Friday, November 20, 2020

On The Origin Of The Home Of COVID-19 - 19

I.

This series includes, among other things, the argument that the "farming and mass slaughtering of cows, pigs, and chickens industry" markets and exports meat products that contain corona viruses (On The Origin Of The Home Of COVID-19, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18).

One of the hypotheses set forth in this series is that SARS-CoV-2 is a descendant of corona viruses that have been found in sewage for many years:

"These findings provide strong evidence that SARS-CoV can be excreted through the stool/urine of patients into sewage system, thus making the sewage system a possible route of transmission."

(Concentration and detection of SARS coronavirus in sewage, Wang 2005, Journal of Virological Methods). Wang's decade and a half old research and perceptions have proven accurate some 15 years later as the descendant virus SARS-CoV-2 (causes COVID-19) has been found in sewage systems all over the place.

In fact, in the USA it is a preferred method of SARS-COV-2 detection now:

"Sampling wastewater is therefore sampling a mix of the total population in the sewershed, and encompasses the large proportion of infected individuals that do not get tested, because they are not or only mildly symptomatic, are reluctant to get tested, are not included in the testing policy or have less access to testing. As a consequence, sewage surveillance better represents the true SARS-CoV-2 circulation in the population. Sewage surveillance is the systematic collection, analysis and interpretation of data on SARS-CoV-2 RNA in wastewater to observe (and provide an early warning of) trends in COVID-19 in the communities. Sewage surveillance has been shown to be sensitive and fast enough to provide an early warning of increasing SARS-CoV-2 in cities. This is important information to support stratified lockdown decisions. Sewage surveillance is aimed to monitor the circulation of SARS-CoV-2 communities; large communities such as inhabitants of a large city, or smaller communities, such as nursing homes, university or office campuses, prisons, and so on. It is a very cost-efficient tool for population surveillance, and also a noninvasive tool, which does not require repeated sampling of individuals (such as nursing home inhabitants) to survey for (absence of) SARS-CoV-2 circulation in that community."  

(Implementation of environmental surveillance for SARS-CoV-2 virus to support public health decisions: Opportunities and challenges, emphasis added). The CDC has guidelines for such surveillance (CDC Wastewater Surveillance Data Reporting & Analytics).

What goes into our mouths is food that comes to us from the "farming and mass slaughtering of cows, pigs, and chickens industry", and what goes out into the sewer systems indicates what came in.

II.

What comes out of us is feces and urine with viral residue of the enteric viruses, and that excrement is combined to form sewage systems.

Exactly as Dredd Blog has hypothesized ("garbage in ... garbage out").

III.

The remaining work for scientists is to isolate the microbe or microbes that are being massacred by toxic chemicals / antibiotics used by the "farming and mass slaughtering of cows, pigs, and chickens industry" so that they are not destroyed along with pathogens.

Avoiding "firing a shotgun into a crowd with one crook in it" is a worthy endeavor.

Update

"Early phylogenetic analyses suggest that SARS-CoV-2 may have evolved between October–December 2019 [9-11].
...
9) Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med 2020; 26(4): 450-2.

10) van Dorp L, Acman M, Richard D, et al. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infect Genet Evol 2020; 83: 104351.

11) Li X, Zai J, Zhao Q, et al. Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2. J Med Virol 2020; 27(10): 25731.
"

(Oxford Academic, emphasis added). BTW, in this series an even earlier date has suggested.

The the next post in this series is here, the previous post in this series is here.


Dr. Bonnie L. Bassler, Princeton University:



Thursday, November 19, 2020

Awe Topsy - 5

What mass grave?
This is the toughest election autopsy in this series (Awe Topsy, 2, 3, 4).

For one thing, the composition of the Senate isn't over until the two Georgia senate runoffs are finalized.

Democrats need both to have effective control of the US Senate (VP Kamala Harris can cast the deciding vote in case of a tie). 

For another thing which is a repeat performance, the polls were once again ghastly.

But the most important thing is that despotism has metastasized in the sense that the despotic minority is now at an existential threat of about 70,000,000 voters.

What that word means supports this election autopsy:

"despotic

A ruler who governs with an iron fist, caring little for the welfare of the people, can be called despotic. Dictators and tyrants are often described as despotic.

