Part of an ongoing serial story Niko followed silently behind Mrs. Stone, but his mind was agitated. He turned over her few words in his mind, much like a jackdaw would look for jewels among pebbles. What did she mean by saying only a fortunate few are welcomed here? Hadn’t he decided on his own … Read more #2 The Beginning part 2
I have come to a conclusion. Perhaps if I had thought about it more carefully at first I would not be surprised. But it has only recently occurred to me that a great deal of the disturbance about evolution—yes, no, theistic, atheistic, guided, unguided, young earth, old earth, Darwinist , near- neutralist, whatever! is about … Read more Not A Simple Question
Part of an ongoing serial story There once was an old woman with a magical house. Every now and again the house would grow a new room, and the old woman would know it was time to expect guests. She never knew who would come, or when, just that some day there would be someone … Read more #1 The Beginning
Why is the world a beautiful place and why does it touch me? When I was 16, my parents gave me a horse. I was a fairly typical teenager— alienated, self-absorbed, and without a way to ground my understanding of the world. I had received a certain worldview from my parents, but it was incomplete … Read more Beauty Leads Us Home
Why is the world a beautiful place and why does it touch me?
was 16, my parents gave me a horse. I was a fairly typical teenager— alienated,
self-absorbed, and without a way to ground my understanding of the world. I had
received a certain worldview from my parents, but it was incomplete and
unsatisfying to me. I think my parents hoped that the horse would liberate me
from my existential crisis. Some sort of animal therapy, perhaps. And it did,
but not in the way they thought.
Picture a hidden city, that though it cannot be seen, is everywhere. Sound crazy? It’s real. And it is the most antic, madcap, crowded yet fantastically efficient city you could ever picture. It’s like Hong Kong sped up to an almost unimaginably manic pace, with all kinds of independent, apparently purposeful activities going on — fast, fast, fast! — conducted by a huge cast of actors (enzymes and other intricately sophisticated molecular machines made of proteins) that go about their business as if it were their business. There, I gave it away. This mysterious city I write about is a microscopic cell, made of DNA, RNA, proteins, and membrane. No doubt you were taught to think of a cell more or less statically, but it is a highly dynamic ever changing entity. How is all this activity coordinated and directed? The answer remains largely mysterious, and the more we find out the more the mystery grows.
We do know this much. The nucleus is where DNA, the cell’s
information storage system, resides. It serves as the cell’s Grand Central
Library, where a good deal of the coordination takes place. DNA, the chief
orchestrator, looks like a tangled mess, but it isn’t, it’s quite organized. It
has to be. Supercoiled DNA packs tightly against the nuclear wall, inactive.
Nearer the center, active chromosomes stake out territories, so that in the center,
their unwound loops of DNA can partner with others in an intricate dance. Clouds
of signal molecules surround these loops, looking for binding sites near genes.
Most genes have multiple binding sites near them. When occupied, the binding
sites send signals— yes, no, no, yes, yes
— that get integrated into one overall signal. When it adds up to yes! a
cascade of events begins — another kind of binding protein sits down on the DNA
like a rider in a saddle, right in front of the gene, and attracts other
proteins to itself, one by one. Then the cluster attracts a wandering machine
called an RNA polymerase, which will copy (transcribe) the DNA into RNA. The
whole complex waits like a race horse in the starting gate until the signal is
given, then bang! the polymerase whizzes off, transcribing DNA into RNA at an
astonishing clip of 30 nucleotides per second.
Sometimes the polymerase jumps between strands, forming an RNA
made from two separate chromosomes. Sometimes polymerases racing in opposite
directions run into each other, like Keystone cops. And sometimes polymerases
run into what are called replication forks, the places where DNA is being
duplicated in order for the cell to divide. The RNA polymerase politely steps
You are probably wondering what the RNA is good for. It gets processed and shipped out to the
cytoplasm, where it is turned into proteins like the polymerase and binding
proteins, or the thousands of other proteins the cell requires. Proteins are the
actors that accomplish things in the cell, and the building blocks from which
things are made. You will meet other examples as we go.