MASC brain "computer"
3. Problem of sex
4. Eukaryotes
[Home] [Site map] [Updates] [Projects] [Contents; 1. Introduction; 2. Philosophy (1), (2), (3), (4) & (5); 3. Religion (1) & (2); 4. History (1), (2) & (3); 5. Science; 6. Environment (1), (2) & (3); 7. Origin of life (1), (2) & (3); 8. Cell & Molecular (1) & (3); 9. Mechanisms (1), (2) & (3); 10. Fossil Record; 11. `Fact' of Evolution; 12. Plants; 13. Animals; 14. Man (1) & (2); 15. Social; 16. Conclusion; Notes; Bibliography A-C, D-F, G-I, J-M, N-S, T-Z]
"PROBLEMS OF EVOLUTION": 8. CELL & MOLECULAR (2) 1. Cell 1. Origin of life is origin of cell 2. Cell's technology is beyond the ability of science to duplicate 3. Cell is a Von Neumann machine 4. Information content of a cell 5. The minimal cell 6. The first cell was irreducibly complex 7. Assembly of first cell was fantastically improbable 2. Molecular 1. Genetic code(s) 1. Origin of genetic code 2. `Chicken and egg' problem 3. Origin of information 1. Not chemical necessity 2. DNA 1. DNA transcription 2. DNA translation 3. DNA replication 4. DNA error-checking 3. Proteins 1. Chaperones 4. Enzymes 5. Molecular machinery 1. Origin of molecular machinery 2. ATP synthase (F1-ATPase) 3. Ubiquitin-Proteasome protein recycling system 4. Myosin-actin muscle molecular motor 5. Nerve cells (voltage-regulated gates, etc) 6.
"PROBLEMS OF EVOLUTION": 8. CELL & MOLECULAR (2) 2. Molecular 1. Genetic code(s) 1. Origin of genetic code "The British biologist John Maynard-Smith has described the origin of the code as the most perplexing problem in evolutionary biology. With collaborator Eors Szathmary he writes: `The existing translational machinery is at the same time so complex, so universal, and so essential that it is hard to see how it could have come into existence, or how life could have existed without it.' (Maynard Smith & Szathmary, 1995, p.81, in Davies, 1998, p.79). [top] 2. `Chicken and egg' problem The origin of life presents a number of basic `chicken and egg' problems. One of the most intractable of these for the evolutionist is the origin of the genetic code (Orgel, 1994, p.54; Davies & Adams, 1998, pp.55-56; Matthews, 1992, p.60). The problem is that the genetic code can do nothing unless it is translated with the help of "at least fifty macromolecular components which are themselves coded in DNA" (Monod, 1971, p.143; Popper, 1974, p.270. Emphasis in original). This therefore "constitutes a really baffling circle: a vicious circle ... for any attempt to form a model, or a theory, of the genesis of the genetic code" (Popper, 1974, p.270). [top] 3. Origin of information 1. Not chemical necessity"For many current origin-of-life scientists, self-organizational models now seem to offer the most promising approach to explaining the origin of biological information. Nevertheless, critics have called into question both the plausibility and the relevance of self-organizational models. Ironically, perhaps the most prominent early advocate of self-organization, Professor Dean Kenyon, has now explicitly repudiated such theories as both incompatible with empirical findings and theoretically incoherent. The empirical difficulties attendant self-organizational scenarios can be illustrated by examining a DNA molecule. The diagram here [http://www.firstthings.com/ftissues/ft0004/articles/meyer.gif] shows that the structure of DNA depends upon several chemical bonds. There are bonds, for example, between the sugar and the phosphate molecules that form the two twisting backbones of the DNA molecule. There are bonds fixing individual (nucleotide) bases to the sugar-phosphate backbones on each side of the molecule. Yet notice that there are no chemical bonds between the bases that run along the spine of the helix. Yet it is precisely along this axis of the molecule that the genetic instructions in DNA are encoded. Further, just as magnetic letters can be combined and recombined in any way to form various sequences on a metal surface, so too can each of the four bases A, T, G, and C attach to any site on the DNA backbone with equal facility, making all sequences equally probably (or improbable). The same type of chemical bond occurs between the bases and the backbone regardless of which base attaches. All four bases are acceptable; none is preferred. In other words, differential bonding affinities do not account for the sequencing of the bases. Because these same facts hold for RNA molecules, researchers who speculate that life began in an "RNA world" have also failed to solve the sequencing problem-i.e., the problem of explaining how information present in all functioning RNA molecules could have arisen in the first place. For those who want to explain the origin of life as the result of self-organizing properties intrinsic to the material constituents of living systems, these rather elementary facts of molecular biology have devastating implications. The most logical place to look for self-organizing properties to explain the origin of genetic information is in the constituent parts of the molecules carrying that information. But biochemistry and molecular biology make clear that the forces of attraction between the constituents in DNA, RNA, and protein do not explain the sequence specificity of these large information-bearing biomolecules. Significantly, information theorists insist that there is a good reason for this. If chemical affinities between the constituents in the DNA message text determined the arrangement of the text, such affinities would dramatically diminish the capacity of DNA to carry information. To illustrate, consider what would happen if the individual nucleotide "letters" (A,T,G,C) in a DNA molecule did interact by chemical necessity with each other. Every time adenine (A) occurred