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Saturday, March 12, 2022

How Microbes Communicate In The Tiniest Language - 3

What are Alarmones?

I. Introduction

Civilizations, societies, and groups wrestle with the concept of "a duty to warn".

In situations where a member of the civilization, society, or group detects a danger to one or all members of that civilization, society, or group, the duty concept kicks in.

During discourse between the general populace and their government, the format, structure, and/or appearance as to what that duty looks like varies from time to time. 

Sometimes they wrestle about the details of the issue of "a duty to warn" over substantial spans of time.

Finally, the rubber meets the road when the uncertainty, religion and law are finally divided at the center line into one side and the other (Uncertainty, Religion, and Law).

A lot of that is altered until, sometimes, "duty" is diminished to the point that no warning is necessary.

To inform by warning of a danger becomes no longer a requirement, it becomes an intrusion (e.g. global warming).

II. The Microbial Alarmone

That human cultural back and forth is not a dynamic that takes place in the microbiome (the world of microbes).

Microbes either have a genetic alarmone or they don't, so "if you see something say something" is a built-in feature (What are Alarmones?, Wikipedia, Alarmones).

Microbiologists point out that this built-in duty to warn via alarmones has been that way for eons:

"All known alarmones are ribonucleotides or ribonucleotide derivatives that are synthesized when cells are under stress conditions, triggering a stringent response that affects major processes such as replication, gene expression, and metabolism. The ample phylogenetic distribution of alarmones (e.g., cAMP, Ap(n)A, cGMP, AICAR, and ZTP) suggests that they are very ancient molecules that may have already been present in cellular systems prior to the evolutionary divergence of the Archaea, Bacteria, and Eukarya domains. Their chemical structure, wide biological distribution, and functional role in highly conserved cellular processes support the possibility that these modified nucleotides are molecular fossils of an epoch in the evolution of chemical signaling and metabolite sensing during which RNA molecules played a much more conspicuous role in biological catalysis and genetic information."

(Alarmones as Vestiges of a Bygone RNA World, emphasis added). Automatic warning systems, eh?:

"Most microbial life exists in a non proliferating state of quiescence that enables survival during nutrient limitation and in stressful environments. A major challenge facing a quiescent cell is how to minimize energy consumption so as to maximize available resources over a potentially extended period of time."

(The alarmones (p)ppGpp directly regulate translation initiation during entry into quiescence). Population control, it would seem, even to the degree of "quiescence" is not beyond normal microbial activity.

III. The Alarmones of Civilizations, Societies, and Groups

The early development of microbial warning systems is probably similar to its early development in civilizations, societies, and groups.

However, the microbial warning system durability and usage is not as robust or long lasting in humans:

"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." [Toynbee]

...

"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]

(How To Enjoy The End Of Bad Choices). Our current civilization, society, and group behavior is an illustration of that:

"Today's IPCC report is an atlas of human suffering and a damning indictment of failed climate leadership. With fact upon fact, this report reveals how people and the planet are getting clobbered by climate change. Nearly half of humanity is living in the danger zone – now.  Many ecosystems are at the point of no return – now. Unchecked carbon pollution is forcing the world's most vulnerable on a frog march to destruction – now. The facts are undeniable. This abdication of leadership is criminal."

(What The Latest [2022] UN Climate Report Says About Our Future, emphasis added). Our civilization, society, and group alarmones are NOT bringing about "a non proliferating state of quiescence".

The microbial warning system gets the message out, so why doesn't good bio-mimicry exist in our current civilization (On The Peak of Intelligence - 2)?

The previous post in this series is here.


Ode to the alarmones:


Friday, March 11, 2022

How Microbes Communicate In The Tiniest Language - 2

Calling all microbes
In the first post of this series Dredd Blog introduced readers to the phenomenon of "the language of microbes".

That introduction was made possible due to the research done by a hard working Princeton University professor and her hard working students (How Microbes Communicate In The Tiniest Language).  

Today's post is a follow-up to that post which probably should have been posted way before now.

Anyway, today's follow-up to that post began as I thought about the astounding revelation that those researchers came upon, which among other things is the discovery that there is both a common language among the huge microbial world of millions of species, as well as a singular variant language between microbes of the same species (ibid).

Since Dr. Bassler also pointed out, in her TED talk video (see below), the astonishing discovery that we humans are composed mostly of microbial DNA and genes, I have done some follow-up research concerning DNA gene matches between homo sapiens and microbes (cf. The Human Microbiome Congress).

My "follow-up research" is a small study that includes only twenty microbe genomes, and three human genomes selected from a GenBank list (see Appendix).

The table in the Appendix contains three human genome excerpt lines, each followed by twenty microbe excerpt lines.

The Appendix also has a help section of seven steps about how to view the appendix data in the GenBank.

