October 23, 2014 | David F. Coppedge

Cell Biologists Use Machine Language

This is a golden age of discovery about molecular machines, but the metaphor may be moving from machinery toward information processing.

Hardly a day goes by without a new discovery of machines in cells doing wonderful things with moving parts.  Thanks to new imaging methods, scientists have clearer vision in the cell than ever before (see Science Daily and Science Insider for examples).  We can only touch briefly on a few of the latest discoveries:

Ribosome:  One part of the ribosome (the RNA-to-protein translator) undergoes a “large scale rotation” by pivoting along a hinge, PNAS reported.  It appears this machine acts like a ratchet with this rotation, moving the messenger RNA through the translation apparatus with every click.

Master switch PKA:  A “powerful biomechanical switch” is described in PhysOrg.  PKA is responsible for coordinating several biological functions.  It has a linker region that “plays a major role in organizing the internal architecture and shape changes the [sic] determine the unique biological functions of PKA.”

Lasso that stray transcript:  The splicesome, Nature reports, has a “lariat” that can “lasso” parts of a messenger RNA it needs to splice.  “The spliceosome enzyme complex removes intron sequences from RNA transcripts to form messenger RNA,” writes Robert T. Batey in “Lariat lessons” the same issue of Nature. “The crystal structure of a lasso-shaped RNA suggests a mechanism for this splicing process.”

Repair shop:  Three articles tell about machines that repair DNA.  Nature describes a molecular scissors capable of “making the cut” where a patch is needed.  Science Daily reported new understanding of how BRCA2 works to repair DNA; this machine is implicated in certain forms of breast cancer when broken.  PhysOrg describes “How to repair tangles in your DNA” which, fortunately, we don’t have to do, because machinery takes care of it automatically.  The opening paragraph is memorable for its implications for intelligent design vs. neo-Darwinism:

DNA damage is a fact of life. On any given day, an organism’s DNA will suffer between 10,000 and 1,000,000 breaks or other damage. These problems are repaired by enzymes in our cells that fix the breaks, remove errors, and maintain the integrity of the genome. One of these DNA repair enzymes acts as a kind of molecular scissors to cut DNA at damage points and resolve tangles that can form when things go wrong. This must be done with great specificity in order to restore the DNA code to its previous state and not generate mutations.

Piston engine:  Yes, the word “piston” really appears in this entry from Science Magazine about how actin filaments and myosin motors allow cells to move by contraction and expansion: “the nucleus can act as a piston that physically compartmentalizes the cytoplasm and increases the hydrostatic pressure between the nucleus and the leading edge of the cell to drive lamellipodia-independent 3D cell migration.

ATP spendthrift:  Speaking of actin, PhysOrg tells about a new finding that solves a 25-year mystery about why actin filaments in bulk use up so much more ATP than individual elements (ATP is the “energy currency” of the cell).  Let’s let them try to explain this:

Basically, what the rate difference mystery means is that somehow actin polymerization accelerates ATP hydrolysis. In other words, as the actin forms a filament, the faster it can use ATP. The effect is cyclical, so that the higher the rate of ATP hydrolysis, the higher the rate at which actin can be depolymerized. This activity leads to a remarkable phenomenon called actin “treadmilling,” which is essential to cellular movement.

Hooray for histones:  That celebratory phrase appears in this article from PhysOrg that also says of these DNA-wrapping proteins: “Histones without DNA are like an instruction manual without words“—i.e., they need the DNA to be able to regulate it.  “The requirement for the presence of histones may help the cell control where the mitotic spindle and the nuclear envelope form,” A lead researcher remarked. “This is particularly important for large cells that need to make sure they are forming these structures in the right spot.

Mighty mitochondria:  There’s a reason why these powerhouses of the cell have stacks and stacks of inner membranes folded on themselves, Live Science says: “This folding vastly increases the surface area for energy production.”  It’s in these membranes where ATP synthase and the other machinery of respiration produce the ATP energy currency needed by all the other machinery of the cell, but that’s not all mitochondria do for us.  The article goes on to describe the “variety of ways” these organelles are vital for cell survival.

Robust photosynthesis:  Corresponding to the mitochondria in animal cells, chloroplasts in plant cells gather sunlight to produce power for the green world.  Researchers publishing in PNAS (see summary on PhysOrg) found out why the membranes in these organelles, called grana, are organized in sandwich fashion.  It allows the repair enzymes to be subcompartmentalized for efficient repair of damaged Photosystem II (PSII) light-gathering antenna complexes.  Even plants get sunburn, you see, and need emergency repairs.  Specialized enzyme machines provide a “multistep repair cycle” to fix the antennas, but need to operate in sequence so as not to get in each other’s way.  The authors were impressed with this organization: “we discover that plants establish reaction order and separation by confinement of the enzymes that catalyze the individual steps to spatially separated thylakoid subcompartments….”

Molecular SupermanPhysOrg describes the Dicer enzyme as a molecular Superman, swooping in to protect the cell from damage during cell division.  Unexpectedly, researchers found that Dicer “controls the release at hundreds of extremely active genes,” not just RNAs.  The conflict is like a plot for a movie:

The problem is that our DNA is constantly in use, with other molecular machines continually plucking at its strands to gain access to critical genes. In this other process, known as transcription, the letters of our DNA are being copied to form a template that will guide the formation of proteins. But these two copying machines can’t occupy the same bit of genetic track at once. Inevitably they will collide — unless a molecular Superman can remove the transcription machinery and save the day.

Electrical wiring:  We save one of the most unexpected discoveries for last: microtubules in cells can apparently conduct electricity.  PhysOrg tells about a team at University of Massachusetts “Imaging electric charge propagating along microbial nanowires.”  The idea that microtubules act like electrical wiring has long been controversial, but molecular biologist Derek Lovley thinks his new images nail it, at least for the bacterium Geobacter.  He thinks the proteinaceous microtubules can pass electrons just like man-made carbon nanotubes do.

Do we have the right metaphor?  The “machine age” of molecular biology is in full swing, but intelligent design advocate Jonathan Wells sees a revolution coming.  Writing in Evolution News & Views, he thinks we’re coming to the end of the machine metaphor.  The new way of conceiving of living things will be to see them as “fundamentally informational.”  His comments come just in time for William Dembski’s new book, Being as Communion, that rigorously argues for information as the basic reality of the universe.

These should be terrible times for Darwinians.  Why don’t they notice their pain?  Why do they still carry on so, chanting their DODO mantras, supporting DOPE and GIDO?  (see the Darwin Dictionary for meaning of these acronyms.)  They are deaf, dumb, and blind by choice: “See no design, hear no design, speak no design,” just like Jesus said and Paul said.


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  • rockyway says:

    Re DNA repair;
    – The cell has been compared to a city… so let’s run with it. Imagine how many things go wrong in a city in a day… and then imagine all the repairs that have to be done daily to keep it running. That might give us a picture of what’s involved with these repair mechanisms, and the importance of them.

    – The steady stream of discoveries at the molecular level speak louder, and far more eloquently, than Richard Dawkins (et al) ever could. The ‘new’ atheists can deny ID all they want, but the realities we see in the cell completely overpower them, and leave them sputtering – as accidentalism becomes less and less plausible all the time.

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