The Way We Die Now

The Way We Die NowThe Way We Die Now by Charles Willeford
My rating: 4 of 5 stars

Pulp Upward Mobility

Of the Hoke Moseley series, this is the most determinedly Pulp of them all and returns to the roots of the genre.

The sense of research, investigation, criminal pursuit have been sidelined to serve Hoke's fall from grace and his middle class redemption (which is the ultimate condemnation, a very personal and punishing hell within the gritty realm of Pulp).

An example of this arises out of his daughter's own emergence into bitter adulthood:
"Suddenly Aileen began to cry. Tears, unchecked, streamed down her cheeks.
"'What's the matter? Why are you crying?
"'Be-because," she said finally, still sobbing, 'because you can't!'"

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Sideswipe

Sideswipe: A Hoke Moseley NovelSideswipe: A Hoke Moseley Novel by Charles Willeford
My rating: 4 of 5 stars

Pulp Burn-out

Willeford has always written from many points of view, and this is a superb example where the separate story lines entwine and intersect naturally. The plot is complex when viewed from a distance, but quite simple when seen from within the eyes of each character.

Willeford also reprises past motifs. One such example is with art. Willeford studied art in France and in Peru. This interests inhabits much of his early writing through his protagonist's own expressed interest in art (often idiosyncratic). This artistic pursuit is fully engaged in "Pick-up," brought to center stage in "The Burnt Orange Heresy," and then here in a surprising and satisfying lesson given by an automobile painter.

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New Hope For The Dead

New Hope for the DeadNew Hope for the Dead by Charles Willeford
My rating: 4 of 5 stars

Pulp Affirmative Action

"Sanchez picked up one of the long-legged dolls. Hoke sniffed the anima of the owner---Patou's Joy, perspiration, cold cream, bath powder, soap, and stale cigarette smoke.
"'You ever notice,' he said, 'how a woman's room always smells like the inside of her purse?'
"'Nope.' Sanchez dropped the doll on the bed. 'But I've noticed that a man's bedroom smells like a YMCA locker room.'"

Later, Hoke trying to make conversation with Ellita Sanchez during the investigation:

"'You Latin girls lead a sheltered life. But the point I'm trying to make is, these marks look like hickeys to me.'
"'Maybe so. From the smile on his face, he died happy.'
"'That's not a smile, that's rictus. A lot of people who aren't happy to die grin like that.'"

Willeford, a retired Army sergeant who began writing Pulp in the service in the early 50's often brings a knowing sensibility of the professional soldier (albeit the civilian version as a police officer). In this regard, Willeford's protagonists (and especially Sgt. Hoke Moseley) have a military background, or have subordinates who are retired sergeants. And with those attributes of a military life of service comes the mix of accommodation and survival skills. This entry in the series is especially illustrative of this with Hoke's solution to his needs balanced with the solution of a crime. I won't say more given it may reveal too much to those who have not read this book.

Willeford also introduces a new (for the time, but fairly common currently) mode to the police procedural, and that is more tightly integrated story line that draws in family. Some may object this has infrequently been a side-show to the genre (the police procedural), and, as such, nothing remarkable. I would argue that Willeford brings in genuine content consistent with the character of Hoke that adds to the continuity of his earliest work; and it meshes as smoothly as Michael Connelly’s Bosch.


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Miami Blues

Miami BluesMiami Blues by Charles Willeford
My rating: 4 of 5 stars

Pulp Haiku

Well, let's just jump into some dialog with Hoke Moseley talking about his dentures:
"'Bout a year ago, I had some abscessed teeth, and the only way I could chew was to hold my head over to one side and chew like a dog on the side that didn't hurt. I was having lunch with Dr. Evans, and after lunch, he took me back to the morgue, shot me up with Novocaine, and pulled all my teeth. Every one of them. Then he made an impression and had these teeth made for me by the same technician who makes all of the Miami Dolphins' false teeth."

A good reason to call this Miami blues.

Then we have an example of character categorization concerning relationships:
"That's some family, isn't it? Incest, prostitution, fanaticism, software ... "

I especially like the software (there is a legitimate tie-in) being chained into this list of perversions.