The "three human genome excerpt lines" does not mean that three people are represented, it is only one person's partial DNA (three chromosomes) which are used to compare to twenty random microbe genomes.

The purpose is to show that matches of microbe gene DNA with human gene DNA vary in quantity of matches.

That "matching" even varies within ourselves, i.e. within one individual, from time to time during our lives (A Cure For Congress & The Supreme Five: Fickle Fecal Transplants, Mitochondrion; On the origin of mitochondria: a genomics perspective).

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



Appendix HMCITTL

This is an appendix to: How Microbes Communicate In The Tiniest Language - 2


To search for the GenBank data in the following table:

1) choose a human or microbe in the table below
2) copy its "GenBank Index Key" column's data
3) click on this link
4) enter that index key data in the search line
5) press the "Search" button
6) GenBank info will appear for your perusal
7) select the "FASTA" link to view the nucleotides



Gene DNA Comparisons (human/microbe)

Definitions:

'Taxonomic Unit Name': 'taxonomic name' of microbe or human;
'GenBank Index Key': the human/microbe GenBank database unique identity;
'Nucleotide Size': number of ACGT molecules in DNA;
'Gene Count': number of genes in the DNA;
'Human Gene Segs In Microbe':
number of human gene DNA segments (10 bp) in microbe DNA;
'Microbe Gene Segs In Human':
number of microbe gene DNA segments (10 bp) in human DNA.


GenBank Data: (enter the GenBank Index Key; select FASTA version)

Taxonomic Unit Name GenBank
Index Key
Nucleotide
Size
Gene
Count
Human
Gene Segs
In Microbe
Microbe
Gene Segs
In Human
Homo sapiens (human) NW_003871055.3 7,283,150 214 ---- ----
Staphylococcus debuckii NZ_CP033460.1 2,691,850 2,600 579 471
Mycoplasma mycoides NZ_CP001668.1 1,084,586 900 1,391 989
Staphylococcus haemolyticus NZ_CP013911.1 2,549,338 2,509 634 496
Rathayibacter tanaceti NZ_CP047186.1 3,214,120 3,044 273 230
Rathayibacter festucae NZ_CP047180.1 4,219,997 3,859 330 260
Pasteurella canis NZ_CP085791.1 2,298,791 2,183 722 628
Staphylococcus aureus NC_007795.1 2,821,361 2,872 883 675
Moraxella bovis CP030241.1 2,839,913 2,881 618 448
Pseudomonas aeruginosa NC_002516.2 6,264,404 5,697 375 291
Pseudomonas brassicacearum NZ_CP034725.1 6,738,544 6,023 382 315
Psychrobacter alimentarius CP014945.1 3,332,539 2,742 574 454
Pseudomonas amygdali NZ_CP042804.1 6,133,558 5,439 432 316
Pseudomonas adelgestsugas NZ_CP026512.1 1,835,598 904 531 409
Acetobacter ascendens NZ_CP021524.1 2,901,846 2,682 463 366
Mycoplasma capricolum NC_007633.1 1,010,023 878 1,232 941
Pasteurella atlantica NZ_CP074346.1 2,301,649 2,209 735 587
Pasteurella canis CP083262.1 2,301,094 2,194 677 539
Shewanella aestuarii CP050313.1 4,029,210 3,506 417 350
Shewanella aestuarii NZ_CP050313.1 4,029,210 3,510 417 353
Pasteurella dagmatis LT906448.1 2,287,213 2,088 604 470
Homo sapiens (human) NC_000020.10 63,025,520 1,059 ---- ----
Staphylococcus debuckii NZ_CP033460.1 2,691,850 2,600 4,851 3,619
Mycoplasma mycoides NZ_CP001668.1 1,084,586 900 9,004 5,670
Staphylococcus haemolyticus NZ_CP013911.1 2,549,338 2,509 4,896 3,897
Rathayibacter tanaceti NZ_CP047186.1 3,214,120 3,044 2,045 2,007
Rathayibacter festucae NZ_CP047180.1 4,219,997 3,859 2,214 1,983
Pasteurella canis NZ_CP085791.1 2,298,791 2,183 4,992 3,869
Staphylococcus aureus NC_007795.1 2,821,361 2,872 5,385 3,802
Moraxella bovis CP030241.1 2,839,913 2,881 3,790 2,888
Pseudomonas aeruginosa NC_002516.2 6,264,404 5,697 2,784 2,440
Pseudomonas brassicacearum NZ_CP034725.1 6,738,544 6,023 3,251 2,696
Psychrobacter alimentarius CP014945.1 3,332,539 2,742 3,990 3,309
Pseudomonas amygdali NZ_CP042804.1 6,133,558 5,439 3,151 2,663
Pseudomonas adelgestsugas NZ_CP026512.1 1,835,598 904 3,536 2,796
Acetobacter ascendens NZ_CP021524.1 2,901,846 2,682 3,595 2,982
Mycoplasma capricolum NC_007633.1 1,010,023 878 8,296 5,681
Pasteurella atlantica NZ_CP074346.1 2,301,649 2,209 5,468 4,127
Pasteurella canis CP083262.1 2,301,094 2,194 4,816 3,604
Shewanella aestuarii CP050313.1 4,029,210 3,506 3,856 3,134
Shewanella aestuarii NZ_CP050313.1 4,029,210 3,510 4,152 3,329
Pasteurella dagmatis LT906448.1 2,287,213 2,088 5,418 4,075
Homo sapiens (human) NC_000021.8 48,129,895 541 ---- ----
Staphylococcus debuckii NZ_CP033460.1 2,691,850 2,600 2,872 2,192
Mycoplasma mycoides NZ_CP001668.1 1,084,586 900 6,079 3,988
Staphylococcus haemolyticus NZ_CP013911.1 2,549,338 2,509 2,515 1,873
Rathayibacter tanaceti NZ_CP047186.1 3,214,120 3,044 935 905
Rathayibacter festucae NZ_CP047180.1 4,219,997 3,859 914 877
Pasteurella canis NZ_CP085791.1 2,298,791 2,183 2,798 2,066
Staphylococcus aureus NC_007795.1 2,821,361 2,872 3,454 2,515
Moraxella bovis CP030241.1 2,839,913 2,881 1,991 1,593
Pseudomonas aeruginosa NC_002516.2 6,264,404 5,697 1,182 1,045
Pseudomonas brassicacearum NZ_CP034725.1 6,738,544 6,023 1,459 1,256
Psychrobacter alimentarius CP014945.1 3,332,539 2,742 2,276 1,859
Pseudomonas amygdali NZ_CP042804.1 6,133,558 5,439 1,660 1,419
Pseudomonas adelgestsugas NZ_CP026512.1 1,835,598 904 1,794 1,492
Acetobacter ascendens NZ_CP021524.1 2,901,846 2,682 2,028 1,721
Mycoplasma capricolum NC_007633.1 1,010,023 878 6,994 4,336
Pasteurella atlantica NZ_CP074346.1 2,301,649 2,209 3,175 2,320
Pasteurella canis CP083262.1 2,301,094 2,194 2,714 2,031
Shewanella aestuarii CP050313.1 4,029,210 3,506 1,891 1,578
Shewanella aestuarii NZ_CP050313.1 4,029,210 3,510 1,890 1,575
Pasteurella dagmatis LT906448.1 2,287,213 2,088 2,556 2,008

