October 17, 2008 | David F. Coppedge

How Cells Thread a Needle

Your challenge today is to invent a machine that can push a wet noodle through a straw.  It can’t pull it.  First it has to grab the end, then push it through without breaking it.  Oh, and there’s a catch; the straw has a plug at the far end and a constriction inside.  Give up?  Maybe you should watch how cells do it.  The mechanism was described by Anastassios Economou in Nature this week.1
    Cells have to do this kind of thing all the time, so they have specialized machinery for the task.  The wet noodles are protein chains in their unfolded state.  The straws are narrow channels through membranes that are normally in a plugged configuration.  Just outside the straw entrance are several precisely-fitted proteins that first attract the chain and cradle it gently between two halves that swivel shut.  As one half tilts, it causes the constriction in the tunnel to open up.  The two parts then fit together like hands, and use a powered motor to gently send the noodle through.
    Economou included a schematic diagram of the five-part mechanism that pushes the proteins through.  (He included a couple of stylized hands to show how the delicate grasping and pushing is done.)  Here’s the caption:

This simplified representation is based on both earlier studies and the new findings.  In this cut-away view of the membrane, the SecA motor lies flat against the cytoplasmic side of the SecY channel (yellow), and consists of a two-domain ATP-powered engine (light and dark blue) and two ‘business-end’ domains (green and magenta; depicted as hands).  a, Initially, the channel pore is sealed by both a constriction halfway through it and a mobile plug domain (not shown) near its exit.  The pre-protein-binding domain of the motor (magenta) is in the open state, exposing an elongated corridor that connects to the entrance of the channel.  This open state is seen in structures of the isolated motor.  b, Swivelling this domain around its stem would allow it to embrace a secretory protein chain.  At this stage, a finger (green) from the second hand of SecA might be in close contact with the chain.  c, When ATP (not shown) is present, the engine conformation changes and the finger could move upwards, pushing or dragging the protein chain into the pore.  This motion, or other conformational changes, leads to the opening of the pore.

Details of this mechanism have only recently come to light.  It appears that the machinery puts a gentle stretch on the chain a few links at a time.  Think how earthworms stretch and compress to move through their underground tunnels.  The scientists believe that the SecA-SecY machinery uses a similar technique to propel the protein chains through the channel.  For really long chains, the machinery can repeat the cycle over and over.
    Economou described how difficult it is to observe these nanoscopic machines at work.  “Solving structures of membrane proteins is not a trivial pursuit,” he said.  There are many questions and projects remaining.  The ultimate one, mentioned in his final sentence, is “determining the dynamics of this astonishing cellular nanomachine.

1.  Anastassios Economou, “Structural biology: Clamour for a kiss,” Nature 455, 879-880 (16 October 2008) | doi:10.1038/455879a.

Evolution was not mentioned in this paper.  The scientists studied this process in those highly-evolved, large, complex animals known as… bacteria.
    OK, Charlie’s got a problem here.  There are half a dozen protein machines involved in this process.  They rotate, swivel and fit together in precise contact.  They are driven by ATP fuel pellets.  The machines must apply the energy precisely for function: in the right direction, in the right amount, at the right time.  Could chance produce such a complex machine?  (Bacteria, in the evolutionary fable, are among the earliest and simplest life-forms to “appear” on the early earth.)
    Do the math.  SecA contains 802 amino acid residues; SecY contains 436.  Our online book calculated that getting a 400-unit protein chain by chance would be one in 10240, even under unnaturally favorable circumstances.  That number is already way, way, way beyond the universal probability bound (i.e., it would never happen anywhere in the universe), and we don’t even have one protein of this multi-protein complex.  If by some wildly, radically, absurd stretch of imagination chance arrived at the right sequence for SecY (the shorter of the two proteins), it would be incredibly more unlikely to get the larger one, SecA, which is not only twice as long, but has to fit like lock and key with the first one.  Each of these protein parts is like that.  They all have to work together.  Calling this irreducibly complex is an understatement.  The machine parts don’t just happen to show up at the cell membrane by a random walk and work together for the first time.  They were designed to do what they do, and they do it exquisitely.
    Evolutionists would have us believe that natural selection tinkers with whatever parts are available, and complexity just happens.  Sooner or later, though, if you carry that logic too far, you wind up tinkering with nothing.  You could tinker with an existing radio, for instance, to make it pick up new wavelengths, but how far back can you push the tinkering metaphor back until you have nothing but a few random pieces of plastic and wire lying around?  The metaphor also suffers from implicit personification, as if the parts would even want to do such things.  Humans impose their sense of design on molecules that have no ability to plan ahead and work together, and no reason to do so.  Left to themselves, they would randomize.
    Economou has given us occasion to discuss economics.  The bankruptcy of evolutionary theory becomes more evident with each new investigation.  Trying to bail it out with public credulity is not going to make it recover.  The Darwin Party oligarchy needs to stop tinkering and tampering, remove its protectionist barricades, and let free inquiry have its way.  Intelligent design has the intellectual capital to inject into the logic markets.  Liquidity will result, knowledge banks will open up, and public confidence will stabilize the scientific institutions.  Freedom to invest in the best explanations, wherever the evidence leads, will once again usher in a prosperous era of bullish science.

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