Is This Any Way To Run A City?

The Mystery of Energy Metabolism

The Hidden City Continued

Biologists argue about which came first, metabolism or replication, or in other words, enzymes or DNA. Other biologists try to square the circle by saying, “We can have both at the same time with RNA.” But there is something missing from all three scenarios, without which they won’t get far. Both metabolism and replication require a means to store and transfer energy.

Modern day cells use a molecule called ATP for this process: adenosine triphosphate. It is related structurally to one of DNA’s building blocks: adenine. Compare their structures. Adenine is a base (double ring structure in orange). Add a sugar to it and it becomes adenosine. Add a phosphate to that and you have a nucleotide. Add two more phosphates, and you have ATP. Adenosine triphosphate.

Ho hum you say. What is so interesting about that?

Think of in this way. You have a computer system that stores its information in codes of four instead of two. Not 0s and 1s, but As, Cs, Ts, and Gs. Adenine is the A. One part of the code. Now imagine you take your computer hardware that does the encoding for A, whatever it is, stick a sticky bit on it, and a rechargeable battery, and suddenly you can light campfires and suck the power from light bulbs.

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#1 The Beginning

Part of an ongoing serial story

Photo by Rohan Shahi on

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 in need of that room, and it was her sacred duty to keep it ready for them.

She and the house had an odd sort of relationship, almost symbiotic. The house needed her as much as she needed the house. I was never sure where the magic came from for those extra rooms, but my guess is that it was from the bond between them. She needed guests to be happy, so the house supplied them.

As you might expect, after years of organic growth the house was a great shambling thing sprawled across a hillside, like something from one of those magical Japanese movies. In fact, the house was so odd it was a wonder anyone ever dared approach it seeking help. But I guess word had got around that the place was safe after all.

So that’s why Niko turned up on a Friday. Trying to look nonchalant, he lifted the old-fashioned door-knocker, only to have the door swing wide. Inside was a cheery little parlor with a fire blazing on the hearth and the old lady knitting a great shawl in one of those bright colors whose names never seem to match the color themselves, like puce or vermillion. “What an odd color!”said Niko out loud, before he could help himself.

“Do you think so?” The old lady peered at the shawl. “I have wondered myself. But this is what Mrs. Oddsworthy asked for specifically. She does have the most extraordinary taste.” She stopped, laid aside her knitting and rose. ‘Oh, but do come in. I am Mrs. Stone. I see you have been invited. I have just the room for you.”

Niko’s mouth, which had gaped a bit during this last bit, hurriedly shut, then opened again and said, ” I don’t know what you mean. Invited?”

Poetry and Philosophy

It might seem odd to introduce a poem by pointing toward a blog on philosophy, but when the poem and the blog are read the connection will be clear.

I deal in controversy, in discourse that is sometimes freighted with more than disagreement. So I wrote the poem on this page 40 years ago while a graduate student, based on a sharp disagreement I had with a friend. She believed one thing and I believed another, and the two could not both be true.

It seems now that my life deals in this situation even more, only the rhetoric and emotions are are stronger, more caustic even.

How are we to deal with this conflict?

Photo by Miraage.clicks at Flickr,
CC BY-ND 2.0

What does epistemology have to say about solving disputes?

“As can be seen, there is no single correct response or strategy to take toward actual cases of disagreement. The unsurprising irony is that the epistemology of disagreement has managed to give rise to a whole new set of disagreements.”

And then, after discussing religious disputes, the articles comes to this conclusion:

 “disagreement must be dealt with in the ordinary way: I’ll state reasons, provide arguments and pinpoint evidence, and you’ll do the same.”

On Truth

The line twixt truth and lies is difficult to see-
It winds and doubles, blurs the mind,
And vanishes unseen.
How then as mortals who would hope
To know the truth can we
Presume to judge on simple lines and clean?
I had a friend who spoke her truth
That was no truth to me.
Whose lies were these, and where
The line to separate between?
For just as I, with pain, had grasped
My truth, she held to what she knew.
And with our private truths like whips
We flailed, to find the root
Of discord and of pain.
No hope in that: the pain did not
Delineate, our differences remained,
And Truth lay somewhere, savaged, in between.

Cellular Self-Sacrifice

A astrocyte (kind of glial cell that provides nutrients to neurons) stained for particular proteins. The purple blue ovals are the nuclei where the DNA is.

We naturally think of death as something awful, a scourge to be dreaded and put off for as long as possible. But biological death has its positive side. Think of self-sacrifice—death for the good of others. That kind of death we think of as altruistic, even noble, attributing it to heroes or saints. And most of us don’t realize that such self-sacrifice is written into our bodies, at the deepest levels of our being.

The process is called apoptosis, in which cells kill themselves from within. It is not death due to overwhelming damage—that’s another process and called by another name. Rather it is a programmed process whereby cells self-destruct. They shred their DNA, internal organelles (specialized parts of cells) condense, and membranes bleb (blister). Then scavenger cells come by and clean up the remnants for recycling.

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The Exchange

A carved rugged cave whose walls ae red and purple. Light enters it from above, The cave represents the carved heart of Jesus
Photo by Ignacio Palu00e9s on
Lord, save me. Gripping sorrow
Blinds me. I stumble pathless, lost,
Bewildered, buffeted, storm-tossed.
Mother Mary, carve some hollow for
My aching heart, so I can see.

Wrung, remorseful, aching,
Blame eats my bones--where find you, Lord,
Within this deep’ning wound?
Mother Mary, carve some hollow for
My aching heart, so I can heal.

I lie upon a knife of my own making,
Etched by accusation.
My only hope your cross.
Mother Mary, carve some hollow for
My aching heart, so I can trust.

Carve the hollow where I hide
within His Heart.
He heals us by his wounds.
Mother Mary, Be my companion
In the dark, until the dead arise
And empty be the tomb.

Beauty Leads Us Home

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 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.

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The Hidden City

Hong Kong Street at night UCLARodent at English Wikipedia [CC BY-SA 2.5 (

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 aside.

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.

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Where the Waters Are

We have almost forgotten, this nation of faucets,
The nature of water,
But it has not forgotten us.
Hissing below the surface
It streams and bubbles from depths
Leaping upward into light
Or oozing, trickling,
Dripping past our guards.
We have forgotten wells,
Those still pools
That can only be found by digging,
Where silence reigns,
And sound and light
Are swallowed,
Then given back doubled,
Showing us ourselves.
We have hidden our springs,
Sealed them up for profit,
Making a commerce of them.
But the waters cannot be forgotten.
Rich in silence
Drawn from the deeps
They pour forth in torrents
And fountains.
When I think of you
I think of waters—
A small pool with lilies adrift,
Catching the overflow of the world,
Or the drops that nestle beaded
Among the mosses.
A place of ferment
Where change is constant,
A place of stillness,
Of quiet generation,
Where I am reflected back at myself
And forced to listen—
Waters that go down to the depths,
Springing out of the bones of the earth