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Pick-Up

Pick-UpPick-Up by Charles Willeford
My rating: 4 of 5 stars

Continuing my conceit of qualifying terms for this genre, I offer:

Pulp Artist

I am always surprised at the humanity that surfaces with Willeford's handling of this cheap and dirty line of reading. He doesn't squirm or coyly turn his face from the squalid overtures offered by the characteristic covers (which I so love---they pack so much promise in an image).

Without beating around the bush, we have a story of two alcoholics, and their descent into the abyss of hopelessness that leads them to suicide. As much as that says, it doesn't reveal what I discovered about how much un-sentimental sympathy Willeford has for them with the existential twist at the end.

The story is simple, but Willeford's technique is solid enough to build nuance into each character's being. There is sex, beatings, murder, the cosmic joke of unasked-for redemption...and a lot of smoking and drinking.

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The Machine In Ward Eleven

The Machine in Ward ElevenThe Machine in Ward Eleven by Charles Willeford
My rating: 4 of 5 stars

Pulp madness

I hesitate to call this a "redux" of another Pulp category, but it does continue Willeford's excellent work in "Pick Up."

I say this in the sense that in that earlier novel, the hero is also (self)committed to a (nearly)psycho ward. The difference here is a stylistic (and internal logical) consistency where the patient isn't entirely aware of all the details. He says as much, and yet as the teller of the tale, where does that put us to judge the facts on the face of the telling?

Droll.

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The Burnt Orange Heresy

The Burnt Orange HeresyThe Burnt Orange Heresy by Charles Willeford
My rating: 3 of 5 stars

Pulp Art redux

As in again?

Yes, this picks up on a theme developed by Willeford in "Pick Up." This isn't accidental because it is underlined (maybe highlighted would be preferable) by both artists' choice of...wait for it...Orange. Especially dark orange.

"Pick Up" is the better novel. This one moves us across the country from Frisco to Florida with the migration of the author. This one moves upscale, but doesn't make the fall anymore deeper (and possibly shallower) than that in "Pick Up."

In a nutshell: derivative.

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Our Lady of Darkness

Our Lady of DarknessOur Lady of Darkness by Fritz Leiber
My rating: 4 of 5 stars

Pulp Fantasy
(only because calling it Horror in place of Fantasy would be a doubling of Pulp which is its own interpretation of middle-class Horror)

I chose to read this out of my stream of Charles Willeford (actually, I was reading "Pick-Up" at the same time) because of another book (how could it be otherwise?) by Don Herron, "The Dashiell Hammett Tour." Within those pages Don Herron offered a writer he and his group ran into on the streets of The City, Charles Willeford. The purchase of Don's book has lead me to wonders of writers who inhabited San Francisco. Don also introduced me to Fritz Leiber, who added many references of Hammett to his novel, "Our Lady...."

Already knowing how Leiber lived in a rent controlled ("Rhodes" historically Rhodema now Union) hotel in the Tenderloin (and which was merely several blocks from my girlfriend's apartment up Nob Hill), it gave me immediate identification.

However, to return to "Our Lady...."

This story is atmospheric and full of the lore of Megapolisomancy. The hero owns an original journal of a man who studied paramental life-forces that defied time and space; and destructive-forces of the city's megalithic monuments. This book, familiar to an expert who wouldn't touch it for his life, contains both the question and the answer to the journal writer's death.

"Our Lady" is invested with the (author's autobiographical) hero's mood of recovering from the alcoholism following the death of his wife years before. Even then, it is neither morose, nor depressive. Instead, the hero is surrounded with comforting and supportive friends who rescue him from the paramental's highly disturbing embrace.

Of interest, and possibly fascination, is the hero's rumination on the many authors and their titles in the field of fantasy and horror genres that were current in the early 1970s.:
Nostig’s "The Subliminal Occult,"
“The Haunter of the Dark,”
"The Outsider,"
Collected Ghost Stories of Montague Rhodes,
“The City of the Singing Flame,”
"Ames et Fantômes de Douleur,"
"Knochenmädchen in Pelze (mit Peitsche),"
"Suspiria de Profundis,"
"The Spider Glyph in Time,"
"Sex, Death and Supernatural Dread,"
“The Thing on the Doorstep,"
“The Disinterment of Venus,”
...and many others.

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Whip Hand

Whip HandWhip Hand by Charles Willeford
My rating: 4 of 5 stars

This is pulp, it reads like pulp, the story is pulp, and the considerably difference here is that the characters are dirt-farm poor pulp.

Distinctions abound as each of these characters has their own point-of-view chapter (or several). Further, their dialect is utterly dirt farmer.

What makes pulp? The scope of their aspirations. Scope is not the same as scale. In terms of scale, pulp characters are going to go for the whole enchilada. Scope reveals that the enchilada is all they plan for. If they are looking for a $1000 bank-roll, in very little time it lands in their lap.

Then what? Scale of aspiration is met, and a world of hurt follows because there isn't enough zeros in $1000 to pay for the mistakes they made getting it.

"Whip Hand" accomplishes the display of this tragic fault across every character.

Charles Willeford has written an existential pulp comedy.

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Matt Helm – Death of a Citizen by Donald Hamilton

Matt Helm - Death of a CitizenMatt Helm - Death of a Citizen by Donald Hamilton
My rating: 4 of 5 stars

In a class of fiction that barely rises above comic strip in character development, Death of a Citizen manages to stay the course, but does it well. Despite the glowing accolades from Tom Clancy on the (re-issue) cover as being real, it is not. It is not literature (the English combine this genre with literature better), but it is good pulp.

Comparisons to Hammett or Chandler are lazy claims. Matt Helm is what could be called a dry drunk, addicted to violence without any redemption (killing Commies won't get you past Saint Peter in this day and age), but he is a good pulp hero.

At the end of the day, Donald Hamilton is a good pulp writer.


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Mystery At Thunderbolt House

Mystery at Thunderbolt HouseMystery at Thunderbolt House by Howard Pease
My rating: 5 of 5 stars

This historical story, set in San Francisco the year going up to the great earthquake, is a broadly disguised fantasy of Pease's own experience of the shake.

Some elements are based upon his recollection of his aunt, who he recalls being pictured high atop a loaded waggon that is transporting her household items away from the destruction.

The story of rags-to-riches, a common Horatio Alger era theme, also mirror's Pease's family suddenly acquiring a windfall inheritance. However, his own family experience is considerably more subdued to the immense wealth his protagonist finds.

Pease said this book was his personal favorite.

Pease's full stories were printed in American Boy Magazine and illustrated by the renowned artist Anton Otto Fischer whose graphic work was found on many covers such as The Saturday Evening Post.

The Black Tanker

If you are interested in the artwork that illustrated Pease's stories, go to:
Pease Images

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Revenge Of The Kremlin

Revenge of the KremlinRevenge of the Kremlin by Gérard de Villiers
My rating: 2 of 5 stars

What a dog.

“Hello, Malko!” he said. “We met briefly about two years ago. I’ll be here for another year before I head back to Langley."

“I won’t forget this, Sir George. Do I have your permission to inform Malko himself?”

"What the hell are you going to do in Moscow, anyway?”
“Pull the lion’s tail,” said Malko

"You realize you’re walking into the lion’s den, don’t you?”

She respected him, and he was secretly in love with her.

He hadn’t realized that Irina Lopukin had friends in such high places. I hope she hasn’t gone to complain about me, he thought.

“They took their revenge on her,” said Malko, feeling troubled. He had caused her death, he knew. “I’ll have flowers put on her grave. She was very helpful.”

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The Woman Chaser

The Woman ChaserThe Woman Chaser by Charles Willeford
My rating: 4 of 5 stars

Pulp cinema?

The modern audience may think Tarantino got there first (at least on film, 1994), but Willeford bookended "Pulp Fiction" with his script, 1960, that made it to the silver screen, 1999, with few, if any, changes.

Pulp cinematic hero? Consider this description:

"Two hundred pounds, the beginnings of a paunch, big size-eleven feet, more enormous yet in red-yellow-and-blue cashmere argyles, thick, hairy arms and basket-ball-player hands, a mat of blue-black chest hair; a sunburned grinning face, and a headful of dark unruly hair, badly in need of cutting. Some dancer! I laughed wildly. In the face of all maternal arguments I had quit taking ballet lessons when I turned fourteen and fell in love with baseball. The hell with it! I assumed an attitude and met Mother’s charming pas de Bourree with outstretched arms and fingers."

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The Black Mass Of Brother Springer

The Black Mass of Brother SpringerThe Black Mass of Brother Springer by Charles Willeford
My rating: 4 of 5 stars

Who would believe Pulp Religion?

Sam Springer has been ordained and called to a small church in the Negro (late 50s) part of Jax Florida. The Right Reverend "Deuteronomy" Springer was an ex-accountant and ex-novelist who had writer's block when he became a civil-rights leader in a bus boycott. Too soon, he becomes the focus of Klan activity, a lot of donation money, and a parishioner's wife. He arrived at this impasse of identity because in his respectable life he faced:

"My monthly payment of $78.60 on my house was five days overdue. My car payment on my three-year-old Pontiac was one month overdue. A small payment, only $42.50 per month, to be sure.... I owed the milkman $5.40 for the current month, the grocer for groceries delivered during the month, the telephone bill, the television repair bill for a new booster for the picture tube, and several other sundry bills, including an unfulfilled pledge at the Unitarian Fellowship Society."

Brother Springer quickly admits (to himself) that he has no "faith," but his sermons do inspire the faithful and fuels social protest. And, yet, true to Pulp formula, life is about booze, cigarettes, money, and sex.

Pulp Canterbury Tales

Pulp Decameron.

Pulp Fabliaux.

Willeford's writing contains all the classic elements of the older genres I allude to above. A theme I see emerging in his early works is the anti-hero embodying the archetype of the Destroyer who brings positive change.

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Windows 10 Update Failure and its Recovery

You have arrived at this post because you searched for one of the following problems:

 Microsoft.Windows.ShellExperienceHost … needs to be installed correctly

or

Error Code 0xC1900200 – 0x20008 (Code 0xC1900202 – 0x20008)

or

Windows 10 upgrade couldn’t update the system reserved partition

or

Your computer is not compatible with Windows10 (the supremely bitter irony when you are updating it)

or ….

If you share the same problem I struggled with for a week, then the resolution could be quite simple.  It requires a tool downloaded from the net, some adjustments of your disk’s partition table, and (yet one more attempt to) update/upgrade.

What follows is not for the faint of heart, but it is within the skill set of any tinkerer.  By that, I mean you know the risks; but if you don’t perform backups of your data–you don’t qualify, and I suggest you back away from this page right now.

Through considerable Googling of the terms above, I found a tool called MiniTool Partition Wizard Free reviewed on PCMag.  There’s your resource for fixing (knock wood) the problem that brought you here.

The necessary operation is to take the OS partition (typically called C:) resize it a bit smaller (be generous, reduce it by at least double the size of the current system reserve partition) and then extend the system reserved partition to make it bigger.  The MiniTool (free version) will let you change the edges of a partition.  Do this at the point where they both neighbor each other.  My situation had the system reserve lined up ahead of C: in the partition table.  If your situation varies from my description, re-read everything for my intention.

FIRST: take memory off from the beginning of C: (this is what I did), and

SECOND: add the same amount of memory to the system reserve’s end.

THIRD: press the button on MiniTool to commit the change.

This rescued me from the useless, repetitive, unproductive efforts of Windows to self diagnose (it never had a clue), and correct the problem (that never was going to happen, this had been going on for every update for a year).

Novel Preview In Kindle Reader Technical Requirements

If you wish to be a reviewer of an unpublished novel of mine, there are several technical requirements you must meet to view my novel in a Kindle reader.  For correspondence, use publisher at this domain.

  1. You must send me your Kindle email address:
    To find your Send-to-Kindle e-mail address, visit the Manage your Devices page at Manage Your Kindle.
  2. You must put my email address in your Kindle account white-list:
    I can only send to your Kindle devices or apps from e-mail accounts that you added to your Approved Personal Document E-mail List. To add my e-mail account, visit the Personal Document Settings page at Manage Your Kindle.

 

Quantum Dot Self Assembly

From A Reactive Peptidic Linker for Self-Assembling Hybrid Quantum Dot–DNA Bioconjugates:

Quantum Dot Bioconjugate Self Assembly

Our goal was to develop a bifunctional peptide linker that could allow easy attachment of DNA oligonucleotides at one end while the other is modified with a polyhistidine tag to facilitate self-assembly of the full peptide-DNA complex onto QDs via metal-histidine interactions.