Despotic is the adjective form of the noun despot, which means "tyrannical ruler." If you live under despotic rule, you probably have few rights and may fear your government. Use despotic to describe rulers that rely on brute force (or the threat of it) rather than the rule of law to keep order. Even if you're not the emperor of your own small kingdom, you might be a despotic boss, intimidating your employees. Might you consider switching to benevolence instead?

adj belonging to or having the characteristics of a despot

Synonyms:
despotical

adj characteristic of an absolute ruler or absolute rule; having absolute sovereignty

despotic rulers”
Synonyms:
authoritarian, autocratic, dictatorial, tyrannic, tyrannical ["tyranny", meaning "cruel or unjust use of power"]

undemocratic
not in agreement with or according to democratic doctrine or practice or ideals

adj ruled by or characteristic of a despot

“moved from a feudal to a despotic order”
“his administration was arrogant and despotic
undemocratic
Synonyms:
not in agreement with or according to democratic doctrine or practice or ideals"

(Vocabulary dot com). Historically, when this condition arises in a society the society is said to be suicidal:

"Toynbee wrote volumes about two dozen or so civilizations that we only think about when we are in a history class or a library, however, unlike us he didn't just skim the surface, no, he followed ugly all the way to the bone:

"In other words, a society does not ever die 'from natural causes', but always dies from suicide or murder --- and nearly always from the former, as this chapter has shown."
(A Study of History, by Arnold J. Toynbee). What? Suicide? Murder? ... He was no ordinary historian was he?

That is just the tip of the iceberg, so to speak, as a world famous encyclopedia points out:
"In the Study Toynbee examined the rise and fall of 26 civilizations in the course of human history, and he concluded that they rose by responding successfully to challenges under the leadership of creative minorities composed of elite leaders. Civilizations declined when their leaders stopped responding creatively, and the civilizations then sank owing to the sins of nationalism, militarism, and the tyranny of a despotic minority.
(Encyclopedia Britannica, emphasis added). Previous posts in this series have zeroed in on the question of what "tyranny" and "despotic minority" meant to him."

(How To Identify The Despotic Minority - 14). Yes, we have nationalism, yes we have militarism, and yes we have a despotic minority (the missing ingredient heretofore is the advent of massive tyranny ... our national tyranny in embryonic at this point).

This election autopsy is also composed of the reality that the largest vote total in history was not for the despot, but was instead for a traditional candidate.

So, not only is there a physical pandemic impacting the USA, but there is a national-soul infection that will erode the nation's character mentioned in the Preamble to the US Constitution ("the general welfare").

UPDATE: An article in Newsweek, authored by Tom Rogers, points out that this election was closer, in terms of relevant votes, than the 2016 election:

"In reality though, the election results were far closer than Biden's nearly 6 million popular vote margin would suggest. The combined total vote margin for Biden in three critical states—Arizona, Georgia and Wisconsin—amounted to only 44,000 votes. This is even fewer than the 77,000 that Trump won by in 2016 across Michigan, Wisconsin and Pennsylvania that gave him the presidency. If Trump had in fact won those 44,000 votes (a tiny fraction of the 150 million cast), the Electoral College vote would have been a 269-269 tie, and the election would have been decided by the House of Representatives. As I have pointed out several times over the last six months, the state delegation-by-delegation vote in the House would have resulted in Trump being reelected."

 (Newsweek, Tom Rogers, emphasis added).

The previous post in this series is here.

Wednesday, November 18, 2020

On The Origin Of The Home Of COVID-19 - 18

Some of my best friends are Germs

Dredd Blog has been pointing out the lack of understanding Western Civilization has of the "germosphere" (Microbial Languages: Rehabilitation of the Unseen).

This same lack of understanding applies to the world of viruses: "Tracing the origins of viruses is difficult ... studying their ancestry requires untangling it from the history of their hosts" (Where did viruses come from?).

Since viruses "can replicate only within a host cell" (The Origins of Viruses), we must ask and answer the question: "What is a host cell?" ("Host cell ... Definition ... noun, plural: host cells ... (1) A cell that harbors foreign molecules, viruses, or microorganisms. For example, a cell being host to a virus."... Biology Online).

Since "viruses ... cannot reproduce on their own" we must also ask and answer the question "why would a host reproduce them".

