Synthetic Biology

These are either the scariest words ever written or the announcement of our impending immortality…

"We make a genome from four bottles of chemicals; we put that synthetic genome into a cell; that synthetic genome takes over the cell," said Dr. Gibson. "The cell is entirely controlled by that new genome."

The scientists didn’t give the new organism its own species name, but they did give its synthetic genome an official version number, Mycoplasma mycoides JCVI-syn1.0.

To set this novel bacterium—and all its descendants—apart from any natural creation, Dr. Venter and his colleagues wrote their names into its chemical DNA code, along with three apt quotations from James Joyce and others. These genetic watermarks will, eventually, allow the researchers to assert ownership of the cells. "You have to have a way of tracking it," said Stanford ethicist Mildred Cho, who has studied the issues posed by the creation of such organisms.

In case you missed it, scientists working for Craig Venter have created, for the first time, a completely synthetic organism by writing computer code to create the desired gene sequences, made the DNA from the code, and then transplanted the DNA in an empty cell, which was taken over by the DNA.

This is literally a turning point in the relationship between man and nature," said molecular biologist Richard Ebright at Rutgers University, who wasn’t involved in the project. "For the first time, someone has generated an entire artificial cell with predetermined properties.

Read the whole story here and ponder what this means for mankind.

Sodium and Potassium

Sensation is an abstraction, not a replication of reality – Santiago Ramon y Cajal

"Every thought, every feeling, every sensation ever experienced by any animal on this planet is the result of sodium entering a cell and potassium leaving the cell…" paraphrased from my notes as spoken by our Biology professor.

Above (Na+/K+-ATPase – aka the Sodium-Potassium Pump)

The path of learning, as we move deeper into the study of biology, has taken us from molecules and the electro-chemical gradient, to cells, tissue, and organs, to plants, and now to animals. The single most important major evolutionary event, for us,  has been the development of the nervous system and the brain. Even at the most fundamental level, understanding how the brain works requires grasping the relationship between electrical and chemical signals. Which, at the end of a long, complicated journey, means understanding the relationship between sodium and potassium.

And, since the development of life is the result of evolution over billions of years, it is not surprising to learn that our dear friends and key chemicals sodium and potassium are found in every process that defines life.

Along the way, it’s become increasingly clear that the same model used to design and operate the most minute molecule has also been used to design and operate every other component of our being, from cells to the higher level organisms of plants and animals. We are simple things, made complex by evolution and size, until the complexity conceals the simple nature of the thing. The fractal (shown below, courtesy of wikipedia) is a good metaphor for this model.

 

If I may grossly over-simplify the concept, every aspect of life requires energy and the ability to communicate. Nature has provided the sodium potassium pump as the agent for both needs. Once again, wikipedia explains:

Membrane potential (or transmembrane potential), is the voltage difference (or electrical potential difference) between the interior and exterior of a cell. Because the fluid inside and outside a cell is highly conductive, whereas a cell’s plasma membrane is highly resistive, the voltage change in moving from a point outside to a point inside occurs largely within the narrow width of the membrane itself. Therefore, it is common to speak of the membrane potential as the voltage across the membrane.

The plasma membrane surrounds the cell to provide a stable environment for biological processes. The membrane potential arises from the action of ion channels, ion pumps, and ion transporters embedded in the membrane which maintain different ion concentrations inside and outside the cell. The term "membrane potential" is sometimes used interchangeably with cell potential but is applicable to any lipid bilayer or membrane.

And how are the differences on either side of the membrane managed? By the sodium-potassium pump, of course…..

Active transport is responsible for the well-established observation that cells contain relatively high concentrations of potassium ions but low concentrations of sodium ions. The mechanism responsible for this is the sodium-potassium pump which moves these two ions in opposite directions across the plasma membrane. This was investigated by following the passage of radioactively labeled ions across the plasma membrane of certain ones. It was found that the concentrations of sodium and potassium ions on the two other sides of the membrane are interdependent, suggesting that the same carrier transports both ions. It is now known that the carrier is an ATP-ase and that it pumps three sodium ions out of the cell for every two potassium ions pumped in.

The sodium-potassium pump was discovered in the 1950’s by a Danish scientist, Jens Skou, who was awarded a Nobel Prize in 1997. It marked an important step forward in our understanding of how ions get into and out of cells, and it has a particular significance for excitable cells such as nervous cells, which depend on it for responding to stimuli and transmitting impulses.

Of course it’s much more complex than my simple phrases, mixed with some pseudo-authority from wikipedia, can possibly explain. But this new student of biology cannot help but read and learn with gobsmacked awe as the (and there’s no other word for it) miracle of evolution and life are explained to him. Simplicity, a successful pattern replicated again and again over time and frequency to build from the atomic to the human level.

All because of sodium and potassium.