Sunday, August 30, 2020

On The Origin Of The Home Of COVID-19 - 17

Fig. 1 See them!
I. The World's First

The world's first Gut Virome Database (GVD) tells us a lot about viruses in homo sapiens:
"The first step in studying viruses in complex communities is being able to detect them. Problematically, identifying viral sequences in large, mixed-community datasets is notoriously challenging.
Further, once viruses are detected there is no standard applied on how viral contigs translate into “species”-level sequences that are to be used as a “working” virus pool for downstream analysis. The lack of viral analysis standards could partly explain the estimated, highly variable (14%–87%) ... rates of virus detection between studies. In addition, factors such as differences in sample processing ... broad under-representation of viral genome space in reference databases ... lack of culturable host gut microbes ... and inter-individual variation add further variability ...
Fig. 2 Antibiotics Kill Helpful Bacteria
Further, although viral reference datasets are being generated at unprecedented rates ... these new data are rarely incorporated for cross-comparisons, which would inflate virus novelty in new datasets and/or leaves many virus sequences undetected. In response to these challenges and to enable virome-centric research in health and disease, we sought to establish a comprehensive, easy-access database dedicated to human gut viruses. This effort would enable future gut microbiome research by augmenting virus detection and helping establish processing standards for human gut viruses."
(The Gut Virome Database Reveals..., emphasis added). I downloaded an early version of the GVD which had fewer rows of data than the latest which I am processing now.

The latest has 33,242 rows which are now in my SQL database, and are being analyzed at this time.

One program is running now, which will be discussed when it finishes comparing SARS-CoV-2 with the phage DNA in the GVD (it finished up, see the appendices).

There are some unprecedented things that have been discovered about "bacteriophages" (phages) in the human enteric virus microbiome.

More on that later in this post.

II. Moving Forward

In this series I have been pointing out that the mass scientific media (the Commentariat) have not been adequately covering the commensal, mutualist, or symbiotic viruses as Dredd Blog has for the better part of a decade now (On The Origin Of The Home Of COVID-19, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16; cf. The Microbes Living in Our Bodies Were Probably Once Evil Pathogens, Smithsonian; Evolutionary origins and diversification of proteobacterial mutualists).

Fig. 3
The mysterious intelligence of single celled creatures has also been under-covered and understudied (the video at the end of this post is shocking in that regard).

The presenter (Eshel Ben-Jacob) at 55 min into video below, details what some would call group co-operation or group-mind at the level of bacteria.

Fig. 4
What we call or name something may not be clear, so let's focus on what the bacteria do.

They do things as if they "knew" what to do, they do things as if they can "see", they do things as if they can communicate effectively with one another.

Fig. 5
When machines do that we call it "AI", the "I" meaning intelligence.


So what is it when living organisms do it?

In Fig. 3 - Fig. 5 (snapshots from the video) two microbes communicate and exchange viruses and other valuables.

The microbes that know how to do something will share that information (and viruses) with other microbes.

What about intelligence in viruses?

What about "machine intelligence" in our gut microbiome (in the zillions of microbes and phages in, on, and around us)?

III. Machine Intelligence

Currently scientists are beginning to point out that there is an incredible amount of "machine intelligence" within the single celled microorganisms we are composed of:
“Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial.” Professor Lithgow said.
Many cellular processes are carried out by molecular ‘machines’ — assemblies of multiple differentiated proteins that physically interact to execute biological functions ... Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.
The most complex molecular machines are found within cells.
Writing in the journal PLoS Pathogens, the team from Queen Mary's School of Biological and Chemical Sciences show how they studied the molecular machine known as the 'type II bacterial secretion system', which is responsible for delivering potent toxins from bacteria such as enterotoxigenic E. coli and Vibrio cholerae into an infected individual.

Professor Richard Pickersgill, who led the research, said: "Bacterial secretion systems deliver disease causing toxins into host tissue. If we can understand how these machines work, then we can work out how it they might be stopped." [or started, or perpetuated as proper and necessary]
(On The Origin of the Genes of Viruses). Indiscriminately "killing anything that moves" is for the inhuman brutality of warmongers (On The Origin of The Bully Religion - 2), but should not be the way of conducting delicate health preserving therapies or food production.

IV. A Look At The SARS-CoV-2
And The Coronavirus Realm Within

While perusing the world's first GVD mentioned in Section I above, I noticed a very large genome which I consider to be a Prophage ("It is not rare for bacteria to contain multiple prophages in their chromosomes, which then constitute a sizable part of the total bacterial DNA" - Prophage Genomics).

The 15 appendices to today's post display analyses of two virus types: 1) coronavirus pre-SARS-CoV-2, and 2) SARS-CoV-2 itself.

Those two are compared to the GVD prophage "Ma_2019_SRR413675", which is the largest one in the GVD (392,017 bases!).

The number of coronavirus genomes compared is 590 viruses, while the SARS-CoV-2 comparison total is 13,827 (the coronavirus and SARS-CoV-2 genomes were downloaded from GenBank).

The process is to: 1) gather a segment of the genome (composed of 10 bases, i.e. a segment of 10 "ACGT's"), 2) search the GVD prophage genome for that sequence, and 3) then move on to the next segment.

That is repeated until the end of the coronavirus or SARS-CoV-2 genome is reached.

A count of the number of matches (a segment of a coronavirus or a segment of a SARS-CoV-2 virus matches a segment in the GVD prophage genome) is shown in the appendices together with the percentage of the coronavirus or SARS-CoV-2 virus segments found in the GVD prophage's genome.

What this teaches us is that elements of coronavirus and SARS-CoV-2 genomes are in our gut microbiome's genome (On The Origin Of The Home Of COVID-19 - 16).

The maximum percent a of coronavirus genome in the human gut (GVD prophage) is:


(Appendix 01), and the maximum percent a of SARS-CoV-2 genome in the human gut (GVD prophage) is:

CNA001371029,904 1,304 43.61%

(Appendix 02). Ok, so on to the appendices.

V. Appendices

Coronavirus 1Appendix 01
SARS-CoV-2 2Appendix 02
SARS-CoV-2 3Appendix 03
SARS-CoV-2 4Appendix 04
SARS-CoV-2 5Appendix 05
SARS-CoV-2 6Appendix 06
SARS-CoV-2 7Appendix 07
SARS-CoV-2 8Appendix 08
SARS-CoV-2 9Appendix 09
SARS-CoV-2 10Appendix 10
SARS-CoV-2 11Appendix 11
SARS-CoV-2 12Appendix 12
SARS-CoV-2 13Appendix 13
SARS-CoV-2 14Appendix 14
SARS-CoV-2 15Appendix 15

VI. Closing Comments

In a future post I plan to show the locations in the GVD phage DNA where these coronavirus and SARS-CoV-2 segments are located. 

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

Long video, but extremely informative:

No comments:

Post a Comment