[114] Even though lipid-like materials were claimed to be detected in the Murchison meteorite,[114],[115] successive research suggested that those compounds were contaminants, rather than endogenous materials.[116] The fabrication of appropriate biomolecules in the interstellar medium is of no significance to the origin of life unless these biomolecules can be delivered unharmed to habitable planetary surfaces. The major question would be: can these noble biomolecules withstand the brutal, scorching delivery to a planetary surface? Even if in some way membrane building blocks landed safely through extraterrestrial resources, decomposition through hydrolysis, photochemical degradation, and pyrolysis would have drastically diminished the quantity of such materials.[34] Hence, we remain with the unanswered question: how did a primitive cell develop its skin?

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4 Re: The Cell membrane, irreducible complexity on Thu May 07, 2015 12:36 pm

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On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells

http://www.gla.ac.uk/projects/originoflife/html/2001/pdf_files/Martin_&_Russell.pdf

All life is organized as cells. Physical compartmentation from the environment and self-organization of
self-contained redox reactions are the most conserved attributes of living things, hence inorganic matter
with such attributes would be life’s most likely forebear. We propose that life evolved in structured iron
monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient
between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor. The
naturally arising, three-dimensional compartmentation observed within fossilized seepage-site metal sulphide
precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes
found in free-living prokaryotes.

The known capability of FeS and NiS to catalyse the synthesis
of the acetyl-methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal
fluid, indicates that pre-biotic syntheses occurred at the inner surfaces of these metal-sulphide-walled
compartments, which furthermore restrained reacted products from diffusion into the ocean, providing
sufficient concentrations of reactants to forge the transition from geochemistry to biochemistry.


The universal ancestor we infer was not a free-living cell, but
rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its
constituents occurred.

Where are the details ?

The first free-living cells are suggested to have been eubacterial and archaebacterial
chemoautotrophs that emerged more than 3.8 Gyr ago from their inorganic confines. We propose that
the emergence of these prokaryotic lineages from inorganic confines occurred independently, facilitated
by the independent origins of membrane-lipid biosynthesis: isoprenoid ether membranes in the archaebacterial
and fatty acid ester membranes in the eubacterial lineage.


Where are the details ?

. The origin of the eukaryotic endomembrane system and nuclear membrane
are suggested to be the fortuitous result of the expression of genes for eubacterial membrane lipid
synthesis by an archaebacterial genetic apparatus in a compartment that was not fully prepared to accommodate
such compounds, resulting in vesicles of eubacterial lipids that accumulated in the cytosol around
their site of synthesis. Under these premises, the most ancient divide in the living world is that between
eubacteria and archaebacteria, yet the steepest evolutionary grade is that between prokaryotes and eukaryotes

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5 Re: The Cell membrane, irreducible complexity on Tue Dec 27, 2016 6:28 pm

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Cell membrane - endoplasmic reticulum,  irreducible complexity and interdependence

http://boscoh.com/protein/looking-at-the-surface-of-a-membrane.html



http://reasonandscience.heavenforum.org/t1973-functions-of-the-endoplasmic-reticulum-and-cell-membrane-endoplasmic-reticulum-irreducible-and-interdependent-complexity#3306

The ENDOPLASMIC RETICULUM cannot exist without the cell membrane. The cell membrane is however sinthesized in the ENDOPLASMIC RETICULUM.

Question: Isn't that  a classic Chicken and Egg problem ? Is it not rational to conclude, that the cell membrane, the ENDOPLASMIC RETICULUM, and the transport vesicles and membrane vesicles and address tags had to be fully functional and fully formed and at the right place right from the beginning ?


http://en.wikipedia.org/wiki/Endoplasmic_reticulum

The endoplasmic reticulum (ER) is a type of organelle in the cells of eukaryotic organisms that forms an interconnected network of flattened, membrane-enclosed sacs or tubes known as cisternae. The endoplasmic reticulum serves many general functions, including the folding of protein molecules in sacs called cisternae and the transport of synthesized proteins in vesicles to the Golgi apparatus. Correct folding of newly made proteins is made possible by several endoplasmic reticulum chaperone proteins

(1) Transport of proteins to the cell membrane (and other locations)

Secretory proteins, mostly glycoproteins, are moved across the endoplasmic reticulum membrane. Proteins that are transported by the endoplasmic reticulum and from there throughout the cell are marked with an address tag called a signal sequence.

Question: How and why did these reticulum membranes evolve in the first place, and specially what survival advantage would they provide to the cell, unless they were able to fully perform their end function, namely being a channel for protein transport ? How did the signal sequence evolve ?


The N-terminus (one end) of a polypeptide chain (i.e., a protein) contains a few amino acids that work as an address tag, which are removed when the polypeptide reaches its destination.

Question : What good would the protein be for, if not employd at the right place in the cell, or outside of it ? How did the organism learn  the right place where the protein had to be employd ? how did the organism survive without being able to send the proteins to the right place to exercise its vital function ?  how did evolution figure out the right destination of given protein ? how did it " learn " to remove the N-teriminus after it reaches its destination ?

Proteins that are destined for places outside the endoplasmic reticulum are packed into transport vesicles and moved along the cytoskeleton toward their destination, whether in the cell membrane or another location. Transport vesicles can move molecules between locations inside the cell, e.g., proteins from the rough endoplasmic reticulum to the Golgi apparatus. Membrane-bound and secreted proteins are made on ribosomes found in the rough endoplasmic reticulum. Most of these proteins mature in the Golgi apparatus before going to their final destination which may be to lysosomes, peroxisomes, or outside of the cell. These proteins travel within the cell inside of transport vesicles.

Question : how were these proteins transported, before the transport vesicles supposedly evolved ? How did the organism survive without these proteins at the right place ? had the transport vesicle not to be existing right from the beginning, in order to provide the transport of the proteins to the right destination ? How did the transport vesicles move inside the cells without the cytoskeleton ?

(2) PROTEIN TARGETING or protein sorting is the mechanism by which a cell transports proteins to the appropriate positions in the cell or outside of it. Sorting targets can be the inner space of an organelle, any of several interior membranes, the cell's outer membrane, or its exterior via secretion. This delivery process is carried out based on information contained in the protein itself. Correct sorting is crucial for the cell; errors can lead to diseases. A protein's sorting code, a specific amino acid sequence, is generated in the ER, where it can be targeted for TRANSLOCATION to the cell membrane.

Question : how did the correct information arise in order to provide correct protein sorting ?  would the cells not have got sick and died many times during trial error of bad mutations , until finding out the right genetic code to produce the right delivery channels and right delivery process ??


(3) The secretory pathway is a series of steps a cell uses to move proteins out of the cell; a process known as secretion. The path of a protein destined for secretion has its origins in the ROUGH ENDOPLASMIC RETICULUM. The protein then proceeds through the many compartments of the GOLGI APPARATUS and finally ends up in a vesicle that fuses with the PLASMA MEMBRANE, dumping the proteins outside of the cell.

Question: Unless the the secretory pathway  in the ROUGH ENDOPLASMIC RETICULUM, the  GOLGI APPARATUS , the transport vesicle, and the vesicle in the cell membrane were not fully evolved and in place right from the beginning, how could proteins move out of the cell to its final destination ?  

All existing biological cells are membrane enclosed workspaces. The cell membrane is the container which holds a cell together. It manages to retain an internal milieu different from its environment within which genetic materials can reside and metabolic activities can take place without being lost to the environment. Existing cell membranes on earth are made of composite mixtures of amphiphilic molecules like phospholipids, sterols, and several other lipids, plus miscellaneous proteins that carry out transport and enzymatic works.

Phospholipids are a class of lipids that are a major component of all cell membranes as they can form lipid bilayers.

http://en.wikipedia.org/wiki/Phospholipid

Phospholipid synthesis occurs in the cytosol adjacent to ENDOPLASMIC RETICULUM membrane. Eventually a vesicle will bud off from the ENDOPLASMIC RETICULUM containing phospholipids destined for the cytoplasmic cellular membrane on its exterior leaflet and phospholipids destined for the exoplasmic cellular membrane on its inner leaflet.

The ENDOPLASMIC RETICULUM cannot exist without the cell membrane. The cell membrane is however sinthesized in the ENDOPLASMIC RETICULUM.

Question: Isn't that  a classic Chicken and Egg problem ? Is it not rational to conclude, that the cell membrane, the ENDOPLASMIC RETICULUM, and the transport vesicles and membrane vesicles and address tags had to be fully functional and fully formed and at the right place right from the beginning ?

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