in a growing genetic sequence, it would likely drag thymine (T) along with it. Every time cytosine (C) found a slot, guanine (G) would follow. As a result, the DNA message text would be peppered with repeating sequences of A's followed by T's and C's followed by G's. Rather than having a genetic molecule capable of unlimited novelty, with all the unpredictable and aperiodic sequences that characterize informative texts, we would have a highly repetitive text awash in redundant sequences-much as happens in crystals. Indeed, in a crystal the forces of mutual chemical attraction do completely explain the sequential ordering of the constituent parts, and consequently crystals cannot convey novel information. Sequencing in crystals is repetitive and highly ordered, but not informative. Once one has seen "Na" followed by "Cl" in a crystal of salt, for example, one has seen the extent of the sequencing possible. Bonding affinities, to the extent they exist, mitigate against the maximization of information. They cannot, therefore, be used to explain the origin of information. Affinities create mantras, not messages." (Meyer S.C., "The Message in the Microcosm: DNA and the Death of Materialism." Access Research Network, 1998. http://www.arn.org/docs/meyer/sm_message.htm) [top]See also Meyer S.C., "DNA and Other Designs," First Things, 102, April 2000, pp.30-38 & Meyer S.C., "The Origin of Life and the Death of Materialism," The Intercollegiate Review 31, No. 2, April 1, 1996. 2. DNA 1. DNA transcription"transcription The process in living cells in which the genetic information of DNA is transferred to a molecule of messenger RNA (mRNA) as the first step in protein synthesis (see also genetic code). Transcription takes place in the cell nucleus or nuclear region and is regulated by transcription factors. It involves the action of RNA polymerase enzymes in assembling the nucleotides necessary to form a complementary strand of mRNA from the DNA template (see also promoter), and (in eukaryote cells) the subsequent removal of the noncoding sequences from this primary transcript (see gene splicing) to form a functional mRNA molecule. The term is also applied to the assembly of single-stranded DNA from an RNA template by the enzyme reverse transcriptase. Compare translation. transcription factor Any of a group of proteins that can increase or decrease the binding of RNA polymerases to the DNA molecule during the process of transcription. This is achieved by the ability of the transcription factors to bind to the DNA molecule (see DNA-binding proteins). Transcription factors contain finger domains, which are often in repeated sequences called multifinger loops. " (Martin & Hine, 2000, p.597) [top]2. DNA translation"translation The process in living cells in which the genetic information encoded in messenger *RNA (mRNA) in the form of a sequence of nucleotide triplets (*codons) is translated into a sequence of amino acids in a polypeptide chain during *protein synthesis (see illustration). Translation takes place on *ribosomes in the cell cytoplasm (see initiation factor). The ribosomes move along the mRNA `reading' each codon in turn. Molecules of transfer RNA (tRNA), each bearing a particular amino acid, are brought to their correct positions along the mRNA molecule: base pairing occurs between the bases of the codons and the complementary base triplets of tRNA (see anticodon). In this way amino acids are assembled in the correct sequence to form the polypeptide chain (see elongation). Translation is terminated by the *release factor." (Martin. & Hine, 2000, pp.598-599) [top]3. DNA replication"DNA replication The process whereby DNA makes exact copies of itself, which is controlled by the enzyme DNA polymerase. Replication occurs at rates of between 50 nucleotides per second (in mammals) and 500 nucleotides per second (in bacteria). The hydrogen bonds between the complementary bases on the two strands of the parent DNA molecule break and the strands unwind, each strand acting as a template for the synthesis of a new one complementary to itself (see DNA-binding proteins). DNA polymerases move down the two single strands linking free nucleotides to their complementary bases (see base pairing) on the templates. The process continues until all the nucleotides on the templates have joined with appropriate free nucleotides and two identical molecules of DNA have been formed. This process is known as semiconservative replication as each new molecule contains half of the original parent DNA molecule (compare conservative replication; dispersive replication). Sometimes mutations occur that may cause the exact sequence of the parent DNA not to be replicated. However, *DNA repair mechanisms reduce this possibility." (Martin & Hine, 2000, p.186). [top]4. DNA error-checking How did a `blind watchmaker' invent error-checking?"Michelangelo once said he did not carve an angel, he only released it from the rock. For the artist this was modesty, but for selection it is simple truth. The "grain" of the wood being carved, i.e., the informational characteristics of the genome itself and the probability structure of genetic phase space (Brooks et al., 1989, define GPS as the probability space of all possible genomes), determine what selection is able to produce. One cannot select a characteristic not already present; a horse breeder cannot produce Pegasus. Clearly, then, the nature of the information encoded on the genome, the genetic programs that can be mutated, are central to understanding natural selection's ability to "create." The information structure however, is far more complex than has been usually assumed. Specifically, the information encoded on the genome reveals hierarchy. It is a hierarchy of described reality, of blueprints for specific cell types, organs, organisms, hives-blueprints of immense stability. Further, these blueprints are organized in a form analogous to a linguistic hierarchy, in which the definitions of the "markers" are written in the code they define-e.g., amino acid code in the encoded description of the structure of the aminoacyl proteins. Nor are these simple descriptions of morphology, but a cybernetic hierarchy of controls, with the goals of the more comprehensive levels buffered by flexibility in the lower levels. Finally, those goals are realized through a temporal (developmental) hierarchy, in which the same goal may be achieved by different paths (Muller and Wagner, 1991). The information that dictates error-checked homeostatic/homeorhytic phenomena must itself be error-checked and cybernetic." (Wilcox D.L., "A Blindfolded Watchmaker: The Arrival of the Fittest," in Buell J. & Hearn V., eds., "Darwinism: Science or Philosophy?," Foundation for Thought and Ethics: Richardson TX, 1994, pp.196-197. http://www.leaderu.com/orgs/fte/darwinism/chapter13.html)"New individuation, the appearance of adaptive complexes (morphological entities) is typically very abrupt for instance, limb structure in Diacodexus (Rose, 1982 & 1987) or the Ichthyostegeds (Coates and Clack, 1991). New "type" forms usually appear suddenly, with the characteristic morphological systems already "individuated"-as defined and error-checked entities (Such definition will almost always require more "bytes" to encode.) Even if possible ancestors that lack the new complex seem to be present (usually at about the same point in time), where do the new control system norms come from? The appearance of new taxa seems to imply the sudden appearance of packages of individuated structural information, but how does closed, error-checked cybernetic feedback start? It may be relatively easy to show that a path across phenotypic space could be progressively adaptive (Kingsolver and Koehl, 1985), but explaining the necessary changes in the underlying genome is a different matter. The two seem identical only because neo- Darwinism has assumed the supply of sufficient additive variability." (Wilcox D.L., "A Blindfolded Watchmaker: The Arrival of the Fittest," in Buell J. & Hearn V., eds., "Darwinism: Science or Philosophy?," Foundation for Thought and Ethics: Richardson TX, 1994, p.202. http://www.leaderu.com/orgs/fte/darwinism/chapter13.html)"In conclusion, it seems to me that there is indeed good reason to suppose that metaphysical assumptions have constrained vision in neo-Darwinian biology. Genomes that contain a high level of encoded morphological diversity in the form of error-checked coherent entities seem to appear with regularity. Neo- Darwinism can explain the exploration of such packages, but it has not proved that it can explain their origin. Based on uniform human experience, the simplest explanation for the appearance of a novel, dense pattern of information is an information-dense source. If available DNA templates seem inadequate, the alternative is a source of order exterior to the genome. Are there any known material sources of sufficient density to act as such sources other than human intelligence? Further, if no adequate material source suggests itself, is not the remaining logical explanation an immaterial source? " (Wilcox D.L. "A Blindfolded Watchmaker: The Arrival of the Fittest," in Buell J. & Hearn V., eds., "Darwinism: Science or Philosophy?," Foundation for Thought and Ethics: Richardson TX, 1994, pp.204-205. http://www.leaderu.com/orgs/fte/darwinism/chapter13.html)"The diverse evidence I presented centers on a single, common problem: a complex and structured genome that is characterized by programmed and error-checked entities, a cybernetic base for biotic reality. Darwinian theory is based on a "bean-bag" view of genetics, on the additive effects of many small effect genes-or perhaps on occasional "macro" mutation. But, in the cybernetic model, those "beans" are best explained as adaptive buffers for the genetic goalseeking machinery. Evidence for adaptive change does not naturally expand into evidence for prescriptive change as it accumulates. Thus, it is not minor anomalies, the occasional genetic tornado, that neo-Darwinism cannot (yet) explain. Rather, it has failed to explain the fundamental realities of biological systems. It has failed to explain the core of the apple. Why then has it been considered an adequate (nay, a necessary and vital) explanation for all of biological reality? ... I conclude that the easy acceptance of neo-Darwinism as a complete and adequate explanation for all biological reality has indeed been based in the metaphysical needs of a dominant materialistic consensus." (Wilcox D.L., "Tamed Tornadoes," in Buell J. & Hearn V., eds., "Darwinism: Science or Philosophy?" Foundation for Thought and Ethics: Richardson TX, 1994, p.215. Emphasis in original. http://www.leaderu.com/orgs/fte/darwinism/chapter13b.html)[top] 3. Proteins 1. Chaperones"In this chapter we have seen how large, multi-protein complexes catalyze specific steps in DNA replication, recombination, and repair. These complexes need to be assembled and disassembled in a highly regulated manner, and current research indicates that chaperones are essential for both the assembly and disassembly processes." (Lodish H., et al., "Molecular Cell Biology," [1986], W.H. Freeman & Co: New York, Fourth Edition, 2002, Fifth Printing, p.491)]"Efficient folding of many newly synthesized proteins depends on assistance from molecular chaperones, which serve to prevent protein misfolding and aggregation in the crowded environment of the cell. Nascent chain-binding chaperones, including trigger factor, Hsp70, and prefoldin, stabilize elongating chains on ribosomes in a nonaggregated state. Folding in the cytosol is achieved either on controlled chain release from these factors or after transfer of newly synthesized proteins to downstream chaperones, such as the chaperonins. These are large, cylindrical complexes that provide a central compartment for a single protein chain to fold unimpaired by aggregation. Understanding how the thousands of different proteins synthesized in a cell use this chaperone machinery has profound implications for biotechnology and medicine. ... To become functionally active, newly synthesized protein chains must fold to unique three-dimensional structures. How this is accomplished remains a fundamental problem in biology. Although it is firmly established from refolding experiments in vitro that the native fold of a protein is encoded in its amino acid sequence, protein folding inside cells is not generally a spontaneous process. Evidence accumulated over the last decade indicates that many newly synthesized proteins require a complex cellular machinery of molecular chaperones and the input of metabolic energy to reach their native states efficiently. The various chaperone factors protect nonnative protein chains from misfolding and aggregation, but do not contribute conformational information to the folding process. Here we focus on recent advances in our mechanistic understanding of de novo protein folding in the cytosol and seek to provide a coherent view of the overall flux of newly synthesized proteins through the chaperone system." (Hartl F.U. & Hayer-Hartl M., "Molecular Chaperones in the Cytosol: From Nascent Chain to Folded Protein," Science, Vol 295, No. 5561, 8 March 2002, pp.1852-1858)[top]4. Enzymes Enzymes are proteins that greatly speed up biological reactions (Hoyle & Wickramasinghe, 1981, p.19). There are about two thousand of them (Hoyle & Wickramasinghe, 1981, p.19). Yet the evolutionist explanation is that "in the primordial soup ... between 3.5 and 4 billion years ago ... self-replicating systems of RNA molecules, mixed with other organic molecules including simple polypeptides" and "began the process of evolution" (Alberts, et al., 1994, p.9). But apart from the problem that there is no evidence there ever was a "primordial soup" (Brooks, 1985, p.118; Denton, 1985, p.261), the three-dimensional surface shapes of enzymes are critical to their function, and that shape determined by the particular sequence of amino acids in the enzyme's structure (Hoyle & Wickramasinghe, 1981, p.20). Of the hundred or more amino acids typically make up an enzyme, about ten to twenty of those amino acids determine the basic three-dimensional structure of the enzyme and these must be in the correct sequence (Hoyle & Wickramasinghe, 1981, p.20). There are also regions of each enzyme called an active site that must be in their correct sequence (Hoyle & Wickramasinghe, 1981, p.20). Now the chance that these ten to twenty different amino acids would just happen to fall into the correct sequence to form a particular enzyme and its active site is about one chance in 1020 (Hoyle & Wickramasinghe, 1981, p.20). However, the problem for evolution is that there are about two thousand enzymes, and the chance of obtaining them all by random shuffling is one in (1020)2000 = 1040,000 (Hoyle & Wickramasinghe, 1981, p.20). This is such a small probability that it would not occur even if the whole universe consisted of organic soup (Hoyle & Wickramasinghe, 1981, p.20; Denton, 1985, p.323)! [top] 5. Molecular machinery 1. Origin of molecular machinery Leading evolutionist Richard Dawkins admits the logical impossibility of random mutation and natural selection producing the molecular machinery that is a required to be in place for natural selection to work (Dawkins, 1986, pp.139-140). He concedes that this could be seen as "a fundamental flaw in the whole theory of the blind watchmaker" and evidence "that there must originally have been a ... a far-sighted supernatural watchmaker" (Dawkins, 1986, p.141). Dawkins blusters that this is "a transparently feeble argument" on the grounds that it "explain[s] precisely nothing, for it leaves unexplained the origin of the Designer" (Dawkins, 1986, p.141). But it is Dawkins' argument which is "transparently feeble," because as Ratzsch points out "the principle that no explanation is legitimate unless anything referred to in the explanation is itself explained ... would effectively destroy any possibility of any explanation for anything" (Ratzsch, 1996, pp.191-192). Or to put it another way, "[t]here is a lot of middle ground, however, between a statement that `explains precisely nothing' and a statement that does not explain everything" (Johnson, 1998a). Dawkins' own explanation for the origin of the "DNA/protein replicating machine" is "sheer unadulterated miraculous luck" (Dawkins, 1986, p.141), apparently forgetting that about a hundred pages earlier he had noted that the probability of a mere 146 amino acid haemoglobin protein assembling itself by chance "is 20 times itself 146 times ... a 1 with 190 noughts after it" (Dawkins, 1991, p.45), that is 20146 or 10190. Yet, as Dawkins himself had earlier stated, the size of just one of these protein machines is about 6,000 atoms (Dawkins, 1986, p.121), which at an average of 16 atoms per amino acids in a protein chain (Shapiro, 1986, p.283), is 375 amino acids required to assemble by chance (which is 20375 or about 10489)! Dawkins later rejects a rival theory of geneticist Gabriel Dover on the grounds that the chance of it happening was "a 1 with 301 noughts after it" (that is 10301), which "is far far greater than the total number of atoms in the entire universe" (Dawkins, 1986, p.315). Yet Dawkins' own chance alternative to design is a 1 with 489 noughts after it! [top] 2. ATP synthase (F1-ATPase) The ATP (adenosine triphosphate) synthase molecular machine, F1-ATPase, is a protein complex found in the membranes of prokaryotes, mitochondria and chloroplasts (Campbell, Reece & Mitchell, 1999, p.159), therefore in all living organisms. It uses the energy of a proton (H+) gradient to drive ATP synthesis (Campbell, Reece & Mitchell, 1999, p.159), the conversion of "food or light into ATP, the energy currency of the cell" (Pearson, 2001). "ATP captures the chemical energy released by the combustion of nutrients and transfers it to reactions that require energy, e.g. the building up of cell components, muscle contraction, transmission of nerve messages and many other functions (Henahan, 1998). "The motor resides within the ATP synthase enzyme and has three main parts each consisting of a number of protein subunits: a cylindrical component within the membrane, a protruding knob, and a rod (or "stalk") connecting the other two parts (Campbell, Reece & Mitchell, 1999, p.159). "The cylinder is a rotor that spins clockwise, at several thousands revolutions per minute, when H+flows through it down a gradient (Campbell, Reece & Mitchell, 1999, p.159; Pearson, 2001). The attached rod therefore also spins, activating catalytic sites in the knob, which is the component that joins inorganic phosphate to ADP to make ATP" (Campbell, Reece & Mitchell, 1999, p.159). The ATP synthase "mushroom cap," they found, contains three identical areas, arranged like a coil, where ATP is made," with "Each area is occupied with a different stage in ATP production" (Henahan, 1998). "As the `stem' rotates, it creates a powerful internal shifting in each of the three coiled sections within the cap" (Henahan, 1998). "This shifting provides the energy to cause chemical changes" (Henahan, 1998). "At one site, the "ingredients" for ATP come together" (Henahan, 1998). "At another site, they assemble as ATP, and at the third site, the rotation readies the fully formed ATP to pop off the synthase molecule, for use throughout the cell" (Henahan, 1998). Adenosine triphosphate synthase is "one of the most complex molecules ever revealed, almost six times larger than the blood molecule hemoglobin" (Henahan, 1998). "It's also one of the tiniest and most powerful motors ever identified" (Henahan, 1998). "Richard Cross, who studies the ATP synthase enzyme, admitted that "We couldn't ever build a motor that small - but nature has" (Pearson, 2001). "The idea that the enzyme might turn like a motor when originally proposed was thought to be "a crazy idea" (Pearson, 2001). Indeed, leading evolutionist J.B.S. Haldane declared in 1949 that "a leap which would imply prevision by a designer," would be "the wheel ... which would be useless till fairly perfect" (Haldane, 1949, p.90)! When "Kinosita's group ... showed the ATP motor turning for the first time ... `It had major impact - seeing is believing' ... `It turned the field on its head' ... `To see it physically going was amazing" (Pearson, 2001). "ATP synthase is just 10 nanometres across: about 50,000 times smaller than" the world's smallest human-built electric motor, which is only 1/64th inch cubed (Ball, 2004a). And "no one has yet figured out how to make such a molecular-scale device from scratch (Ball, 2004a). So the problem for evolution is to expla how a `blind watchmaker' (natural selection - Dawkins, 1986, p.21) could make a motor that is "50,000 times smaller" than the smallest motor made by a highly intelligent human designer with modern technology. However, the evolutionist problem is that the ATP synthase molecular motor is found in all free-living organisms, being essential to the production of the cell's energy, and is therefore a prerequisite to life, and therefore to natural selection itself! So evolutionists must explain how "one of the most complex molecules ever revealed" (Henahan, 1998), assembled itself without natural selection! "The F0F1 Complex: Proton Translocation Through F0 Drives ATP Synthesis by F1. ... the F1 complex is only part of the ATP synthase complex. F1 is attached by a short stalk to complex F0, which is embedded in the inner mitochondriai membrane at the base of the stalk. ... We now know that the F0 complex serves as the proton translocator, the channel through which protons flow when the electrochemical gradient across the membrane is being used to drive the ATP synthase activity of the F1 complex. Thus, the functional unit is the F0F1 complex. The F0 component provides a channel for the exergonic flow of protons from the outside to the inside of the membrane, thereby tapping into the pmf, or driving force, of the electrochemical proton gradient, and the F1 component carries out the actual synthesis of ATP, driven by the energy of the proton gradient. ... The ... F1 headpiece The bacterial F1 headpiece consists of three a and three ß polypeptides, organized as three aß complexes that form a catalytic hexagon. The catalytic site for ATP synthesis and hydrolysis is located on the ß subunit; the a subunit serves as an ATP/ADP-binding site, thereby promoting the catalytic activity of the ß subunit. The stalk consists of three polypeptides: gamma (y), delta (d), and epsilon (E). These subunits extend into both the F1 and the F0 structures. ... The d and e subunits are required for assembly of the F0F1 complex, and the y subunit appears to rotate as protons move through the channel in the F0 structure ... The F0 complex consists of polypeptides a, b, and c, with 1 a subunit, 2 b subunits, and 9 to 12 c subunits present in the functional complex. The c subunits are thought to be organized in a circle, forming the proton channel through the membrane. The a and b subunits apparently stabilize the proton channel. In addition, subunit b binds to the stalk, thereby anchoring the F1/stalk structure to the F0 base. ... Despite years of intense research, we do not yet fully understand the mechanism whereby the exergonic flow of protons through F0 drives the otherwise endergonic phosphorylation of ADP to ATP by F1. However, research in this area was greatly stimulated by the publication in 1994 of the structure for the F1 complex from bovine heart mitochondria, as determined by X-ray crystallography. Significantly, each of the three aß complexes has a distinctly different conformation, a finding that supports the binding change model ... This mechanism envisions that each of the aß assemblies exists alternately in one of three conformations-loose (L), tight (T), and open (O)-with each of the three assemblies in a different conformation at any point in time. ATP synthesis is thought to proceed in four steps. In step (1), ADP and Pi bind initially to an aß assembly that is in the L state. Step (2) involves an energy-dependent change to the T conformation, accompanied by the conformational change of another aß assembly (which has a previously synthesized ATP molecule bound to it) from the T to the O conformation. The bound ADP and Pi at the T site then react to form ATP, with the release of water (step (3)). That ATP remains bound but the previously synthesized ATP molecule at the other site is released. The F1 complex then rotates 60° to position the next aß assembly for binding of ADP and Pi, in readiness for the next cycle (step 4 ). The most remarkable feature of this model is that the differences in binding affinities of the three aß assemblies are thought to be caused by a physical rotation of the y subunit in the center of the (aß)3 catalytic hexagon! The y subunit extends from the F1 headpiece down the stalk to the circle of c subunits in the F0 complex. Proton transport through the c channel involves protonation and deprotonation of a specific aspartate residue (Asp61) in a particular c subunit, causing structural changes in the portion of the c subunit that interacts with both the y and e subunits. These subunits appear to move progressively from one subunit c to another, and the torque of that movement is thought to cause the physical rotation of the y subunit. According to this model, F0F1 is a "rotary engine" in which the electrochemical energy that is released as protons pass through the F0 component and is transduced into mechanical energy, which then drives the conformational changes of the aß assemblies that lead to ATP synthesis. In other words, the F0F1 complex is an electrochemical-to-mechanical-to-chemical energy transducer-and the smallest rotary engine in the world! Or, in the words of one author, "a splendid molecular machine." (Becker, Kleinsmith & Hardin, 2000, pp.438-440) "The molecular weights of the three components of the E. coli F0F1 are about 321,000 for F1 (a3/ß3), 65,000 for the stalk ( yde), and 144,000 for F0 (ab2c10). The total molecular weight for the assembled complex (a3/ß3ydeab2c10) is therefore about 530,000." (Becker, Kleinsmith & Hardin, 2000, p.439). [top] 3. Ubiquitin-Proteasome protein recycling system Professors Aaron Ciechanover, Avram Hershko and Dr Irwin Rose" "won the 2004 Nobel prize for chemistry" "for work in the 1980s" "discovering the human body's method of getting rid of rogue proteins that ultimately lead to diseases like cancer." "They "found that the unwanted proteins which could, for example, lead to errors in cell replication or genetic coding are `labelled' for destruction with a molecule called ubiquitin. It sends them to "waste disposal" units, called proteasomes, where they are chopped into small pieces ... the process by which the body exercises quality control." The "role of protein breakdown in such processes was `absolutely fundamental'. "There is nothing in the cell that can work without some role of ubiquitin or its cousins" (Johnson & Brown, 2004). "The cell's custodial duties have turned out to be much more than just taking out the trash. Rather, they act like a sophisticated inventory control program. The quick removal of specific proteins tells the cell when to divide, when to turn on or turn off various functions, when to die. .... The disposal of proteins is `crucial to almost any cellular process that anybody has studied.' ... a small protein consisting of just 76 amino acids. ... [is] in every tissue of every organism higher than bacteria, from fungi to yeast to frogs to people. ... the ubiquitous protein: ubiquitin. ... the cell attaches to proteins it wants destroyed. The process of attaching ubiquitin takes energy ... The tagged proteins are taken to barrelshaped chambers floating in the cell cytoplasm called proteasomes, which slice the proteins into bits that are then recycled into new proteins. For example, the protein-destroying process plays an important role when a cell divides, because of proteins called cyclins that change at each step of the process. `These are proteins that ... tell the cell what stage they are at in the cell cycle' ... `To go from one stage to the next, you need to get rid of these cyclins very suddenly.' In people, about 1,000 of the genome's 35,000 genes appear to take part in the ubiquitin system. `A large fraction of the genome is dedicated to this pathway'... In addition, some genes that were initially identified as tumor suppressors now appear to be involved with ubiquitin ..." (Chang, 2004a). The "yeast 26S proteasome contains over two million protons and neutrons and is the largest nonsymmetrical molecule mapped to date. ... It serves as an intracellular waste-disposal and recycling system. Tiny molecules within the proteasome attach markers (called ubiquitin) to waste material ... the first job of the 26S proteasome, after identifying a tagged protein, is to unfold, untwist, and unravel it. This function is performed by an apparatus at each end of the proteasome. Once the targeted protein is straightened out, the proteasome drags it into its core and cuts the protein into segments. These segments are precisely measured by a `ruler' inside the proteasome. The cut-up pieces are then ejected from the proteasome, and a `sanitation' fleet (other proteins) drives by to pick them up and sort them, separating the stuff that can be reused from the stuff that cannot. The complexity of such systems ... reflect a mind-boggling quantity, not to mention quality, of information. Where did that information come from? Who structured these molecules and taught them to perform their functions? Did blind chance and random process?" (Ross, 1997). If evolutionists really think that the `blind watchmaker', random mutation and natural selection, created the ubiquitin tagging and proteosome protein recycling system, then why do they waste time on such comparative trivia as peppered moths and finch beaks? Explaining the origin of the proteosome, a protein that destroys other proteins, and then ubiquitin a protein that tags other proteins that have defects, and then putting them both together into a system, would be a far more impressive demonstration than fluctuations in moth shades of grey and millimetre cyclic fluctuations of finch beaks! [top] 4. Myosin-actin muscle molecular motor "The machinery of muscle, for instance, has gangs of proteins that reach, grab a `rope' (also made of protein), pull it, then reach out again for a fresh grip; whenever you move, you use these machines. ... If a hobbyist could build tiny cars around such motors, several billions of billions would fit in a pocket ... Simple molecular devices combine to form systems resembling industrial machines." (Drexler, 1992, p.8). "myosin A contractile protein that interacts with actin to bring about contraction of muscle or cell movement. The type of myosin molecule found in muscle fibres consists of a tail, by which it aggregates with other myosin molecules to form so- called 'thick filaments'; and a globular head, which has sites for the attachment of actin and ATP molecules." (Martin & Hine, 2000, p.395). "myosin The predominant protein of the myofibrils of muscle cells. It has an unusual shape for a protein, having a globular head and a rod-like tail" (Allaby, 1999, p.348). "actin A contractile protein found in muscle tissue, in which it occurs in the form of filaments (called thin filaments). Each thin filament 'consists of two chains of globular actin molecules, around which is twisted a strand of tropomyosin and interspersed troponin. Units of muscle fibre (see sarcomere) consist of actin and myosin filaments, which interact to bring about muscle contraction (see also sliding filament theory). Actin is also found in the *microfilaments that form part of the cytoskeleton of all cells" (Martin & Hine, 2000, p.7) "sarcomere Any of the functional units that make up the myofibrils of voluntary muscle. Each sarcomere is bounded by two membranes (Z lines), which provide the points of attachment of actin filaments; another membrane (the M band or line) is the point of attachment of the myosin filaments. The sarcomere is divided into various bands reflecting the arrangement of the filaments ... During muscle contraction the actin and myosin filaments slide over each other ... and the length of the sarcomere shortens: the Z lines are drawn closer together and the I and H bands become narrower" (Martin & Hine, 2000, p.531). "sliding filament theory A proposed mechanism of muscle contraction in which the actin and myosin filaments of striated muscle slide over each other to shorten the length of the muscle fibres (see sarcomere). Myosinbinding sites on the actin filaments are exposed when calcium ions bind to troponin molecules in these filaments. This allows bridges to form between actin and myosin, which requires ATP as an energy source. Hydrolysis of ATP in the heads of the myosin molecules causes the heads to change shape and bind to the actin filaments. The release of ADP from the myosin heads causes a further change in shape and generates mechanical energy that causes the actin and myosin filaments to slide over one another..." (Martin & Hine, 2000, p.550) [to be continued] [top] 5. Nerve cells (voltage-regulated gates, etc)"Nerve cells have a long tail, which carries an electronic impulse. The tail can be several feet long, and its signal might stimulate a muscle to action to control a gland, or report a sensation to the brain. Like a cable containing thousands of different telephone wires, nerve cells are often bundled together to form a nerve. Early researchers considered that perhaps the electronic impulse traveled along the nerve cell tail like electricity in a wire. But they soon realized that the signal in nerve cells is too weak to travel very far. The nerve cell would need to boost the signal along the way for it to travel along the tail. After years of research it was discovered that the signal is boosted by membrane proteins. First, there is a membrane protein that simultaneously pumps potassium ions into the cell and sodium ions out of the cell. This sets up a chemical gradient across the membrane. There is more potassium inside the cell than outside, and there is more sodium outside than inside. Also, there are more negatively charged ions inside the cell, so there is a voltage drop (50-100 millivolts) across the membrane. In addition to the sodium -potassium pump, there are sodium channels and potassium channels. These membrane proteins allow sodium and potassium, respectively, to pass through the membrane. They are normally closed, but when the electronic impulse travels along the nerve cell tail, it causes the sodium channels to quickly open. Sodium ions outside the cell then come streaming into the cell down the electrochemical gradient. As a result, the voltage drop is reversed and the decaying electronic impulse, which caused the sodium channels to open, is boosted as it continues on its way along the nerve cell tail. When the voltage goes from negative to positive inside the cell, the sodium channels slowly close and the potassium channels open. Hence, the sodium channels are open only momentarily, and now with the potassium channels open, the potassium ions concentrated inside the cell come streaming out down their electrochemical gradient. As a result, the original voltage drop is reestablished. This process repeats itself along the length of the nerve cell until the impulse finally reaches the end of the cell. ... the process depends on the intricate workings of the three membrane proteins. The sodium -potassium pump helps set up the electrochemical gradient, the electronic impulse is strong enough to activate the sodium channel, and then the sodium and potassium channels open and close with precise timing. How, for example, are the channels designed to be ion-selective? Sodium is about 40 percent smaller than potassium, so the sodium channel can exclude potassium if it is just big enough for sodium. Random mutations must have struck on an amino acid sequence that would fold up just right to provide the right channel size. The potassium channel, on the other hand, is large enough for both potassium and sodium, yet it is highly efficient. It somehow excludes sodium almost perfectly (the potassium -to -sodium ratio is about 10,000), yet allows potassium to pass through almost as if there were nothing in the way. The solution seems to be in the particular amino acids that line the channel and their precise orientation. For potassium, moving through the channel is as easy as moving through water, but sodium rattles around-it fits in the channel, but it makes less favorable interactions with the amino acids. ... Nerve cells are constantly firing off in your body. They control your eyes as you read these words, and they send back the images you see on this page to your brain. They, along with chemical signals, control a multitude of processes in our bodies. For example, our cardiovascular system runs twenty-four hours a day, seven days a week without our giving it a conscious thought. Our nerves control muscle motion that expands our lungs to draw in outside air and pump blood through the heart.... Biology is full of incredibly elaborate, complex machines. If you are beginning to suspect that Darwinism has no compelling explanation for them, you're right. Aside from vague hypotheses that have more speculation than hard fact, evolutionists have no idea how such machines could have come about by the unguided forces of nature." (Hunter, 2003, pp.30-34) [top]6."The mind's 'Enigma machine'," Daily Telegraph, 24 January 2006, Roger Highfield reports ... Scientists have discovered how codes are processed within the brain. ... Seth Grant Prof Seth Grant says his team have uncovered a 'whole new level of complexity' in the brain. Now a remarkable effort has shown how the proteins described by 200 of these genes make a fundamental piece of the machinery of thought, revealing the human brain is at least 1,000 times more powerful than previously estimated and providing profound new insights into mental illness. A working human brain is the most complex known object in the universe and weaves an average of a million connections every second between its 100 billion nerve cells. By one estimate, if you connected a Pentium 4 computer, each containing tens of millions of transistors, to every connection on the global internet, the average brain would still be 100 times more powerful. To reveal how genes build and run this awesome chemical computer, scientists in Cambridge and Edinburgh focused on the synapse, the junction through which nerve cells transmit information for the biological computations that underlie feeling, perception and thought. The team broke down synapses into their component molecules and analysed them using a method called mass spectrometry, identifying more than 1,000 different proteins. Then the scientists found the genes that described them and studied which proteins interacted with each other. The effort revealed how 200 proteins worked together in a crucial molecular signalling machine that they christened MASC, unveiled in the latest issue of the journal Molecular Systems Biology. The team at the Wellcome Trust Sanger Institute and the University of Edinburgh believe it marks a new leap from genes to cognition, revealing how the MASC is in itself a chemical computer which further boosts the power of the brain by around 1,000 fold. "The synapse has far more computational power than we realised," said Prof Seth Grant of the Sanger, head of the mind machine team. The discovery of a "computer within a computer" offers a new way to understand how information is processed in the brain. "We have uncovered a whole new layer of complexity," said Prof Grant. The MASC can turn patterns of activity generated by messenger chemicals called neurotransmitters into the changes in nerve cells that form memories. It is like "the Enigma Machine of World War II, which was used to convert one code into another," said Prof Grant, who revealed its innards with Dr Andrew Pocklington, Dr Douglas Armstrong and Mr Mark Cumiskey. ... [top]
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Created: 3 November, 2003. Updated: 11 February, 2006.