There are many reasons why hosts of viruses would reproduce the viruses within them:

 "Most consider viruses to be parasites, where infection benefits the virus, but decreases the fitness of the host. Now consider other scenarios, such as commensals and mutualists. A virus can be commensal, the virus benefits while host fitness is unaffected. A virus can be mutualistic, in which both organisms benefit and fitness increases. Such viral associations may provide advantages that promote evolution and biodiversity. Also consider that one virulent virus among a sea of non-virulent viruses does not equate to pathogenesis. Unless transmission and recovery rates are high, pathogenicity may be an evolutionarily poor strategy for viral survival. More likely, pathogenesis is the exception and not the rule, with more instances being discovered of viruses having cooperative roles with the host. There are many instances where an organism cannot exist without beneficial viruses ... endogenous retrovirus syncytin expression in the placenta of mammals allows for the development of the placental syncytium. This syncytial fusion creates a barrier for the placenta, which in part keeps the fetus from being rejected by the mother’s immune system. Viruses can also modulate the immune system and restore dysbiotic conditions ... It is becoming evident that viruses have the potential to be something more than parasites in a holobiont, which revises conceptions of how viruses impact host interactions."

(The Intra-Dependence of Viruses and the Holobiont, Grasis, JA, 2017). Equally interesting is what is inside the host that does the replication of mutualistic viruses:

Nucleobase/nucleotide comparisons

"The protein-based molecular motors rely on an energy-rich molecule known as adenosine triphosphate (ATP), which is basically a nucleotide having three phosphate molecules that play a vital role in its energetics, and make it an indispensable commodity of life. The machines described in this section, the F0-F1 ATPase, the kinesin, myosin, and dynein superfamily of protein molecular machines, and bacteria flagellar motors all depend, directly or indirectly, on ATP for their input energy."

(Molecular Machines, bold added). That "(ATP),which is basically a nucleotide" is found abundantly in the DNA/RNA sequences of viruses. 

Specifically, the particular molecular machine that does the work of microbe replication is the ribosome (The ribosome as a molecular machine).

That is why Dredd Blog has presented the argument in this series that SARS-CoV2 is generated by the injection of toxic chemicals / antibiotics into the food system by the "mass slaughtering of cows, pigs, and chickens industry", thereby killing beneficial microbes which host beneficial (mutualistic pre-SARS-CoV2) viruses within them (On The Origin Of The Home Of COVID-19, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17).

The next post in this series is here, the previous post in this series is here.




Monday, November 16, 2020

Quantum Oceanography - 4

World Ocean
The ocean is a deep subject which we have mapped less than we have mapped the Moon and Mars. 

Today's post is a study of certain aspects of the World Ocean Database user's manual (Johnson, D.R., T.P. Boyer, H.E. Garcia, R.A. Locarnini, O.K. Baranova, and M.M. Zweng, 2013. World Ocean Database 2013 User’s Manual. Sydney Levitus, Ed.; Alexey Mishonov, Technical Ed.; NODC Internal Report 22, NOAA Printing Office, Silver Spring, MD, 172 pp, doi:10.7289/V5DF6P53. The manual is available for a no-cost download at http://www.nodc.noaa.gov/OC5/WOD13/docwod13.html).

That manual presents, among other things, maximum and minimum ocean temperatures and salinity values at thirty-three (33) ocean depths.

Snapshots of those values are presented in Appendix QO-1

Those thirty-three WOD depths (L1-L33) also make-up the five Pelagic Depths (Epipelagic, Mesopelagic, Bathypelagic, Abyssopelagic, and Hadopelagic) which are depicted in the graphs in Appendix QO-2 and Appendix QO-3.

Those depths are:

L1-L9.......Epipelagic.........(10-200m)

L10-L18...Mesopelagic.....(201-1000m)

L19-L29...Bathypelagic.....(1001-4000m)

L30-L32...Abyssopelagic...(4001-5500m)

L33..........Hadopelagic......(>5500m)

In a paper I recently quoted from, the authors complained that "long‐term, continuous observations of temperature deep within the ocean are exceedingly rare" (In Search Of Ocean Heat - 9).

Let me point out that those "observations" (measurements) are not so exceedingly rare that scientists Johnson, Boyer, Garcia, Locarnini, Baranova, Mishonov, Levitus, and Zweng were unable to ascertain relevant maximum and minimum values for those ocean depths around the globe (see WOD link in the first paragraph of this post, and Appendix QO-1).

The next post in this series is here, previous post in the series is here.

QO4-1

This is an appendix to: Quantum Oceanography - 4

Featured below are screen-shots from Appendix 11 of the World Ocean Database manual.

They display maximum and minimum values for temperature and salinity at ocean depths around the globe.







QO4-3

This is an appendix to: Quantum Oceanography - 4 

Top three pelagic depths are graphed in various ways below: