Sunday, April 5, 2020

#Viruses An introduction to what they are and how they work

Artistic enhancement of a transmission electron microscope image of the COVID-19 virus.


This is an actual transmission electron microscope image of the virus. Colors are added after the scan is complete.
  • In June of 1973, I began teaching biology at Monte Vista High.
  • If this “story” wasn’t part of my first year’s teaching, it arrived soon thereafter.
  • Originally presented on a chalkboard, then a whiteboard, then via an overhead projector, and in the 1990s and beyond as Apple's early presentation software then PowerPoint, the original diagrams were hand-drawn.
  • Mercifully for you, the diagrams in this PPT are not.
  • Of course, although you do get better visuals, you don't get the "show" that my lecture was. <snicker>

This post is long in scrolling, but not in verbiage. Hang in there.

An important aside

This is important information because

Viruses 
  1. are not made up of cells.
  2. reproduce only in a host using their cellular equipment.
  3. DO have DNA or RNA.
  4. don't grow or develop.
  5. use a cell's energy, not their own.
  6. don't respond to their environment, except to go dormant.
  7. don't control anything about their internal or external environment.
  8. DO mutate DNA or RNA. HIV and other viruses mutate so frequently that the chance of developing a vaccine for them is LITTE TO NO CHANCE.

Conclusion of the Aside:

  • A LIVING ORGANISM MUST "DO" ALL 8 LISTED ITEMS.
  • VIRUSES "DO" ONLY TWO OF THEM.
  • VIRUSES ARE NOT ALIVE. YOU CANNOT KILL THEM. 
  • More on this later.



The Saga of Victor the Virus 

Hosts of viruses tend to be species or scientific classification group-specific. They don't infect every organism they make contact with.

This comic strip illustrates how a bacteriophage (a virus that attacks bacteria) works.  

Viruses that attack your cells function in the same way.  In fact, it's easier for a virus to enter your cells because your cells don't have cell walls.

If you think about what kinds of molecules cells need to function (Hint: Include protein in your list!) and what the outside of a virus is made of, you might be able to figure out why viruses can enter your cells easily.

Victor is a Bacteriophage-a type of virus that attacks only bacteria
Cold viruses are Adenoviruses.
A retrovirus contains RNA, not DNA. It mutates after every few replication cycles of each version of the virus.
Additional types of viruses.












A viral particle approaches a bacterial cell wall.

Yellowish shapes are bacteriophages.
Upon contact with the bacterium, the virus uses enzymes in its base plate to digest a hole in the bacterial cell wall.


All viruses, as you should recall, do only one thing VERY WELL:  reproduce.  However, 
the virus must be inside a host cell or it cannot reproduce. 
To get inside the host bacterium, the contractile sheath contracts, and the viral DNA is injected into the bacterium.  

Aside #2.

  • Your cells have membranes as their outer border, not cell walls
  • Viruses that infect your body don't need to inject anything into your cells because the outer covering of viruses contains proteins. 
  • When viruses "land" on your cells, your cell membranes recognize the virus as a source of protein. 
  • Sensing the protein as food, the cell membrane engulfs the virus and brings it inside the cell. 
  • The virus does nothing to gain entrance exept land on the cell membrane. 

End of Aside #2


Sometimes the viral DNA attaches to the bacterial DNA.  This temperate phage is replicated every time the bacterium divides.  The herpes viruses that cause cold sores in you are like this. The virus can remain inside the bacterial hosts, or your lip cells, for years.  

But isn't an intact virus more than DNA?

Correctamundo!  

Now that we find out that "Victor" is a lot like Clark Kent.  Just like inside Clark is Superman, inside the protein coat of the virus is the functioning part:  DNA.  

DNA must enter the host or nothing will happen. Once inside the bacterium, two possible endings to the story exist. Bacteria (or your lip cells) are not aware that they are infected.  Pretty boring.


Under certain conditions, like radiation from the sun at the beach, can cause the virus to "escape" from its place in the bacterial DNA.  When the virus escapes, it leads to …

An environmental signal can trigger the virus DNA to exit the bacterial chromosome and switch to the lytic mode.

For example, when triggered
Herpes simplex-1 --> Cold sores
Exposure to ultra-violet radiation in sunlight is one trigger of  Herpes simplex-1 to begin the lytic cycle that ends in cold sores.


The second possible ending resulting from a virus infecting a cell is known as the lytic cycle.  Many viruses never exist in the temperate condition; the lytic cycle is their normal process.

Using the host bacterium's (or your lip cell's) enzymes and energy sources, the viral DNA replicates itself.  The multiple copies of the viral DNA direct the ribosomes of the cell to begin making viral coat protein. 
Something, scientists do not know what triggers the virus sub-parts to combine, or how virus sub-parts assemble into virus particles. One of my professors said that step convinces many researchers of the existence of God.

During the lytic cycle, the host cell is destroyed (lysed).  An enzyme is produced which weakens the cell membrane (and wall if the cell is a plant, fungus, or bacterium) of the host.  The cell boundary ruptures. 


Thousands of newly assembled virus particles are released into the environment to infect other cells.

Vaccines usually damage viral DNA.  Since damaged DNA cannot function properly, these attenuated viruses cannot infect and lyse hosts.  

Radiation is used to damage viruses.  Just like radiation is harmful to the DNA in your cells, it is harmful to viral DNA as well.  That is why many hospitals use ultra-violet lights in operating rooms between surgeries.

One use of the word "kill" I don't like at all is when it's used in reference to viruses. There are ways to damage viruses and reduce or eliminate their ability to infect cells and use those cells' internal structures to replicate.

You can't kill something that was never alive.

Closing Aside
Since viruses are not alive, antibiotics do not have any effect on most viruses. There are anti-viral drugs, of course, but medicine used for first aid or bacterial infections are useless against viruses.

Remember that the outer coating of a virus is protein, sometimes phospholipids, also found in your cell membranes, are present, too. If conditions exceed the range where a virus can function, the proteins begin to denature. They unfold from their functional form to a non-function form. Non-functional protein is recognized by your cells and is not ingested like functional proteins are.

An egg white is made of proteins When a raw egg is cracked, the white isn't white, it's opaque. When you cook the egg white, nothing happens until the temperature reaches the critical temperature. 

Denaturation is the physical changes in protein when it is exposed to abnormal conditions in the environment.
Mechanical agitation, heat, acid, high salt concentration and alcohol can cause proteins to denature.
(Denaturation can only occur in protein foods)
When proteins are denatured, what happens is that the protein bonds are broken down and the natural state of the protein structures is unraveled and becomes a single strand of amino acids. 
http://aifujita-moleculargastronomy.weebly.com/denaturation-and-coagulation.html

Egg white protein coagulates, this occurs after denaturing, between 144° F and 149° F (62.2° C and 65° C).  I couldn't find agreement among various websites for the temperature extremes that are functional limits for the COVID-19 virus.

Bottom Line

  • Avoiding or limiting time in areas where COVID-19 might be found and washing your hands are your best protective actions against this disease. 
  • Dawn is an excellent choice to combine with water because Dawn helps dissolve the outer layer of the virus making it less appealing to your cell membranes. 
  • In addition, it washes easily off your skin, taking whatever it traps with it. That's why they use it on oil-covered animals after oil spills.

Many illustrations in this post are from a PowerPoint Copyright 2008, Pearson Education, Inc., publishing as Pearson Benjamin Cummings. If you'd like to see the entire PPT or a version that goes into more depth, email me for either or both URLs.

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Wednesday, April 1, 2020

#Immunity Basic information on types and how to get them

Because of the pervasive reminder of the current threat from the COVID-19 virus, I'm posting two blogs on the BASIC biology of immunity and viruses. The focus of this blog is IMMUNITY.

You can download the original Powerpoint I used in my Biology classes for MANY years. It has sound effects and animation of text/diagrams entry and exit. :-)






The technology of vaccines has improved over time.
In the past, many vaccines used "attenuated" pathogens. These were heated or treated with chemicals and damage the pathogen to the point it
  • would not replicate or
  • its reproduction was slowed enough for human immune systems to defeat them.

Sometimes the pathogen won and people vaccinated got the disease the vaccine was supposed to protect them from. 
  • That is extremely rare these days.

Now pathogens involved (bacterium or virus) is neutralized before the vaccine is made. 

Another blog post today explains what viruses are and how they infect organisms.




If you have comments or questions, please leave them on Blogger. I reply to all the comments received.

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I invite you back to the blog on virus structure and function posted later on 4/1. 
No fooling!

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My Christian Context. Posts M/W of discussion questions. Thursdays - Timeless Truths. Fridays - Expressions of Faith. https://mychristiancontext.blogspot.com/  

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Monday, March 30, 2020

#amwriting Idea Farming—growing your plot #4—The Backyard Garden (Part II)



This is the fourth blog on story farming. In this one, the focus is—The Backyard Garden (novella-length pieces).

