What points to design, simplicity, or complexity?

What points to design, simplicity, or complexity?

https://reasonandscience.catsboard.com/t3250-what-points-to-design-simplicity-or-complexity

I hear from time to time, that simplicity, not complexity, is the hallmark of design. I think that is what we can observe in the universe. All the awe-inspiring diversity of stars, galaxies, planets, life forms, ecology, landscapes, and so forth is built based on just four fundamental forces of energy, six fundamental mathematical equations, four Building blocks of life, a genetic alphabet of four letters, and a genetic code, that assigns 64 códon words to 20 amino acids. So it is basically both, designed simplicity, combined with the complexity that comes from it, that points to design.

On top of that, physical forces and laws are fine-tuned. And the genetic code and the amino acid set are optimal amongst millions of less adequate alternatives.

The fundamental forces must be finely adjusted to the extreme to permit life
https://reasonandscience.catsboard.com/t1339-fine-tuning...

The laws of physics must also be finely adjusted to permit carbon-based life
https://reasonandscience.catsboard.com/t1336-laws-of...

No DNA double Helix, no life

And that depends on the hydrogen bond forces for Watson-Crick base pairing which must also be just right, and they depend on the isomeric configuration of the nucleobases of purines and pyrimidines. There is almost an infinite number of possible setups.
https://reasonandscience.catsboard.com/t2591-biochemical...

If we employ weightings to allow for biases in translation, then only 1 in every million random alternative genetic codes generated is more efficient than the natural code.
https://pubmed.ncbi.nlm.nih.gov/9732450/

In 2015, a scientific investigation was performed to test 100 million different sets of twenty amino acids. They measured three chemical properties: size, charge, and hydrophobicity, and compared it to the standard amino acid alphabet. Only six are better able to explore “chemistry space” than the twenty amino acids that life uses. That suggests that life’s set of amino acids is finely tuned to one part in 16 million.
https://www.nature.com/articles/srep09414

Parsimony, Fine-tuning, and optimality of sets = 

Complexity creates simplicity that gives rise to complexity: A close circle that points to a designed setup. 

I frequently hear atheists claiming that simplicity, and not complexity is the hallmark of design.  Imagine that we would be civil engineers having the task of building a skyscraper. We would employ many different materials and building blocks, various types of cement, metal beams, floor tiles, strong cables, ventilation shafts, electric cables and wiring for the electrical systems, etc., etc. Quite a long list of materials.

Now consider that all matter in the universe is made of atoms. The earth, life, and our bodies. Everything. The properties of atoms are basically defined by protons and electrons. Everything we see can be built by merely these two subatomic particles - protons and electrons. They are so incredible that they can be used to build everything in the universe! The same applies to our bodies, which are made just of four basic building blocks: Amino acids, nucleotides, phospholipids, and carbohydrates.

Now another paradox: C.Wood (2022): The positively charged particle at the heart of the atom is an object of unspeakable complexity, one that changes its appearance depending on how it is probed. High school physics teachers describe them as featureless balls with one unit each of positive electric charge — the perfect foils for the negatively charged electrons that buzz around them. College students learn that the ball is actually a bundle of three elementary particles called quarks. But decades of research have revealed a deeper truth, one that’s too bizarre to fully capture with words or images.

“This is the most complicated thing that you could possibly imagine,” said Mike Williams, a physicist at the Massachusetts Institute of Technology. “In fact, you can’t even imagine how complicated it is.”

The proton is a quantum mechanical object that exists as a haze of probabilities until an experiment forces it to take a concrete form. And its forms differ drastically depending on how researchers set up their experiment. Connecting the particle’s many faces has been the work of generations. “We’re kind of just starting to understand this system in a complete way,” said Richard Milner, a nuclear physicist at MIT.
https://www.quantamagazine.org/inside-the-proton-the-most-complicated-thing-imaginable-20221019/

The same goes for the building blocks of life. While just a limited set is used to construct the amazing variety of organismal forms in life, the synthesis of these building blocks is enormously complex.

William Martin and colleagues from University Düsseldorf’s Institute of Molecular Evolution give us also an interesting number: The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H2, CO2, and ammonia (NH3) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment. Seventy-seven core reactions involve the hydrolysis of high-energy phosphate bonds, furthermore suggesting the presence of a non-enzymatic and highly exergonic chemical reaction capable of continuously synthesizing activated phosphate bonds. CO2 is the most common carbon-containing compound in the core. An abundance of NADH and NADPH-dependent redox reactions in the autotrophic core, the central role of CO2, and the circumstance that the core’s main products are far more reduced than CO2 indicate that the core arose in a highly reducing environment. The chemical reactions of the autotrophic core suggest that it arose from H2, inorganic carbon, and NH3 in an aqueous environment marked by highly reducing and continuously far from equilibrium conditions.

Comment: Imagine each of the 404 reactions depends on a complex molecular machine. Another example we find in David Goodsell's excellent book: Our Molecular Nature, page 26:
Dozens of enzymes are needed to make the DNA bases cytosine and thymine from their component atoms. The first step is a "condensation" reaction, connecting two short molecules to form one longer chain, performed by aspartate carbamoyltransferase. Other enzymes then connect the ends of this chain to form the six-sided ring of nucleotide bases, and half a dozen others shuffle atoms around to form each of the bases. In bacteria, the first enzyme in the sequence, aspartate carbamoyltransferase, controls the entire pathway. (In human cells, the regulation is more complex, involving the interaction of several of the enzymes in the pathway.) Bacterial aspartate carbamoyltransferase determines when thymine and cytosine will be made, through a battle of opposing forces. It is an allosteric enzyme, referring to its remarkable changes in shape (the term is derived from the Greek for "other shape"). The enzyme is composed of six large catalytic subunits and six smaller regulatory subunits. Take just a moment to ponder the immensity of this enzyme. The entire complex is composed of over 40,000 atoms, each of which plays a vital role. The handful of atoms that actually perform the chemical reaction are the central players. But they are not the only important atoms within the enzyme--every atom plays a supporting pan. The atoms lining the surfaces between subunits are chosen to complement one another exactly, to orchestrate the shifting regulatory motions. The atoms covering the surface are carefully picked to interact optimally with water, ensuring that the enzyme doesn't form a pasty aggregate, but remains an individual, floating factory. And the thousands of interior atoms are chosen to fit like a jigsaw puzzle, interlocking into a sturdy framework. Aspartate carbamoyltransferase is fully as complex as any fine automobile in our familiar world. And, just as manufacturers invest a great deal of research and time into the design of an automobile, enzymes like aspartate carbamoyltransferase have been finely tuned  and now, Goodsell adds just five words at the end of the sentence - over the course of evolution..