QDtaglinkerDNA

We have developed a conjugation strategy based on metal-affinity-driven
interactions between CdSe-ZnS core-shell QDs and proteins or peptides appended with polyhistidine (Hisn) tags. … The His tag drives self assembly by interacting directly with the metallic surface …


  1.  (DNA) DNA conjugates of target DNA are thiolated (sulf-hydride group attached):
  2. (linker)  The synthesis of the peptide module was performed by standard solid-phase peptide synthesis (SPPS) on Rink amide resin to create the desired His6-Cys sequence.
    The crude peptide was precipitated, and the final bifunctional reactive linker His6-Cys(Ac)-S-S-Py was obtained through a direct disulfide exchange reaction.
    (the initial reactive chemistry for His6 attachment to thiolated-DNA is one of the fastest and most common linkage chemistries used in bioconjugation)
  3. (tag)  Functionalization of free 5‘-thiol DNA with the peptide linker (4) to yield the His6-tailed oligo (5) was rapid and straightforward …
    and the mixture was allowed to react anywhere from 1 h to overnight
  4. (Quantum Dot)  The His tag drives self assembly by interacting directly with the metallic surface [of the Quantum Dot]

The QD-peptide-DNA conjugates were further characterized by atomic force microscopy (AFM) imaging, where association of oligos with a central QD was observed only for samples made of QDs mixed with His6-peptide-DNA …


We also demonstrate the potential utility of this His-reactive-peptide modification of DNA by assembling and testing a QD-DNA molecular beacon that specifically detected the presence of its complementary sequence.

The potential of this reactive linker was demonstrated by self-assembling several QD-DNA conjugates as well as a QD-MB construct able to discriminate between different sequences of DNA. A variety of other applications, such as highly luminescent multilabeled hybridization probes, are possible using this construct. Preforming MB sensors with different color QDs and then mixing them may allow “multiplexing”.  Beyond nanoparticle-MBs, this selfassembly technique may be applicable to attaching biomolecules to a variety of other similarly prepared surfaces.


Quantum Dot Bioconjugate Self Assembly

And now for the shortened version.  Above, you will see a very stylized expression of the process of self-assembly.  Again, we will do this by steps:

  1. Obtain the His6 tags (Polyhistidine-tag)
  2. Obtain Cy5 dye (a fluorescent/fluorophore nano particle)
  3. Obtain the Thiolated DNA
    1. Label the Thiolated DNA with Cy5 dye, the dye becoming a quenched fluorophore;
  4. Obtain the Quantum Dots
  5. Combine where:
    1. The Thiolated DNA, which has an affinity for the one end of the His6 tag, becomes attached;
    2. The His6 tag, which has an affinity for the DHLA covering of the Quantum Dot, becomes attached;
    3. (not a production step, but found in the illustration prior to the addition of the complementary DNA) Excite the batch with high energy light as seen in the center of the graphic where:
      1. the proximity of the Cy5 particle in the His6–Thiolated DNA and the Quantum Dot allows the molecular beacon to absorb energy through FRET (Förster resonance energy transfer) and emit a color shifted light in fluorescence;
  6. (not a production step, but, rather, the set-up for a test of the marker beacon) Obtain and add Complementary DNA to the process
    1. the molecular beacon (the His6–Thiolated DNA–Cy5) unzips, and takes on the Complementary DNA;
  7. (not a production step, but, rather, a test of the marker beacon) The right side of the graphic shows the action the new bioconjugated Quantum Dot undergoes to stimulation by (a now second) high energy light to emit a color shifted light in fluorescence.

Rogue NanoVirus Design Elements And Products

Designing a NanoVirus has been a work in progress, and if I dare say so (noting a certain irony), an evolution.  First, the components:

Quantum Dots

A quantum dot is a one dimensional construction.  It is usually less than 10nm wide (yes, that contradicts the notion of one dimension when it has height, width, and length, but at the quantum scale it is suitable).  By selection of material, shape, and size, various optical properties can be set.

Size (nm) Emission Peak (nm) Color
2.2 [10] 495 blue
2.9 [10] 550 green
3.1 [11] 576 yellow
4.1 [10] 595 orange
4.4 [12] 611 orange
4.8[11] 644 red
7.3 [10] 655 dark red

A QDot is often made of toxic elements such as CdSe (Cadmium Selenium).  For biomedical applications this needs to be covered without disturbing the optical qualities of the QDot.

To be useful, the quantum dot needs to be functionalized.  This means the QDot is attached with strands or layers that can, in turn, selectively bind to larger structures.  Another means of attachment is through bio-conjugation which allows for protecting the QDot in a wide variety of harsh media.  This leads to the application of DNA or nucleotides.

QDot Coatings for Tagging

The metals used to construct quantum dots are toxic.  For biological applications, it is necessary to cover them while still retaining the optical qualities and the possibility of making attachments.

One such coating is Dihydrolipoic acid.

QDot Tags for Functionalization

For a quantum dot to be useful beyond responding to ultraviolet light with fluorescence, a tag is added that allows for attachments.  These attachments are simple handles that will attach, in turn, to complex oligonucleotides to become functionalized.  These oligonucleotides are chosen to attach, once again, to target RNA/DNA strands.  This target will then have a marker beacon to aid viewing the site at which the target resides.

Cy5 fluorophore

Probe Ex (nm) Em (nm) MW Quantum yield
Cy2 489 506 714 QY 0.12
Cy3 (512);550 570;(615) 767 QY 0.15 [5]
Cy3B 558 572;(620) 658 QY 0.67
Cy3.5 581 594;(640) 1102 QY 0.15
Cy5 (625);650 670 792 QY 0.27[5]
Cy5.5 675 694 1128 QY 0.28[6]
Cy7 743 767 818 QY 0.28

Cyanine variants exhibit various optical properties.  Within this post, it is limited to being used as a quenched fluorophore that engages through FRET with the quantum dot.

Molecular Beacon

Molecular beacons are hairpin shaped RNA/DNA fragment molecules with an internally quenched fluorophore, the Cy5 above, whose fluorescence is restored when they bind to a target nucleic acid sequence. This is a novel non-radioactive method for detecting specific sequences of nucleic acids. They are useful in situations where it is either not possible or desirable to isolate the probe-target hybrids from an excess of the hybridization probes.

Oligonucleotide (DNA)

From Wikipedia:

Short DNA or RNA molecules made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, library construction and as molecular probes.

DNA Origami

From the work of Paul Rothemund:

DNA Origami is the manipulation of single strands of M13mp18, a folding of a long single strand of this viral DNA aided by multiple smaller “staple” strands.

The simpler description is that DNA can be sliced and diced into short strands that are stiff, and then those strands can be connected/configured into triangles, squares, pentagrams, hexagons….  These planar elements can then be assembled into three dimensional pyramids, cubes, tubes, buckyballs….

DNA Tiles

From the work of Erik Winfree:

The creation of two-dimensional lattices of DNA tiles using the “double crossover” motif. These tile-based structures provided the capability to implement DNA computing.

DNA computing performs the standard operations of comparing, sorting, counting, and such, but are not intended to replace a word-processor or spreadsheet program.

sgRNA

single guide RNA contains bases in both repeat and spacer regions of a single RNA strand.  In a CRISPR application (see below), repeater and spacer has the following meanings:

Repeat–a pattern of bases that are recognized by dCas9 by their being palindromes (the sequence of bases are lined up to read the same both ways).  Repeats signal that the pattern of bases that follows the repeat is a spacer.

Spacer–a short pattern of bases that have been stripped out of a virus’ DNA.  The length is sufficient to uniquely identify the virus’ past visit, and to engage Cas9 (dCas9 if the spacer is engineered) to act upon the agent that introduced the DNA recently (for a bacteria, it would sense the invasion of a virus based on a past infection).

Cas9

CRISPR associated protein 9.  This protein 9 is specifically associated with the host bacteria Streptococcus pyogenes it inhabits.  Protein 9 is a DNA library of virus DNA samples from the bacteria’s past experience of being attacked by viruses.  Protein 9 is called a single guide RNA (see above).

Cas9 performs an interrogation on an intruding virus by unwinding that virus’ DNA and checking if it is complementary (matches) to any 20 basepair spacer region of the guide RNA. If the DNA substrate is complementary (matched) to the guide RNA, Cas9 cleaves the invading DNA.  This recognition method effectively eliminates the virus.

However, for applications beyond this specific protein 9 and this specific bacteria, Cas9 has the unique ability to bind to essentially any complement (matching) sequence in any genome when provided with a tailored guide RNA.

When Cas9 is used informally as a research or engineered process outside of the specific bacteria, Streptococcus pyogene, it is frequently described as a mutant/mutation of Cas9, or as dCas9 (see following).

dCas9

dead CRISPR associated protein 9.  A Cas9 variant used for both mechanistic studies into Cas9 DNA interrogative binding and as a general programmable DNA binding RNA-Protein complex.  Some might prefer to associate the d in dCas9 to the d in endonuclease-deficient.

dCas9 and its guide RNA can be used to interrogate DNA to then

  • restore that DNA and release it; or
  • remove the matching sequence from that DNA and release it shortened; or
  • clip that DNA and disrupt it; or
  • remove the matching sequence and insert a new sequence into the DNA and release it; or
  • block assembly of transcription factors leading to silencing of specific gene expression; or
  • activate genes when fused to transcription activating factors.

dCas9-Fusion

A “split-fusion” approach is where the sgRNA (see above) is split into two inactive halves that only regain functionality when the two halves are co-joined at a particular site.

CRISPR

CRISPRs are part of a bacteria’s DNA recognition and adaptive immunity system.  This acronym merely names the organization of elements that enable this system, and is not in itself any separable component.

CRISPRs (clustered regularly interspaced short palindromic repeats) are segments of DNA containing short repetitions of base sequences. Each repetition is followed by short segments of “spacer DNA” from previous exposures to a bacterial virus or plasmid. It is pronounced “crisper.

By delivering the Cas9 protein and appropriate guide RNAs into a cell, the organism’s genome can be cut at any desired location.

The CRISPR/Cas9 system is an immune system that confers resistance to bacterial DNA and viruses and provides a form of acquired immunity.

CRISPRa

CRISPR activator library for transcriptional activation

CRISPRi

CRISPR interfering library for transcriptional repression

Enteric Nervous System

The enteric nervous system (ENS) or intrinsic nervous system is one of the main divisions of the nervous system and consists of a mesh-like system of neurons that governs the function of the gastrointestinal system. It is now usually referred to as separate from the autonomic nervous system since it has its own independent reflex activity.

Microbiome

Some of the microbes in the human body can modify the production of neurotransmitters known to occur in the brain.

Bacteroides fragilis

From: Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders, Elaine Y. Hsiao, et al.

Bacteroides fragilis corrects gut permeability, alters microbial composition, and ameliorates defects in communicative, stereotypic, anxiety-like and sensorimotor behaviors.

NanoVirus Product

At the structural level, the virus is composed of DNA origami, folded into a shape suited as a delivery mechanism much like the capsid of a virus.  QDots functionalized with DNA serve as the vertices and edges of the construction.  The QDot heads one or more long tails of DNA.

Within this capsid structure is an DNA tile program, and an sgRNA in a dCas9 (see both above).

Howard Pease Offers Post San Francisco Earthquake Credits

Here are Howard’s comments on his personal success of melding his own life experience into his novel The Mystery of Thunderbolt Mansion:

I could even see the end of my book, the five of us trudging uphill with thousands of other refugees, with all we owned on our backs or in our arms, heading for open country to sleep by night under falling ashes and to watch by day a sun swinging across the sky like a blood-red moon through the smoke. I even had my theme to lie hidden behind the story’s action: “Wealth does not always bring happiness.”

My story would be an attempt to dramatize a struggle with human values, material vs. spiritual. My family would learn the difference between false values, fleeting values and basic values. At the end we would hold fast to the old enduring values, with my family once more closely knit.

While the Baxters learned to come down to earth before catastrophe struck them, my own family as usual would have to learn the hard way. Later, to my surprise, I realized that my father’s aunt Mary had left me a delightful inheritance, my own favorite of my twenty-two books of fiction.

Howard Pease’s Family Experience of the San Francisco Earthquake

If you have read Howard Pease’s The Mystery of Thunderbolt Mansion, then you can see the authenticity of his story in this reminiscence:

I could remember only confused bits of the day following that ominous dawn, with newsboys crying “Extry—extry!” with word pictures of San Francisco shaken into rubble, and the spreading fires and no water to fight with because of the broken water mains, and Mama going about her housework with a strained expression because her younger sister, my aunt Libby, worked and lived in the City right in the path of the flames; then the second day with worse news of the fires spreading and joining in one immense holocaust and the militia ordering thousands of refugees to walk back toward the hills; and then the third day with the army dynamiting all the buildings and houses along Van Ness Avenue in hope of halting the flames. No one but rescue crews could enter the City except doctors and nurses and wagons bringing medicines and water, and all these disappeared into the darkness of smoke. And where was Aunt Libby? After ten days we learned that she had been seen with several people from her boarding house seated high on bedding in a beer truck driven by a friend of hers, heading for the slopes of Twin Peaks. This sounded like my aunt Libby, all right. She always came out on top.

First Experiences of the San Francisco Earthquake

The following material is taken from Howard Pease’s Writing In Depth.  It contains biographical material obtained nowhere else.  In this section, Howard recalls his childhood experience of the San Francisco Earthquake of 1906.  The unique characteristic of this excerpt is that Howard is describing how he crafted this event into his book Mystery At Thunderbolt House.

Flash! On the instant I had a complete book laid out before me like an architect’s design. Our inheritance in Chapter One. My own family as a boy moving to San Francisco with a new way of life leading to bickering, arguments, mishaps, frustration, clashes, all ending the good family life we had once known and only now appreciated. Then the final section with the earthquake at 5:13 on the morning of April 18th, as I remembered it, wakening in Stockton, eighty miles from the center of the quake, with my room trembling all round me. And I could see myself jumping out of bed in my long cotton-flannel nightgown and rushing into the hall and seeing my parents in the same kind of nightgowns standing at the open front door. And while the terrifying tremor went on I could see past them to the two big elms at our curb swaying and shivering as in a wind. And I could still hear my mother’s firm voice repeating the ninety-first psalm: Thou shalt not be afraid of the terror by night, nor of the arrow that flieth by day.

I will continue this selection in another posting to bring in the stories of his family members in San Francisco in these fateful days.

Progression of The Reveal

Part 12, appearing by page 70-something, seems to be the place to do the reveal.  This is a dialogue between Carson and Sean about what Carson hopes to achieve through self-experimentation with a virus that reprograms his nervous system.

I label this post as the progression because I’ve been working and re-working the first 100 pages for several months.  To put that into context, the novel has been roughly 320 pages long when the first draft was finished a year ago.  Originally, the reveal bubbled to the surface of the story at least 100 pages later.  This was not satisfying.

Over the course of those months, the reveal has been moving backwards toward the opening pages making it a better story.

At some point, I will have to pickup at page 120-something and move forward into a new narrative arc.  It could easily wipe out half of the original.  Future posts will offer their own reveal on that possibility.

Wade's Manifesto

I believe in the importance and goodness of Wade’s people.

This band of young men and women take on challenges that hint at success, promise failure, but always reward with rich experience.

Wade’s people are passionate about their work and tightly bonded with their team.

The challenges they choose and the risks that come with them are the essence of today’s start-up culture.  Wade’s people bring their edge of creativity to the fringes of town that are more bohemian than corporate campus.

Their challenges occupy a shifting moral landscape that bring them into disturbing contact with complex issues.  I believe in how Wade’s people define themselves through their healing recovery from failure.

747 Data

The following graphic reveals how much data is available to computers on a commercial 747.

A display of all recorded flight senors on this 747.

A display of all recorded flight senors on this 747.

This chart reveals nearly two minutes of flight data.  It begins at the left, at 20:18:40 (40 seconds after 8:18PM).  It continues on to the right, at 20:20:20 (20 seconds past 8:20PM).

As a narrative in the experience of a passenger:

  • the 747 is sitting at the end of the runway for the first 10 seconds.
  • the 747 has all four throttles full on at 10 seconds in.  Maximum thrust is achieved at 10 to 15 seconds later where all four engine lines level off (lines marked EPR for Engine Pressure Ratio).
  • Longitudinal Acceleration (the pressure you feel pushing you into the seat back at take-off) also tracks up through this same 10 to 15 seconds.
    For the nearly two minutes, it varies between 0.20 and 0.25 G.  A 150 pound individual would feel at least 30 pounds of pressure pushing them into the seat back.
  • Vertical Acceleration (the pressure you feel pushing you into the seat pan).  There is none until lift-off which occurs at 20:19:40.  At that time, you feel 0.15 G of force pushing you into your seat with 16 or more pounds of pressure.  There is also a corresponding increase of pressure against the seat back.

These are all familiar to the traveler.  Other data may be compared to discover all other activities going on during flight, like the pilot pressing the microphone transmit key at the top of the graphic.

One major point of interest.  There is a lot of noise in some of the data.  Some of it is genuine representations of what is going on.  Other data is corrupted.