Wednesday, August 10, 2022

Seaports With Sea Level Change - 23

Port of NY/NJ

Over a decade ago Dredd Blog began to take a look at the concepts of sea level rise (SLR), and a bit later to consider sea level fall (SLF).

Several series resulted (e.g. Will This Float Your Boat?, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,  and many more on the Series Posts (N-Z) page at the headings with "SEA LEVEL" in them).

The issue is now discussed in a wide variety of internet venues (e.g. What is high tide flooding?; US high tide flooding breaks records in multiple locations; Climate change impacts on seaports: A growing threat to sustainable trade and development) to name a few (see also the posts under the "EXTINCTION" heading on Series Posts (A-M) page.

In this current series (Seaports With Sea Level Change, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22) the focus is on individual sea ports that also involve Container Ship international trade.

Here is the previous update on Seaports:

(HTML) Single
Coastline Countries
(HTML) Multi
Coastline Countries
Coastline Graphs
Appendix: A-CAppendix: A-CAppendix: A-C
Appendix: D-GAppendix: D-GAppendix: D-G
Appendix: H-LAppendix: H-LAppendix: H-L
Appendix: M-OAppendix: M-OAppendix: M-O
Appendix: P-TAppendix: P-TAppendix: P-T
Appendix: U-ZAppendix: U-ZAppendix: U-Z

Closing comment

The zone between the lines is a place for us to keep our eyes on:

"The municipalities and states are pointing to the costs they’re shouldering because of climate change. The sea level is expected to rise by three feet along San Mateo’s shoreline by 2100, drowning ecosystems, parks, neighborhoods, and infrastructure alike. Baltimore faces dozens more extreme heat days per year, severe storms, and a four-in-five chance of flooding above nine feet by 2100. Boulder’s many injuries include wildfires, drought, flooding, extreme heat days, higher transmission of insect-borne diseases, and increased ground-level ozone pollution.

The suits allege that the energy companies misrepresented the harms of fossil fuels through subterfuge. They funded 'dozens of think tanks, front groups, and dark money foundations pushing climate change denial.' Not mincing words, the attorneys for San Mateo wrote that the fossil fuel companies’ conduct was 'so vile, base, and contemptible that it would be looked down upon and despised by reasonable people.'”

(Why Is Merrick Garland Sticking with Donald Trump on Climate Lawsuits?).

The previous post in this series is here.

Dr. Jerry Mitrovica

Shorter video:

at ~31:14: "By taking the [global] average you're assuming something, and you're assuming it implicitly. You're assuming what we call the bathtub model." - Dr. Mitrovica

Tuesday, August 9, 2022

Quantum Biology - 13

Bones Doll
I. Background

The old song about this bone "is connected to" that bone, and so forth, is a simple way to teach kids some of the basics about the human anatomy (see first video below).

But, you don't have to tell them that those bones are not directly connected, that there is a flexible entity called cartilage between them, because teaching concerns basics first, then the beyond.

The same thing goes for quantum biology in the sense that we are taught that three nucleotides are connected together to make a Codon, a Codon 'leads to' an amino acid, and those amino acid atoms are 'connected together' by a ribosome machine to make a protein, and so forth.

Again, they don't have to tell us that the atoms are not "directly connected", that the molecules are not "directly connected", or that there is a flexible entity (space & forces) between them, because quantum physics teaching also concerns basics first, then the beyond.

II. Appendix

Today's appendix (Appendix QB13) shows the amino acid atoms, and the spaces between them, of a list of human chromosomes, followed by several virus and/or microbe genomes.

The first twenty-four of them depict the smallest amino acid strings in a human chromosome, and the final ones depict the same thing (smallest "CDS" location) in one virus and three microbes. 

The structure is: 

('[one uppercase letter]':[a formula listing atomstheir quantity]), and the spaces between them ("~") ... Example: "('M':C5H11N1O2S1)~('A':C3H7N1O2)~ ..."

They epitomize the codon/amino acid/protein construct which "ribosome machines" process, as depicted in the second video below, and as described by this quote from that video:

"These are tiny molecular machines, and they are doing this inside your body - right now. To understand why, we have to zoom out. Every day, in an adult human body, 50 to 70 billion of your cells die. Either they're stressed, or damaged, or just old. But this is normal - in fact, it's called "programmed cell death". But, to make up for all these lost cells, right now, billions of your cells are dividing, essentially creating new cells. And that process of cell division, also called mitosis -- well, it requires an army of tiny molecular machines. So, let's take a closer look. DNA is a good place to start - the double helix molecule we always talk about. This is a scientifically accurate depiction of DNA, created by Drew Berry at the Walter and Eliza Hall Institute of Medical Research. If you unwind the two strands, you can see that each has a sugar-phosphate backbone connected to the sequence of nucleic acid base pairs, known by the letters A, T, G and C. Now, the strands run in opposite directions, which is important when you go to copy DNA. Copying DNA is one of the first steps in cell division. Here, the two strands of DNA are being unwound and separated by the tiny blue molecular machine called "helicase". Helicase literally spins as fast as a jet engine! The strand of DNA on the right has its complementary strand assembled continuously. But the other strand is more complicated, because it runs in the opposite direction. So it must be looped out with its complementary strand assembled in reverse, section by section. At the end of this process, you have two identical DNA molecules, each one a few centimeters long, but just a couple nanometers wide. So, to prevent the DNA from becoming a tangled mess, it is wrapped around proteins called "histones", forming a nucleosome. These nucleosomes are bundled together into a fiber known as chromatin, which is further looped and coiled to form a chromosome, one of the largest molecular structures in your body. You can actually see chromosomes under a microscope in dividing cells. Only then do they take on their characteristic shape. Otherwise, the DNA is more strewn inside the nucleus. The process of dividing a cell takes around an hour in mammals, so this footage is from a time-lapse. You can see how the chromosomes line up on the equator of the cell. Now, when everything is right, they are pulled apart into the two new daughter cells, each one containing an identical copy of DNA. Now, simple as this looks, the process is incredibly complicated and requires even more fascinating molecular machines to accomplish it. So, let's look at a single chromosome. One chromosome consists of two sausage shaped chromatids, containing the identical copies of DNA made earlier. Each chromatid is attached to microtubule fibers, which guide and help align them in the correct position. The microtubules are connected to the chromatid at the kinetochore, here colored red. The kinetochore consists of hundreds of different proteins working together to achieve multiple objectives. In fact, it's one of the most sophisticated molecular mechanisms inside your body. The kinetochore is central to the successful separation of the chromatids. It creates a dynamic connection between the chromosome and the microtubules. For a reason no one's yet been able to figure out, the microtubules are constantly being built at one end and deconstructed at the other. While the chromosome is still getting ready, the kinetochore sends out a chemical "stop" signal to the rest of the cell, shown here by the red molecules, basically saying, "this chromosome is not yet ready to divide." The kinetochore also mechanically senses tension. When the tension is just right, and the position and attachment are correct, all the proteins get ready, shown here by turning green."

(Transcript excerpt, Second Video Below, emphasis added). Did you notice that at some machine locations the process takes place at jet engine speeds?

III. Discussion

In a previous post (Quantum Biology - 12) I discussed a paper ("Paper One") where a "postdoc" student waxed imaginary:

"if I were a small protein sitting on a replicating chromosome, could I tell which DNA segment belongs to which sister DNA? Physicists like questions like that, whether they are rooted in physics or biology. "

(ibid). He will do just fine in the doll factory of imaginative biology, but nevertheless he brings up the point I am emphasizing in these series (Quantum Biology, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12; Small Brains Considered, 2, 3, 4, 5; The Doll As Metaphor, 2, 3, 4, 5, 6, 7, 8).

That point, that emphasis, is about an important consideration/question, which is:


(Machines at work, Video Two below). It reminds me of a Nietzsche quote:

“Insanity in individuals is something rare – but in groups, parties, nations and epochs, it is the rule.”

(see e.g. Friedrich Nietzsche). So then, can an individual atom or a group of atoms "suffer" insanity? 

That question reminds me of a recent chess game:

"In something out of Black Mirror meets Queen's Gambit, a chess robot accidentally broke the finger of its seven-year old opponent during an exhibition in Moscow, The Guardian reported. The child apparently moved his piece too soon and the robot grabbed his finger and squeezed it, causing a fracture before help could arrive. 'The robot broke the child’s finger,' said Moscow Chess Federation president Sergey Lazarev."

(A chess-playing robot broke its seven-year-old opponent's finger). The big problem I am pointing out is not obvious, no, it is very subtle.

IV. Closing Comments

That big problem in scientific circles, i.e., that malfunctioning thought process, is anthropomorphism ... fusing human thinking/cognition with inanimate objects we call machines.

Videos Three and Four (below) feature scientists who are seriously considering that question in terms of quantum mechanics principles (but without the anthropomorphism).

The previous post in this series is here.

Video One: "Dem bones ..."

Video Two: "The Ribosome machine ..."

Videos Three and Four "Quantum Consciousness of Small Brains ..."

Appendix QB13

This is an appendix to Quantum Biology - 13

1) click on the link you want to check out,
2) Notice: "Due to the large size of this record, sequence and annotated features are not shown. Use the "Customize view" panel to change the display",
3) click on "Customize View" at the upper right hand corner,
4) click on the "Customize 'button',
5) click on the "Gene,RNA,and CDS features only" button,
6) search for all or part of the sequence letters (example:
7) remember that these letters represent ONLY ONE "CDS" amino acid/protein sequence location in the genome, and that they are the smallest "CDS" location letters (it's the idea we are contemplating, not the whole thing).

























End of Chromosomes





Saturday, August 6, 2022

Quantum Biology - 12

Fig. 1 Close up of a cell's brain?

I. Background

I recently read "The Bacterial Chromosome: A Physical Biologist's Apology. A Perspective." (Paper One) and "Nuclear speed and cycle length co -vary with local density during syncytial blastoderm formation in a cricket" (Paper Two).

Today I am ready for another post here on Dredd Blog.

One reason for that is that Paper One featured E. Coli genome and Paper Two featured a cricket genome; furthermore, since according to the authors those blasted syncytial  blastoderm dynamics are here because "physics and biology have worked together during the course of evolution" (Paper One) which is whimsical, metaphorical, and teleological "playing with dolls" as when a Mars rover "made friends with a pet rock" (The Doll As Metaphor - 8).

Evidently the pet rock and the rover overcame the time-warp between them with a time travel trip so "working together" emerged in a syncytial-time-blasted episode of "physicists will continue to enter biology until one day the boundary between the two disciplines disappears."

Anybody read Shakespeare's 2087 time-travel book "working together in the boundary"? ("time keeps on slippin' into the future" ... see video below).

It's a perfect time, then, to fuse Small Brains Considered, 2, 3, 4, 5 with Quantum Biology, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, because "physics and biology" are not living things, and genomes are made of atoms, i.e., inanimate objects that are not alive.

II. Appendices

There is only one appendix to today's post (Appendix QB-12), which contains counts of the number of amino acids coded for and featured in a previous post's appendices (Small Brains Considered - 5).

Those appendices: A, B, C, D, and E (The count tables are linked to those appendices).

They featured, among other things, information concerning a cricket genome, an E.Coli genome, a human chromosome, and several others, for the purpose of showing the amino acid, codon, and atomic similarities.

III. Discussion

For starters, notice that the human chromosome (Appendix A) shows counts of hundreds of thousands, while the other counts (non-human) are for the most part less than one thousand (Appendix QB-12).

However, consider this:

"There's about a trillion human cells that make each one of us who we are and able to do all the things that we do. But you have 10 trillion bacterial cells in you or on you at any moment in your life. So, 10 times more bacterial cells than human cells on a human being. And, of course, it's the DNA that counts, so here's all the A, T, Gs and Cs that make up your genetic code and give you all your charming characteristics. You have about 30,000 genes. Well, it turns out you have 100 times more bacterial genes playing a role in you or on you all of your life. So at the best, you're 10 percent human; more likely, about one percent human, depending on which of these metrics you like. I know you think of yourself as human beings, but I think of you as 90 or 99 percent bacterial. (Laughter) And these bacteria are not passive riders. These are incredibly important; they keep us alive. They cover us in an invisible body armor that keeps environmental insults out so that we stay healthy. They digest our food, they make our vitamins, they actually educate your immune system to keep bad microbes out. So they do all these amazing things that help us and are vital for keeping us alive, and they never get any press for that. But they get a lot of press because they do a lot of terrible things as well. So there's all kinds of bacteria on the earth that have no business being in you or on you at any time, and if they are, they make you incredibly sick."

(Small Brains Considered - 4, transcript excerpt/quote from video of Dr. Bassler, emphasis added). This is important for researchers to consider.

I have complained about microbiologists and virologists use "host" when the appropriate term is "epi-host" because most ACGT and U nucleotides are contained in a microbe host (eukaryotes/prokaryotes; only they can replicate viruses).

Non-microbial cells (human/animal/plant) do orders of magnitude less replication, if any, because for one thing those cells are less plentiful as Dr. Bassler points out in the quote above.

Furthermore, a virologist says it is erroneous not to know what virus host (what microbe) a virus was extracted from for sequencing its genome:

"In principle, a plaque assay is remarkably simple: prepare a dilution series of a phage lysate, mix dilutions well with ali­quots of a growing culture of their host bacteria ... plaque as­says for counting phages do not work if you have − or suspect you have − lots of phages in a sample but the host bacteria are difficult or impossible to culture on plates, or − even worse − not known."

(Of Terms in Biology: The Polony Method, emphasis added). Most virology papers and media news never mention the host bacterium, instead they do the worst case scenario which is to only mention the "epi-host" (human, cow, chicken, bat, ect.) which the actual host microbe is in. 

IV. Closing Comments

Virology blog’s take on it: 

“Viruses are not living things. Viruses are complicated assemblies of molecules, including proteins, nucleic acids, lipids, and carbohydrates, but on their own they can do nothing until they enter a living cell. Without cells, viruses would not be able to multiply. Therefore, viruses are not living things … Viruses don’t actually ‘do’ anything.” 

(Virology 101; Virology Blog, 2004). That is my understanding as well, which is why I have criticized the use of metaphor, teleology, and doll's play.

Especially when discussing microbes and viruses (Small Brains Considered, 2, 3, 4, 5; The Doll As Metaphor, 2, 3, 4, 5, 6, 7, 8).

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

Time keeps on slippin' into the tik tok:

Biology stuck in the middle with Physics:

Appendix QB-12

This is an appendix to Quantum Biology - 12

Appendix A Amino
Acid Counts

Amino Acid Count
A 204,021
R 171,446
N 105,293
D 143,629
C 65,752
Q 147,972
E 223,499
G 194,669
H 75,007
I 127,649
L 293,627
K 177,071
M 63,839
F 107,848
P 193,692
S 262,594
T 160,379
W 35,018
Y 79,973
V 178,484

Appendix B Amino Acid Counts

Amino Acid Count
A 173
R 56
N 158
D 62
C 41
Q 69
E 77
G 212
H 65
I 356
L 523
K 82
M 231
F 310
P 131
S 320
T 178
W 88
Y 145
V 176

Appendix C Amino Acid Counts

Amino Acid Count
A 961
R 474
N 754
D 706
C 433
Q 508
E 668
G 834
H 259
I 715
L 1,346
K 828
M 308
F 698
P 549
S 936
T 1,051
W 157
Y 636
V 1,128

Appendix D Amino Acid Counts

Amino Acid Count
A 155
R 53
N 173
D 69
C 45
Q 73
E 65
G 217
H 68
I 351
L 519
K 66
M 276
F 304
P 130
S 302
T 191
W 86
Y 149
V 161

Appendix E Amino Acid Counts

Amino Acid Count
A 63,829
R 35,863
N 26,172
D 34,190
C 7,667
Q 29,724
E 37,056
G 48,517
H 14,785
I 39,289
L 70,921
K 28,150
M 18,611
F 25,899
P 29,626
S 39,284
T 36,224
W 10,406
Y 18,980
V 46,655