Dredd Blog: Quantum Biology

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 atoms_{their 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:

"CAN AN ATOM OR A GROUP OF ATOMS 'THINK'?"

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