#4 Room

Part of an ongoing serial story

Zephan rolled his shoulders, trying to release some tension, and then rubbed his hands across his face. He didn’t know what to do now. Voices that called to him from flames! He must be crazy!

“Mom, please tell me everything you can about the house and that old woman who seems to run it. If I am to go back, I need to know who they are and what they want.” He spoke quietly, but with a firmness beyond his year

“Her name is Mrs. Stone. As far as I can tell, she is as old as the house and still going strong. She is solid as a rock, immovable in her opinions, flinty-eyed when it comes to mischief, but she has broad shoulders and a soft heart for the sorrowful. Go to her when you are in trouble, and you will receive unfailing aid,”

“But the house, Mom?”

“I don’t know, honey. All I know is that people staying there are given jobs to do, some of them pretty heroic. Like the time Lester led a herd of sheep down the mountain in a crashing thunderstorm at night. Good thing he and his dog know that mountain like the back of their hands, er, paws. I just had to learn not to feel sorry for myself, and one day to marry and have a son.” She sighed wearily. “I don’t know what else to tell you.”

“Can I trust them?” Zephan asked quietly.

“With your life, ” she said swiftly. “They saved mine, you know. I was a proud, heartless girl the day that fall blinded me, and drove the will to live out of me.” She reached out for him, and he took her hand. “Ask anyone who knew me then, and they will tell you that blindness was the best thing that ever happened to me. But I will add, no, it is the best only because of Mrs. Stone and the house.”

“Why do you say the house, Mom? Do you mean the people living in the house?” Zephan released her hand, frowning.

She smoothed her skirts, tilting her chin up a little. “No. Though they did help. It was the house.” Then she smiled. “It is alive, Zephan. It knows what you want and what you need, and when to give them both. It is like the world’s best parent, only it never speaks directly, only indirectly. And it is full of love, infinite love, for each one within it. You know, it’s funny, but there’s always room for one more. It always seems to know when someone’s coming. It’s the house that tells Mrs. Stone, you know.”

The snap of resin popping and wood burning was the only sound for a while. Both mother and son seemed far away in quiet conversation with themselves. Finally, Zephan roused himself. As he scooped up his backpack, it was apparent something had changed. He no longer looked like someone to be bullied; he had grown into a young man in an evening.

The Ultimate Recycler

a power grid reaches straight up to a blue sky. Demand for power is high how do we meet our own demand for power?
Photo by Pixabay on Pexels.com

When a city starts out with a major energy deficit, there are two changes that should be made: to be really, and I mean really efficient at recycling the critical resource, or to buy more energy.

What about in biology? Cells are like cities, right?

We already know from the previous post https://anngauger.blog/2019/11/23/is-this-any-way-to-run-a-city/ that the cell has an energy budget that is out of balance based solely on biosynthesis and use of AT.P It is in a predicament. It has an extreme shortfall in ATP in its balance sheet, needing six ATP just to make one. ATP is a high energy molecule. All that energy has to be loaded into the molecule during its synthesis by using up other ATP molecules.

The chemical structure of ATP shows three high energy phosphate bonds.

If chemical A is necessary for the synthesis of more chemical A, then A has the power of replication (such systems are known as autocatalytic systems). …We find that intermediary metabolism is invariably autocatalytic for ATP.

Kun et al., Genome Biology 2008, 9:R51

The cell needs to have ATP before it can make ATP, and it has to have more ATP than it can make. Can the cell rescue its metabolic state by bringing in ATP from outside? Sure, indirectly– if it eats biological material other cells have made, it can get ATP by breaking down glucose into pyruvate, and then pyruvate into citrate, and then ultimately, the energy is harvested and and a net gain in ATP is produced. The glucose to pyruvate digestion happens in the cytoplasm, but the citrate to final energy harvest all occurs in marvellous mysterious voyagers in our cells called mitochondria.

Mitochondria are the microscopic power plants of the cell whose purpose is to take citrate and convert it to ATP,

the cell’s energy currency. Resembling miniature blimps with corrugated double membranes, they carry out an interlocking series of chemical reactions that squeeze out every last possible ATP from the breakdown of glucose. It’s a highly efficient, environmentally friendly process.  Everything is recycled — one part of the process is called the citric acid cycle because it regenerates itself with each new round. In fact, everything cycles.

Most cells have many mitochondria, whose characteristic wrinkled stroma serve to increase the interior membrane surface area. Think of a bag with a much bigger bag neatly tucked in folds inside. Embedded in that folded inner membrane are all machinery of energy production that makes life possible. And that machinery is considerable. An ensemble of multiple proteins come together to make 5 protein complexes, shown in the picture below. In complexes 1-4, energy in the form of electrons is received by them and cycled through and, then using some of that energy to pump protons across the membrane. As citrate is gradually broken down, compounds like NADH or succinate are produced, and shunted off to the electron transport chain, and they also contribute to the process.

Even the last high-energy electrons from the breakdown process are not wasted: a chain of proteins in the inner membrane passes these electrons like little hot potatoes from one to another, using the energy of each transfer to pump hydrogen ions across the membrane, so that a molecular machine called ATP synthase can take advantage of the hydrogen gradient to create even more ATP.  


The protein structures of the electron transport chain of the mitochondrion. These complex structures harvest energy and pump protons so that AdP can be recycled back to ATP.
The protein complexes of the mitochondrial electron transport chain, showing the flow of molecules in and out of the mitochondrion at each stage. doi: https://doi.org/10.1371/journal.pbio.1001129.g001

In the drawing you can see the direction of H+ flow out and then in again, and how many different proteins make up each protein complex. There are 5 complexes, whether in an animal, or a plant.


The fifth complex is ATP synthase. This is where the miracle happens that makes life possible. ATP synthase harvests the energy of the proton gradient to recycle ADP to ATP. Like a turbine in a hydroelectric plant, ATP synthase lets the hydrogen ions flow back across the membrane through itself, rotating as the ions pass through, and As it rotates it adds a phosphate to ADP at each crank, thus restoring ATP to use.

ATP synthase is the name of the protein complex that performs the ADP to ATP conversion. A video is listed that describes its action.

https://doi.org/10.7554/eLife.43128.002

The engine ATP synthase is 98% efficient at what it does! Human machines can’t approach that. But this is what permits life. We burn through our body weight in ATP every day. Just breathing burns ATP.

Right now, within your bodies this little engine is cranking away. Without this machine, oxygen-dependent life could not exist. Strong statement, but I stand by it.

To put it all together, in all life’s glorious improbability and elegant design, will require another post. And I haven’t even gotten past the beginnings of biochemistry.

For a video: ATP Synthase: The power plant of the cell

Comes a King

originally written in 2017

Epiphany
What star is this, shines clear and bright?
Why come these shepherds in dark of night?
From stable there shines a heavenly light—
My heart it trembles at such a sight. 
A glorious King has come here to be born,
A wonder of wonders on this Christmas morn.
 
The baby lies in a manger bare
Joseph and Mary attend him there
The shepherds kneel in wonder and awe 
The infant King born in a stall
Come to take away our sin,
Born that we might be born again
 
His star in the east the prophets foretold
And wise men bringing wealth untold--  
Frankincense a priest’s offering,
Myrrh for burial, gold for a king.
This King a priest born to suffer and die
Then rise again, glorified.
 
The only wise God asleep on the hay
Is Wonder Counselor born this day
Mighty God become helpless for all 
This paradox brings a sense of awe.
Prince of Peace, born to end all strife,
He conquers death and brings new life.
 
Who could have foretold such a wondrous thing
What once was hidden from prophets and kings?
That God would take on a human form
And be born among us on Christmas morn,
Because he took flesh he knows the ways
That sin and grief attend our days.
His sacrifice took away our sin.
Restoring the gift of His life within. 
 
 
 
 
 
 
For unto us a child is born, unto us a son is given: and the government shall be upon his shoulder: and his name shall be called Wonderful, Counsellor, The mighty God, The everlasting Father, The Prince of Peace.
 
 
 
 
 
 

#3 The Mission

Part of an ongoing serial story

Photo by Miro Alt on Pexels.com

Niko edged through the door, hoping his mother wouldn’t notice.

“Zephan? Where have you been? I wanted you to go and get more goat cheese from Mr.Raintree before nightfall.” She spoke quietly, without reproach, but simply describing how it had been.

Zephan grimaced. He had forgotten. “I went to the old house on Hearthstone Hill. You know the one. Bruiser had dared me, and I thought you would rather have me go than have me come home with torn and dirty clothes again.”

She turned her face in his direction eagerly. “Really? You went there? Did you try the door?”

Read more

Joy Comes in the Morning

Photo by Simon Matzinger on Pexels.com

Psalm 30

A Psalm. A Song at the dedication of the temple. Of David.


I will extol you, O Lord, for you have drawn me up,
    and did not let my foes rejoice over me.
O Lord my God, I cried to you for help,
    and you have healed me.
O Lord, you brought up my soul from Sheol,
    restored me to life from among those gone down to the Pit.[a]
Sing praises to the Lord, O you his faithful ones,
    and give thanks to his holy name.
For his anger is but for a moment;
    his favor is for a lifetime.
Weeping may linger for the night,
    but joy comes with the morning.

Home At Last

 Homesick hungry weary lonely
Hearts beleaguered, yet unbowed
‘Still we seek thee ancient beauty
Shining prospect glimpsed through cloud.
Bright horizon, distant city
Where our joy cries out ,”Believe!”
Where our hearts are stilled and gentled
Love the atmosphere
We breathe.

Hearts that long for such a morning
Find no ease in emptiness—
Ancient beauty sate our yearning
Slake our thirst for holiness
For with thee the new day dawning
Soft and sweet all dread now ceasing
Peace and righteousness shall kiss 
And joy will ring out love’s
Great Feast.

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.

Read more

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

https://philosophicaldisquisitions.blogspot.com/2010/08/oppy-on-disagreement-part-3.html

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.