Sunday, March 6, 2022

Quantum Biology - 4

Fig. 1 Transcription: DNA~>mRNA

In this and other Dredd Blog series the subject of "quantum origins" has been contemplated.

Those origins are hypothesized to have taken place over a span of time beginning with the big bang.

Over the eons following that origin, it is said that carbon and other relevant atoms were produced in stars (The Uncertain Gene - 2).

Whatever the exact origin, that star-made carbon is now also found in DNA and RNA molecules within living things referred to as "carbon based life forms".

It is also found in abiotic (non-living) carbon-containing viruses (On the Origin of the Genes of Viruses, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17).

How the "conglomeration" of big bang stuff was rearranged into carbon in stars is described in various conflicting stories (If Cosmology Is "Off," How Can Biology Be "On?", 2).

The "conglomeration" is hypothesized to be an ever-changing entity, which is said to have evolved into the quantum conglomerations we now study in genomics.

But more than that, within the conglomeration (at some time before DNA and RNA emerged) was the earliest chemist cum atomic surgeon.

That quantum surgeon became capable of removing specific atoms from DNA molecules in order to make RNA molecules (Some Of My Best Friends Are Germs).

Specifically, I am focusing on the instant when thymine 'T' (C5H6N2O2) was changed into uracil 'U' (C4H4N2O2).

That would have to be done by removing one carbon atom and two hydrogen atoms from the thymine (The Tiniest Scientists Are Very Old, 2).

A contrary hypothesis is that RNA emerged within the conglomeration first, because it is a more simple segment (fewer moving parts) of the conglomeration, thus, one carbon atom and two hydrogen atoms were added to uracil 'U' (C4H4N2O2) to make thymine 'T' (C5H6N2O2).

Without that quantum surgery, among other things, there can be no DNA~>RNA or RNA~>DNA (Fig. 1).

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


Trillions of quantum surgeries per second:




A friendly virus reports back to us about what it is like to enter into a vastly larger single-celled host [in doll magic language: "to take control over its highly complex machines"] (The New Paradigm: The Physical Universe Is Mostly Machine).