Why DNA translation requires thought and planning

Have you ever tried writing a coded message? In order to do it you must first plan a coding scheme.

Your coding scheme determines what key information is required to both encode and decode your messages.

The fun part is when you share the decryption key with your friends. Writing and reading the original message even before encoding it already requires a certain level of intelligence and cognitive abilities that is far above and beyond any other creature on earth besides humans. So, it’s safe to say that only human level or higher cognitive abilities can read, write encode and decode written messages, right?

During my book launch presentation, I presented a handout to the participants and challenged them to decode words that were written in DNA code. The point of the exercise was to highlight the level of intelligence that was required to perform the task.

Afterwords, the participants could discuss whether such tasks could ever be expected to be performed by chance processes. In other words, the participants would have a better understanding of whether human level or higher cognitive abilities could be clearly seen within the coded messages that were made?

Creationism and Intelligent Design is the understanding that the level of complexity found within a thing made from scratch, has ALWAYS been recognized as directly corresponding to and directly proportional to the minimum level of cognitive abilities required to make it. That recognition goes from computers, rocket ships to written novels, computer code to integrated circuits, nano machines, forensic science, crime investigation, and on to the origin of life and of the universe.

The complexity that is clearly seen within your coded messages is also recognized as directly corresponding to and directly proportional to the minimum level of cognitive abilities that was required for you to make your coded messages.

When we examine a document and find that it contains (A) high accuracy, precision, and significant specified complexity that form instructions that controls (B) assembly mechanisms that produce (C) functional 3-D parts that also have high accuracy, precision, and significant specified complexity that allows (D) the parts to perform specific goal directed behavior, what details can we assume about advanced cognitive abilities that wrote such instructions? And can we also assume that such abilities to write such code to be beyond the capabilities of natural undirected chance processes?

We have (A) DNA —-> (B) assembly mechanisms —-> (C) 3-D parts —-> (D) the parts perform specific goal directed behavior.

All life on earth is formed that way and starts with (A) the extremely complex design and assembly information found within DNA code.

DNA contains the genetic instructions that code for protein chains such as is similar to the beads chained together in this image, which in turn fold into 3-D structures to form cellular parts and carry out various functions essential for the cell's structure and activities.

The scientific method comparing origin of life by natural processes versus Intelligent Design

I posed this question to AI: “Please provide a detailed list of plausible steps that could have led to the formation of DNA and functional proteins from basic chemical components by way of design by an intelligent agent regardless of its realm. Please reexamine each step, taking into account the significant challenges posed by chiral purity (the uniform 'handedness' of biomolecules), the effects of water, and the presence of oxygen on early Earth. Additionally, consider how these challenges might be addressed by the advanced cognitive abilities of an intelligent agent.”

Here is AIs response:

“Exploring the formation of DNA and functional proteins from basic chemical components through the lens of design by an intelligent agent involves hypothesizing how such an agent might address the challenges of chiral purity, water, and oxygen on early Earth. Below is a detailed list of plausible steps that could have led to the creation of these complex biological molecules, with a focus on how an intelligent agent could overcome the significant challenges inherent in natural processes.

1. Selection and Preparation of Raw Materials

• Step: The intelligent agent would select the necessary raw materials, including specific types of amino acids, nucleotides, and other organic molecules, with the appropriate chiral purity.

• Addressing Chiral Purity:Challenge: In natural processes, amino acids and sugars are produced in racemic mixtures (equal amounts of left- and right-handed forms), but life requires homochirality (left-handed amino acids and right-handed sugars).Design Solution: An intelligent agent could selectively synthesize or separate only the left-handed amino acids and right-handed sugars, ensuring that the biomolecules formed have the correct chirality necessary for biological function. This selection process could involve advanced techniques for recognizing and sorting chiral molecules, something difficult for undirected natural processes to achieve consistently.

• Addressing the Effects of Water and Oxygen:Challenge: Water tends to hydrolyze (break apart) bonds necessary for forming complex polymers, and oxygen can oxidize and degrade organic molecules.Design Solution: The intelligent agent might create a controlled environment that minimizes the destabilizing effects of water and oxygen. This could involve the use of protective barriers, such as hydrophobic environments or protective vesicles, and careful regulation of oxidative conditions to prevent the degradation of sensitive molecules during synthesis.

2. Synthesis of Nucleotides and Amino Acids

• Step: The intelligent agent would precisely design and synthesize nucleotides and amino acids with the correct chirality and functional groups.

• Addressing Chiral Purity:Challenge: Naturally occurring synthesis of nucleotides and amino acids would result in mixed chirality, reducing the likelihood of forming functional DNA or proteins.Design Solution: By employing advanced chemical knowledge and techniques, the intelligent agent could ensure that only the desired chiral forms are synthesized. This could be done through controlled synthesis pathways that favor one chirality over the other or by using specialized catalysts that promote homochirality.

• Addressing the Effects of Water and Oxygen:Challenge: Water can prevent the formation of stable bonds between nucleotides and amino acids, and oxygen can oxidize and damage these molecules.Design Solution: The agent might employ protective mechanisms during synthesis, such as creating a non-aqueous environment or using antioxidants to protect against oxidative damage. Additionally, the agent could design molecules with protective groups that prevent degradation during assembly.

3. Polymerization into DNA and Proteins

• Step: The intelligent agent would guide the polymerization of nucleotides into DNA and amino acids into proteins, ensuring proper sequence alignment and bond formation.

• Addressing Chiral Purity:Challenge: In natural settings, forming polymers with mixed chirality results in non-functional molecules.Design Solution: The agent could employ precise control over the polymerization process, ensuring that only homochiral monomers are used. This could involve advanced molecular machinery or techniques that specifically recognize and incorporate the correct chiral forms into the growing polymer chains.

• Addressing the Effects of Water and Oxygen:Challenge: In water-rich environments, the formation of stable polymers is difficult due to hydrolysis, and oxygen could oxidize the nascent DNA or protein chains.Design Solution: The agent might carry out polymerization in a controlled, water-free environment or within protective compartments that shield the growing polymers from water and oxygen. This could involve the use of specialized vesicles or other protective structures that allow for the precise assembly of DNA and proteins without the risk of degradation.

4. Folding and Functionality of Proteins

• Step: The intelligent agent would ensure that the newly formed proteins fold correctly into their functional three-dimensional shapes.

• Addressing Chiral Purity:Challenge: Correct folding of proteins depends on the homochirality of amino acids. Proteins with mixed chirality would likely misfold and be non-functional.Design Solution: The agent could utilize advanced folding mechanisms, such as molecular chaperones or folding catalysts, specifically designed to ensure that proteins achieve their correct three-dimensional structure. These folding mechanisms would be precisely calibrated to the chiral composition of the proteins, ensuring functional conformation.

• Addressing the Effects of Water and Oxygen:Challenge: Water can interfere with the delicate folding process, and oxygen can cause oxidative damage to amino acid side chains, leading to misfolding or loss of function.Design Solution: The agent might control the environment to optimize conditions for proper folding, such as maintaining low water activity or using reducing environments to prevent oxidative damage. This controlled environment would mimic the intracellular conditions found in living cells, where protein folding is tightly regulated.

5. Assembly and Encapsulation into Protocells

• Step: The intelligent agent would assemble the DNA, proteins, and other necessary biomolecules into protocells, creating a functional unit capable of self-replication and metabolism.

• Addressing Chiral Purity:Challenge: Functional protocells require that all their components—DNA, RNA, proteins—have the correct chirality for biochemical interactions to proceed efficiently.Design Solution: The agent could precisely assemble these components with strict attention to chiral purity, ensuring that the biochemical machinery within the protocell operates correctly. This assembly process would involve the careful alignment of molecules to facilitate interaction and function.

• Addressing the Effects of Water and Oxygen:Challenge: The formation of stable protocells in a water-rich, oxygenated environment is challenging due to the risk of hydrolysis and oxidation.Design Solution: The agent might encapsulate the protocells in protective membranes that regulate the internal environment, maintaining optimal conditions for biochemical reactions while shielding the internal components from harmful external factors like water and oxygen. These membranes could be designed to allow selective permeability, controlling what enters and exits the protocell.

6. Initiation of Self-Replication and Metabolic Processes

• Step: The intelligent agent would initiate self-replication mechanisms within the protocells, ensuring the propagation of genetic material and the continuation of metabolic processes.

• Addressing Chiral Purity:Challenge: Self-replication requires the precise replication of homochiral DNA, RNA, and the correct synthesis of homochiral proteins.Design Solution: The agent could design replication machinery that is highly specific, ensuring that only homochiral substrates are used during DNA and RNA replication. This machinery would be engineered to minimize errors and maintain the integrity of the genetic material through successive generations.

• Addressing the Effects of Water and Oxygen:Challenge: Replication processes are vulnerable to hydrolysis (which could break down nucleic acids) and oxidation (which could damage DNA and RNA).Design Solution: The agent might design the replication machinery to operate within microenvironments that protect against water and oxidative damage. This could include specialized enzymes that repair any oxidative damage or molecular systems that actively remove water or oxygen from the vicinity of replication processes.

7. Optimization and Refinement of Biological Systems

• Step: The intelligent agent would continuously refine the biological systems, optimizing them for greater efficiency, adaptability, and resilience in varying environments.

• Addressing Chiral Purity:Challenge: Maintaining and refining chiral purity is essential for the continued functionality of biological systems.Design Solution: The agent could implement feedback mechanisms that detect and correct any deviations in chirality, ensuring that all future generations maintain the correct homochirality. These mechanisms could involve advanced biochemical pathways that monitor and enforce chiral consistency.

• Addressing the Effects of Water and Oxygen:Challenge: Over time, the effects of water and oxygen could degrade biological systems, leading to the loss of function or fidelity in replication.Design Solution: The agent might design redundant systems and repair mechanisms that mitigate the effects of water and oxygen over time. This could involve antioxidant systems, dehydration reactions, or other protective processes that maintain the integrity of biological molecules despite environmental challenges.

Conclusion

In this design-by-intelligent-agent framework, each step in the formation of DNA, proteins, and protocells would involve overcoming the inherent challenges posed by chiral purity, water, and oxygen. An intelligent agent, equipped with advanced cognitive abilities and knowledge of biochemistry, could precisely control the synthesis, assembly, and function of these biological components in ways that undirected natural processes cannot.

This approach hypothesizes that the agent could bypass or mitigate the obstacles that would otherwise hinder the formation of life, such as ensuring homochirality, protecting against hydrolysis and oxidation, and optimizing biological systems for stability and function. While speculative, this framework offers a potential explanation for how life's complex molecular machinery could have originated under conditions that would otherwise pose significant challenges to naturalistic processes.”

I deal with many of these issues in my book: