Cells Know Their Physics

first_imgAt the microscopic level of cells, forces come into play that are unfamiliar to us at the macro level: quantum mechanics, Brownian motion, and subtle elastic forces that we might overlook.  Two recent papers in the Proceedings of the National Academy of Sciences explored physical mechanisms cells use to good advantage.  Good thing cells know their physics, or we could not exist.    In a paper in PNAS by a team at the University of Oregon,1  Harland, Bradley, and Parthasaranthy explored the forces at work in cell membranes, which they called “nature’s most important two-dimensional fluid” composed of lipid bilayers.  What keeps the membrane intact?  “It is generally assumed, for lack of evidence to the contrary, that homogeneous lipid bilayers are simple Newtonian fluids – that is, purely viscous two-dimensional liquids incapable of an in-plane elastic response.  To the contrary, “we find that membranes are not simply viscous but rather exhibit viscoelasticity, with an elastic modulus that dominates the response above a characteristic frequency that diverges at the fluid?gel … phase-transition temperature,” they said.  This means that the membrane is stretchy and it requires force to pull it apart.  “These findings fundamentally alter our picture of the nature of lipid bilayers and the mechanics of membrane environments.”    As for why this matters, “The fluidity of membranes is crucial to functions such as the assembly of proteins into signaling complexes and the controlled presentation of macromolecules at cell surfaces” – i.e., we could not live without membranes that know how to take advantage of viscoelastic properties.  “At the level of single proteins, rapid conformational changes on the part of transmembrane proteins such as ion channels and pumps must couple to the local lipid environment;” they said at the end of their paper; “whether this environment is viscous or elastic must therefore influence any molecular model of protein function.”  The authors did not mention evolution in their paper.    Another team at UC Davis explored the quantum mechanics of an important molecular machine – the Complex I macromolecular complex.2  This machine employs a railroad-like piston and coupling-rod mechanism (07/07/2010, 09/22/2010) to create the proton gradient that drives ATP synthesis.  This process is vital to all life: in humans – and in respiring bacteria – it takes the energy from food and stores it as chemical energy in ATP molecules that are used like currency to pay for most of the energetic activities in the cell.  Complex I transfers two electrons from NADH and passes them like hot potatoes down a series of cofactors in the long arm of its L-shaped structure.  One of the electrons is apparently used for control, and the other gets passed 90 angstroms (a fair distance on the scale of proteins) to a ubiquinone molecule for the next stage of energy transfer.  This happens in the cell’s power plants, the mitochondria.  The electron pathway includes a flavin molecule, water molecules, and eight iron-sulfur (Fe/S) clusters in two conformations, each acting alternately as donors and acceptors of the electrons – creating an electrical current.    Hayashi and Stuchebrukhov found that Complex I takes advantage of electron tunneling – a phenomenon in quantum mechanics – to pass the electrons down the chain.  Tunneling occurs when a particle faces an energy barrier that seems insurmountable, but makes it through somehow, because in the probabilistic world of quantum mechanics, a particle, being wavelike and having a wave function, has a probability distribution of where it might be located, due to the uncertainty principle.  There’s a certain probability the particle will be found on the other side of the barrier.  It’s as if a soldier at a castle could magically appear on the other side of the wall without climbing over it.  “In this paper we use state-of-the-art electronic structure calculations to show that the mechanism of electron transfer is quantum mechanical tunneling, as in the rest of electron transport chain;” they said.  Another surprise was that water molecules in path amplify the efficiency of transfer many-fold: “the water between subunits of complex I plays the critical role in mediating electron transport.”  Here’s how they summarized their findings:The whole electronic wiring of complex I is obtained by combining tunneling pathways of individual processes, as shown in Fig. 3.  It is clear that specific peptide residues serve as electronic wires connecting neighboring Fe/S clusters; individual electron tunneling paths involve up to three protein residues, including two cysteine ligands and one additional key residue (Table 1).  Notably, the clusters in the protein are oriented in a specific way—corner to corner—with Cys [cysteine, an amino acid] ligands mostly pointing toward each other, which is clearly the most efficient way to transfer electrons from one cluster to another.In addition, they noted that the “wires” employ thermodynamics to good effect: “the tunneling orbitals in the core regions are constantly changing on the time scale of thermal dynamics of the local protein environment, which is much faster than that of the slowest electron transfer.”  This “mixing” is another efficiency mechanism: “If there were no mixing of the electronic states, the incoming and outgoing electrons would tunnel from the same gateway atom of a cluster, which obviously is very inefficient because of the additional tunneling distance.”    On top of all those efficiencies, the water molecules help even more: “With water present between the subunits, the tunneling rates are dramatically increased by two to three orders of magnitude,” they said with evident surprise and delight: “The internal water at the subunit boundaries is therefore an essential mediator for the efficient electron transfer along the redox chain of complex I.”    Did these scientists bring evolution into the story?  Only to show it had not happened here: “The key residues identified in this study as mediators of electron transfer (Table 1) are remarkably conserved among different organisms.”  To test that conservation, they watched what happened with mutants.  The electron transfer rate decreased dramatically.  All the elements of the chain appear to be precisely tuned for optimum efficiency.  Even though water can “repair” some tunneling paths if gaps are created by mutations, they were not prepared to say evolution produced this finely-tuned pathway for electrons.  “Yet there is conservation of specific residues along the paths described above, and whether it was evolutionarily determined or not remains to be examined further.”  That was all they had to say about evolution.  In essence, they shuttled off the question to someone else, but left open the possibility that it was not evolutionarily determined.  What is the alternative?    Their concluding paragraph revealed a bit of emotion about all this: “It is remarkable that the most fundamental energy-generating machinery in cells is based on the wave properties of electrons, which allow for an efficient transport of energy-carrying particles along the chain of redox cofactors toward molecular oxygen via quantum tunneling as demonstrated by this study.”1.  Harland, Bradley, and Parthasaranthy, “Phospholipid bilayers are viscoelastic,” Proceedings of the National Academy of Sciences, published online before print October 25, 2010, doi: 10.1073/pnas.1010700107.2.  Hayashi and Stuchebrukhov, “Electron tunneling in respiratory complex I,” Proceedings of the National Academy of Sciences, published online before print October 25, 2010, doi: 10.1073/pnas.1009181107.Notice the precision of these machines.  The efficiency of electron transfer in Complex I, for instance, depends on precisely-placed amino acids and water molecules down a fairly long chain.  The fact that these amino acids are “conserved” (i.e., unevolved), only means that they cannot be altered without severe consequences (like death).  It does not mean that they evolved into that configuration—that would be a logical fallacy.  Both creationists and evolutionists realize that mutations occur – a cosmic ray could hit the molecule or a gene, or an editing error could result in a different amino acid being inserted.  Many of these will cause death.  The ones that do not may allow the organism to survive and reproduce (genetic drift and stabilizing selection).  Over time, mutations can accumulate (mutational load) at rates that are not well understood (despite the evolutionary “molecular clock” that circularly depends on evolution as an assumption), but genetic drift and stabilizing selection are level or downhill processes.  They are only creative if you believe the Tinker Bell myth already (10/08/2010).  How did the first microbe even get off the starting line without Complex I and ATP Synthase already in place?  Evolutionists imagine stepping stones, but never provide them.  It’s like imagining stepping stones to Hawaii or across the Grand Canyon with no evidence – just the belief that they had to be there for evolution to get across the chasm.  Well, guess what.  Some people have no need of that hypothesis.    The elegant, functional structures of these molecular marvels should make us stand in awe of their Creator.  Scientists dare not utter such thoughts.  Look again at that circumlocution in the second paper, “whether it was evolutionarily determined or not remains to be examined further.”  The position of the authors about evolution vs design is unknown to us, but that statement is about as close as a scientist can safely get these days to saying, “Darwin was a mush-head” and still get published in PNAS.  Thoughtful readers can look at the evidence and draw their own conclusions.(Visited 14 times, 1 visits today)FacebookTwitterPinterestSave分享0last_img read more