A good backyard garden might have different areas of plantings—like an anthology. But it might also have a focus that must be a single unit to be properly appreciated—like a fruit tree… or a novella.

The anthology approach to a back yard garden is like a buffet with stations. Each planted area makes a statement on its own. You might have roses, ground cover, annual color, and a perennial shrub border. Then again, you might have none of that—and still have a very nice backyard garden.

The novella approach to a back yard garden is like a meeting where lunch is catered and consists of ONLY one specific portion for each guest. No matter where you look, it’s evident that this backyard is a rose garden, a vegetable garden, or whatever the focus is.

ANTHOLOGIES used to be common forms of book publication. At one time, I had shelves of them in my collection.



But, the last post focused on short stories.

NOVELLA is defined by Merriam-Webster as: 

(1) a story with a compact and pointed plot; or 
(2) a work of fiction intermediate in length and complexity between a short story and a novel. 

Whether you choose the first or second definition, the process of growing a novella is similar. 

In definition (1), the plot itself is emphasized. In definition (2), the length is the focus. Some definitions of novella include the idea of “morality tale” in them. 

In general, novellas are more commonly associated with the novel than the short story. However, in some anthologies, novellas are included—generally in a segregated section of the book.

According to Writer’s Digest, “Novellas generally run 20,000-50,000 words.” 

Reverse Image, volume 3 in the Traveler’s HOT L series is almost 28,000 words. It is a novella in every respect as described in this blog.

If you have a point you are trying to make, I recommend the short story over the novella. Writing shorter forces you to FOCUS on where you’re going. If you ramble in a novella, it’s a lot like wandering through a back yard that’s just had plants stuck in where there is space. Over time, or pages in a novella, the garden gets so overgrown that finding any specific plant, or idea in a novella, is nearly impossible. When any plot becomes so convoluted or obscure that your reader can’t follow it, they will stop reading.

I close with the most important lessons in writing for the backyard garden. 

1.    Prune the plants. Edit judiciously. Remember the goal is completeness, not length.

2.   Keep it weed-free. Edit judiciously. Remember the focus of your story.

3.   Fertilize when needed. Edit judiciously. Remember to flesh out plot points as needed to move the story forward.

4.   Remove dead or dying plants. Edit judiciously. Remember that even the best plot point in the wrong story is an impediment.

Next blog: Idea Farming—growing your plot #5—The South Forty – The Novel

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Monday, March 23, 2020

#amwriting Idea Farming—growing your plot #3—The Backyard Garden - Anthologies



This is the third of six blogs on story farming. In this one, The Backyard Garden (anthologies and/or novella-length pieces) is the topic.

Herbaceous plants are most common as seasonal color and are heavily represented in color pots and hanging containers. They have a short life—usually one or two years. Their purpose is to project a specific feel in a very defined space. They never get very tall because their stems cannot add additional “wood” to their stems as they grow. Think petunias and green beans.

Woody stems are associated with perennial plants—those that live over two years. These plants do have wood-producing cells in their interiors and are capable, in some species, of growing to considerable height and circumference. Think rose bushes and oak trees.
Herbaceous plants are the short stories of the botanical world. Not from the life span, but because they are limited in size. As a writer of short stories, you learn to “stop when the story is done.” Overwriting in a short story causes the entire plant/story to suffer and ultimately collapse under its own weight.

Some plants present an illusion of herbaceousness. Bonsai specimens are woody plants that have been carefully and judiciously pruned over an extended time to present a miniature version of the plant. This type of short story is ripe for converting into a full-sized version of itself—expanding a short story into a longer piece.

Traveler’s HOT L – The Time Traveler’s Resort is filled with examples of short stories, all around or significantly less than 5000 words long, that were bonsai versions of longer stories. Combining the increased length with a common theme, in HOT L it's time travel, provides a perfect storm of stories in the anthology.

I invite you to investigate Sir Isaac's Car, another example of a themed anthology.


WARNING!
Not all short stories are bonsai. The vast majority of short stories are herbaceous plants. If you try to expand a short story that lacks the woody tissue needed to support the added verbiage, your story will never be what you want it to be, or even what it was before you bloated it.

When you finish writing a short story, put it aside. Ask two or three people to be beta readers of the story. Carefully consider the feedback from the beta readers. If there are any commonalities like “you jumped from A to B without explanation, or “where did character X come from,” or “what happened to character X,” suggests you might need to expand the length of the story. 

Try this.
Think of a story idea for a short story.
Write an outline or a plotline.
Write a short story no longer than 500 words
You'll find it's easier to write long than short!

 This post does not discuss novellas. More on that next week.

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Monday, March 16, 2020

#amwriting #authors Idea Farming—growing your plot #2—Container Gardening


In this post, the second blog on story farming, the focus is Container Gardening (short stories). To review, here's the complete list of story gardens.



  • Container (short stories)
  • Backyard (anthologies and/or novella-length pieces)
  • The South 40 (the novel)
  • Mega Farming (the book series).


  • Given a choice, I’d write almost exclusively short stories. Something is satisfying in planting and growing a tale in just a few hundred to a few thousand-word container, analogous to a pot or raised bed garden, as opposed to tens of thousands of words in gardens of larger size.

    Once you choose a seed, it’s imperative to prepare the soil. Even when writing a short story, having an end in mind when you begin a story is critical. Remember that the harvest from your container is a short story, complete with a planned ending.

    Start with a premiseIf you don’t know what your end product will be when you write, how will know when your finished?

    Consider your target length. Most short-story competitions have word count limits. Three thousand words is a common limit. Aiming for a specific numerical goal is good practice in the discipline of writing without the fluff.

    Minimally, the cultivation of container gardens involves 
    • a rough outline, 
    • character sketches, 
    • some plans for what your characters will discuss in dialog format. 


    Determine the pecking order among characters before you begin or you'll find yourself re-writing to correct contradictory actions and dialog.

    "Sir Isaac's Car" is a short story anthology of mine. It is a series of stories, all between 1500 and 5000 words in length. I recommend it as for examples of different ways to explore the same characters. The stories are written in the first-person perspective, something that sounds easy, but isn't. More on that in a later blog.

    Anthology publications:
    "What goes around" (9735 words) in 

    A World Unimagined: An Anthology of Science and Speculative Fiction exploding the boundaries of your imagination.


    "Drop by Drop" (4580 words) in
    If you have never written a short story, or only written a few, I encourage you to take the time to grow one soon. You’ll find out that writing shorter is more challenging in many regards than writing longer. 

    But, it’s excellent practice in honing your storytelling skill.

    Next week: Idea Farming—growing your plot #3—The Backyard Garden


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    Monday, March 9, 2020

    #amwriting #authors Idea Farming: Growing Your Plot #1


    This is the second blog on story farming. This one describes the required components for a healthy plot harvest. Future posts describe farming methods.
    • Container (short stories)
    • Backyard (anthologies and/or novella-length pieces)
    • The South 40 (the novel)
    • Mega Farming (the book series).

    The last blog is a pro/con commentary on each method with advice on when it’s appropriate to use ideas from each in a type of farming for effective cross-pollination. 
    Because you want a good crop/plot, we start with basic needs.

    Soil
    While it is possible to produce sizable crops with hydroponics, most plants are grown in soil. 
    • Dirt is not soil. 
    • Soil contains an abundance of organic and inorganic materials that help nourish the plant and keep the roots anchored.

    In your plot garden, the soil is your experience as a reader and writer. 
    In the same way that plants grow best in rich soil, without a good grasp of what it takes to make a good story, you’re pretty much doomed as a writer.
    Seed.
    A mature seed contains an embryo plant that’s waiting for the right conditions to grow into a plant.
    • Unless the mature idea for your story is present in your plot-seed when you start writing, you’ll find that growing a story is impossible. 

    At the minimum, have a basic outline in writing when you begin.
    “The Law." 
    All plants require Light, Air, and Water (LAW) to grow. 
    • Take away any of these three requirements, you break the law, and your plant dies.
    • Plots also die when requirements aren’t met. 

    You need 
    • believable characters, 
    • reasonable plot points, 
    • realistic dialog 

    to keep your plot-plant alive.
    Cultivation/weeding/pruning.
    Gardeners and farmers know that 
    • keeping the soil loose, 
    • removing weeds, and, if the plant requires it,
    •  judicious removal of shots/limbs that are dying, dead, or growing in the wrong direction

    are mandatory actions to an abundant harvest. 

    You must cultivate the plants in your plot gardens.
    • Keep your mind’s soil loose and open to new and alternate ideas. 
    You must week your plot garden. 
    • Be willing to admit that some of what you’ve written is more weed than crop and remove those post-haste. 

    Some of the verbiage you write is good, but not in the story you’re writing—that’s where pruning comes in. 
    Cutting good stuff to keep your plot growing (MOVING FORWARD) is essential.

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    Emailcrd.author@gmail.com

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