The Genetic Code and Protein Synthesis: by Chance, Mutations, Natural Selection, or Intelligence?
Since the introduction of cell
theory in 1838, our understanding of biological cells and their functions has expanded significantly. Ongoing research has revealed
critical insights into cellular components such as proteins, biological machines, DNA structure, the genetic code and its involvement
in protein synthesis, RNA and its roles, protective mechanisms, and cell signaling. The complexity inherent in these systems raises
a fundamental question about their origins. Part 1 will address the genetic code and the process of protein synthesis, while Part
2 will consider whether random events, mutation, natural selection, or intelligence provide the most plausible explanation for the
emergence of such complexity. This discussion excludes evolutionary hypotheses that lack substantive evidential support.
Part 1 – The
Genetic Code and Protein Synthesis
Proteins and the genetic code
Proteins are vital components of all living organisms, playing indispensable
roles in nearly every biological process, such as cell division, the synthesis of other proteins, structural support of cells and
tissues, digestion, speeding up chemical reactions, cell signaling, the immune system, channels to allow particular substances in
and out of the cell, and transport of things within and between cells. [1][2][3][4] Each protein is encoded by DNA and RNA through
a nearly universal genetic code conserved in all organisms, with few exceptions. [5][6][7] Structurally, proteins are formed of extensive
chains of amino acids joined by peptide bonds. Notably, only 20 distinct amino acids of the roughly 500 amino acids in nature [8] are
routinely found in protein molecules. Of these 20 amino acids, 11 are synthesized endogenously by the human body; the remaining 9
either cannot be produced in adequate amounts or at all, needing their acquisition through dietary intake. [9] Chirality, which will
be addressed in detail later in this article, plays a vital role in the structure and function of proteins and other biomolecules.[10]
The precise number of different protein types present in the human body is still uncertain, though prevailing estimates range
from approximately 20,000 to over 100,000. [11][12] Titin, recognized as the largest protein in humans, includes more than 34,000
amino acids and plays a critical role in muscle elasticity, functionality, and stability. [13][14][15] In comparison, the smallest
protein in the human body has 44 amino acids. [16] Proteins typically are 300 to 500 amino acids in length. [17] The largest documented
protein, found in the golden algae Prymnesium parvum, consists of 45,212 amino acids. [18]
Chromosomes, DNA and RNA
A chromosome is
a thread-like structure made of a single molecule of deoxyribonucleic acid (DNA) coiled around proteins. All animal and plant cells
have chromosomes - the number, size and shape vary among organism types. Humans normally have 23 pairs of linear chromosomes, each
made up of lengthy DNA strands that are coiled tightly around histone proteins.
DNA has a double helix structure, resembling a twisted
ladder. Its sides are made of alternating deoxyribose sugar and phosphate, while its rungs are composed of paired bases. A nucleotide
is a subunit of DNA or RNA composed of one sugar, one phosphate group, and one base. DNA has four bases: adenine (A), thymine (T),
cytosine (C), and guanine (G). Adenine pairs only with thymine, and cytosine pairs only with guanine, which supports the molecule's
stability. In total, there are approximately 3.2 billion bases in the human genome. [19] Histones are essential for the structural
organization of DNA – compaction to fit in the cell, gene expression.
Ribonucleic Acid (RNA), unlike DNA, consists of a single
strand, uses ribose sugar instead of deoxyribose, has uracil (U) in place of thymine, and is not coiled around proteins. Because of
these differences, RNA is structurally much less stable than DNA.
In animal, plant, fungal, and protist cells, DNA is almost exclusively
housed within a specialized compartment - the nucleus. [20] RNA resides both in nucleus and cytoplasm of biological cells.
The Genome
and the Genetic Code
The genome encompasses all genetic material contained within an organism's DNA. In humans, approximately 1–2%
of this DNA, known as coding DNA, handles encoding proteins via the genetic code, while the remaining 98–99%, referred to as non-coding
DNA, does not directly code for proteins or use the genetic code. Non-coding DNA instead contributes significantly to the regulation
of gene expression, supports RNA synthesis, and maintains the structural integrity of the genome. According to research by ENCODE
published in September 2012, 80.4% of the human genome shows functionality in at least one cell type. [21] [22] ENCODE’s leading analyst
coordinator, Ewan Birney, said “it’s likely that 80 percent will go to 100 percent.” [23] Various biological science entities define
"functional" in diverse ways.
The genetic code provides the directives for the order in which amino acids are assembled into proteins.
In the code, each nucleotide is denoted by one of the bases — C, A, G, T, or U. Sequences of three nucleotides, known as codons, specify
individual amino acids or serve as stop signals during protein synthesis. For instance, the codons UUA, UUG, CUU, CUC, CUA, and CUG
all specify leucine, while AUG exclusively encodes methionine, which typically starts protein synthesis but may be cleaved later.[24] The stop codons UAG, UAA, and UGA serve as termination signals in translation, marking the end of polypeptide elongation rather
than coding for amino acids.
How is the genetic code transcribed to messenger RNA?
“Transcription is highly regulated through promoter
sequences, enhancers, repressors, transcription factors, and epigenetic modifications.” [25]
Before the genetic code is translated
into a protein, it must first undergo transcription into messenger RNA (mRNA). This process is helped by an RNA polymerase enzyme,
with support from a transcription factor protein and a helicase enzyme. Initially, RNA polymerase binds to the gene’s promoter region,
found at once upstream of the coding sequence; however, transcription cannot begin until both the transcription factor and helicase
are properly positioned. The transcription factor ensures that transcription initiates at the correct site on the gene and regulates
gene expression in response to various signals. Upon receiving an activation signal, helicase begins unwinding and separating the
DNA into coding and template strands moving in the 5’ to 3’ direction. [a] RNA polymerase then follows on the template strand in the
5’ to 3’ direction, synthesizing a complementary precursor mRNA strand from the exposed template strand, substituting uracil (U) for
thymine (T). [b] While transcription proceeds, the coding and template strands rejoin behind. As it transcribes, RNA polymerase not
only adds complementary nucleotides to the growing RNA strand but also employs several mechanisms to proofread and correct any errors.
It continues this process until it meets a terminator sequence that marks the end of transcription.
The direction of transcription
is critical as transcription in the reverse direction will reverse the letters in the genetic code. In most cases, this will cause
the wrong amino acid to be placed in the wrong position in the protein chain. For example, UCC codes for serine but CCU codes for
proline. [26]
Right after precursor mRNA is synthesized, a 5’ cap is added to shield it from enzymes that could break it down and provide
crucial binding to the ribosome. The next step is splicing. Some genes in nuclear cells have introns, which are noncoding regions
situated between exons, the segments that code for proteins. When the mRNA is created, these introns are transcribed along with the
exons into the precursor mRNA and must be removed; otherwise, the genetic information will not translate accurately. Splicing removes
the introns. Splicing takes place inside the nucleus through a series of reactions conducted by the spliceosome, which consists of
small nuclear ribonucleoproteins (snRNPs). [27] There are also some introns that can splice themselves. [28] Then, precursor mRNA
is finished into mature mRNA with the addition of a polyadenine tail on the 3’ end to protect it from degrading enzymes.
Protein synthesis
is an energy demanding process. Adenosine Triphosphate (ATP) and Guanosine Triphosphate (GTP) are the primary sources of this energy.
How
is mRNA translated to proteins?
Once a mature mRNA has been synthesized, it is transported (through a nuclear pore in eukaryotes) to
a ribosome, a large molecular machine, where translation takes place.
The ribosome forms around the start codon (AUG) during initiation
of translation and the first tRNA carrying the amino acid methionine binds to the start codon. Ribosomes translate the mRNA codons
in the 5’ to 3’ direction. As the ribosome moves along the mRNA strand, each transfer RNA (tRNA) molecule—carrying both its specific
amino acid and an anticodon loop—recognizes and binds to matching codons on the mRNA. [29] (Typically, there are 20 different tRNA
molecules, one for each amino acid.) In this way, tRNAs deliver their amino acids in the precise order specified by the mRNA's codon
sequence. [30] Before continuing to the next codon, the ribosome facilitates a peptide bond between the amino acids. Translation proceeds
in this manner until meeting a stop codon and after a short pause, the tRNAs and the completed protein are cleaved off into the cytoplasm.[31]
In nucleated cells, up to ten million ribosomes may exist within the cytoplasm. [32] Ribosomes themselves typically consist of
three or four ribosomal RNA molecules, along with approximately 40 to 80 distinct ribosomal proteins. [33]
A subset of proteins emerges from the ribosome requiring further conformational modification to achieve functionality. This final folding process is helped by molecular chaperones, which are themselves proteins that rely on ATP for energy. Various chaperone molecules are used depending on the specific protein and the cellular environment.
Part 2 – Evaluating the Evidence
Did the genetic code result from intelligence?
Codes
are generated through deliberate and intelligent actions designed to achieve specific goals. Some examples of this include:
1. Language can be conceptualized as a system of codes, using words or characters as symbols to stand for ideas, objects, or actions.[34] It is governed by grammatical rules that decide how these symbols may be structured to convey meaning. Communication through
language entails encoding thoughts into linguistic forms and then decoding them by the listener or reader to extract meaning. [35]The origins of language are debated, but most agree it appeared through cognitive processes rather than chance. In biblical accounts,
God spoke creation into existence, Adam and Eve used language, and all people originally shared a single language before the Tower
of Babel.
2. International Morse code, a system of dots, dashes, and spaces used in telecommunications to encode
Latin letters and Indo-Arabic numerals was preliminarily proposed by Samuel Morse, developed by Alfred Vail, and revised by Friedrich
Gerke. [36][37]
3. During World War II, Nazi Germany used an advanced cipher machine with rotating wheels and a plugboard
to encrypt and decrypt messages by turning plain text into code. This machine was conceived, designed, and constructed by intelligent
people.
4. Password and ID generators do not rely solely on chance; they are purposefully crafted through thoughtful
design and development. Even though many programming languages offer built-in functionalities for generating random codes, these capabilities
are the result of deliberate work by skilled professionals.
5. Artificial intelligence (AI) does not always require human
intelligence to function, but it could not exist without planning, coding algorithms by programmers, gathering of data, and training
models. [38]
Also, the genetic code holds information necessary for synthesis of proteins, the building blocks of all
life. And information according to information laws requires an intelligent sender. [39][40][41]
Why is there a genetic code
and what are its implications?
The genetic code plays a vital role in the complex cellular processes that generate the many proteins
essential for life. It holds instructions to create potentially over 100,000 different proteins, with at least one chain composed
of tens of thousands of amino acids. However, these instructions depend on specific biological systems to transcribe, transmit, and
translate them; without this machinery, the information is ineffective. Constructing such a system required planning and anticipation,
qualities defined as the ability to foresee and prepare for future requirements [42]. Chemicals alone lack the capacity for foresight
or thought. Achieving this level of complexity is possible only through cognitive reasoning by an intelligent designer.
The chirality
problem
Chiral molecules are characterized by their inability to align perfectly with their mirror images. These two unique, non-superimposable
forms are called enantiomers and are categorized as “left-handed” (L) and “right-handed” (D) types of chirality.
All types of biomolecules
display homochirality, which means they have consistent handedness. This applies to amino acids (except glycine), proteins/enzymes,
sugars, and nucleotides. In living systems, most amino acids are L-chiral, with glycine being the exception because it is not chiral.
Proteins are built from these L-chiral amino acids. Sugars usually have D-chirality, with only a few exceptions, and nucleotides also
generally show D-chirality. However, during transcription, nucleotides can temporarily shift to L-chirality due to torsional strain. [43]Homochirality “is essential for the proper functioning of biological processes.” [44] Some ways that chirality affects biological
processes:
1. Chirality plays an essential role in biological systems by allowing molecules to align
precisely with specific binding sites, such as those within enzymes that help biochemical reactions. This exact correspondence contributes
to the accuracy and efficiency of vital biological processes, including metabolism and genetic information transfer. [45]
2. Except for glycine, all amino acids used in proteins have D-chirality. “If a protein were built with a mix of L- and D- amino acids,
it would be unable to fold into the precise three-dimensional shape necessary for biological function.” [46] Glycine, being achiral,
allows proteins to fold with sharper turns. Additionally, the precise order of amino acids decides both how accurately a protein folds
and its biological effectiveness.
3. “DNA could not be stabilized in a helix if even a single wrong-handed
monomer were present, so it could not form long chains. This means it could not store much information, so it could not support life.”[47]
4. D-chiral sugars are vital for enzyme and receptor recognition affecting metabolism. [48]
“It is
a scientifically verifiable fact that a random chance process, which forms a chiral product, can only be a 50/50 mixture of the two
optical isomers. There are no exceptions.” [49] The origin of homochirality in living things continues to be an important topic for
evolutionary scientists. The possibility that intelligence engaged in creating homochirality cannot be eliminated.
Is it possible for
all proteins essential to life to originate by chance?
While experiential evidence suggests that highly improbable events may occur,
the likelihood of some outcomes is so minimal that it is reasonable for rational individuals to disregard them in their deliberations.
“(I)f
every event in the universe over its entire history were devoted to producing combinations of amino acids of the correct length in
a prebiotic soup” there would be “roughly 1 out of a trillion trillion - of the total number of events needed to have a 50 percent
chance of generating … any functional protein of modest length.” [50]
A cell forming by chance requires “at least one hundred
functional proteins” forming “simultaneously in one place.” An estimated probability of this happening is 1/102000 [51]
The
probability of all essential proteins for an organism arising by random processes is exceedingly small, which shows that their presence
may be attributable to alternative factors.
Was the genetic code formed through natural selection or mutation?
Natural selection has
no consciousness and therefore no foresight. It only functions by selecting among the genetic information that is already there to
adapt to environments. In the process no added information is available, but some information is lost.
Mutations do not lead to evolution
but devolution where information is corrupted which usually results in decreased functions.
“For any conceivable favorable mutation,
a species must pay the price or bear the burden of more than 1000 harmful mutations of the gene... As mutational load increases with
time, the survival of the species will be threatened as matings produce a greater percentage of offspring carrying serious genetic
defects.” [52]
Since genetic information is continually degraded or lost, it's logical to think that it was once in a better state,
like how a wound-up clock gradually runs down over time. Mechanisms exist to protect the genetic code from mutations.
What cellular
mechanisms exist to safeguard genetic information, and what are the broader implications of these protective processes?
Corrupted genetic
information can lead to genetic disorders including cancers. The cell employs various mechanisms to protect its genetic information
and remove errors and replace them with the correct components including:
1. The genetic code is “arranged
to minimize error in protein sequences and structure.” [53]
2. Cells use strategies to exclude molecules
with incorrect chirality, such as L-chiral sugars and D- chiral amino acids, from their internal processes.
3. During replication, DNA polymerase conducts proofreading to detect errors and stops while errors are being corrected before continuing.
4. In eukaryotes (cells with a nucleus), the genetic material in the nucleus is protected by a double
membrane, while nuclear pores control the passage of molecules between the cytoplasm and nucleoplasm.
5. DNA repair incorporates a collection of cellular mechanisms dedicated to finding and correcting damage in DNA molecules that encode
the genome [54]. Each cell daily experiences 10,000 to 1,000,000 individual molecular lesions in its DNA. [55] [56] DNA repair is
therefore needed constantly during the life of the cell.
6. During transcription, RNA polymerase employs
various mechanisms to proofread and correct errors.
7. Messenger RNA undergoes capping and receives
a polyadenine tail to safeguard it from enzymatic degradation.
8. The genetic code has degeneracy whereby multiple
codons code for the same amino acid. This redundancy adds an added layer of protection as certain codon errors will not cause the
wrong amino acid to be substituted into the protein chain.
The creation of cellular mechanisms that safeguard genetic information
involve foresight as their existence results from the anticipation of future harm unless certain actions are prepared and started.
Foresight, as said earlier, requires intelligence.
Which originated first: proteins, the genetic code, or were both set up simultaneously?
Currently, genetic information encoded in DNA is transcribed by proteins into messenger RNA (mRNA), which is then conveyed to ribosomes—complexes
composed of ribosomal proteins and ribosomal RNA—for translation into proteins with the aid of transfer RNA. The synthesis of proteins
today requires homochirality, the genetic code, DNA, RNA, pre-existing proteins, the right amino acids, and energy. For functional
protein synthesis to take place in the distant past, all the necessary components had to be present. If these components were added
gradually over billions of years as some evolutionists hypothesize, no biological proteins would form until every part was available;
thus, it is argued that all components must have come together simultaneously, suggesting intelligent design. It is also important
to note that needing existing proteins to form the first protein seems contradictory and almost impossible to explain scientifically—it
could even be considered a miracle.
What does a nearly universal genetic code for proteins across all organisms today imply?
The fact
that there is a nearly universal genetic code, with few exceptions, does not imply that all organisms have a common ancestor; that
is merely an evolutionary assumption. [57][58][59] Considering the evidence that codes come from intelligence, what should be clear
is that all organisms had a common intelligent designer who varied the code in those few cases where it was helpful.
Conclusions
The
genetic code has been proposed as evidence of an intelligent origin, based on arguments that information-bearing codes are exclusively
the product of intelligent entities. Additionally, it is suggested that the complexity of protein synthesis requires foresight, defined
as the ability to anticipate and plan for future requirements, which entails cognitive processes typically associated with intelligence.
Mechanisms such as random chance, mutation, and natural selection are regarded as lacking foresight and, therefore, considered inadequate
for independently assembling all necessary components for protein synthesis.
Effective protein synthesis mandates the simultaneous
presence of homochirality in biological chemicals, DNA, RNA, the genetic code, various proteins, appropriately matched amino acids,
biological machinery for transcription, transportation, and translation of the genetic code into proteins, protective systems against
errors, and sufficient energy sources all within a single location. The absence of any one part prevents the occurrence of protein
synthesis, challenging theories that support incremental evolutionary development over lengthy periods. Moreover, the intricate biological
mechanisms and processes involved in protein synthesis often require more than intelligence alone; they present a paradox wherein
existing proteins are needed to produce new proteins, prompting inquiry into how first protein formation could occur without significant
intervention.
Notes:
[a] The 5’ end is the end with a phosphate group and the 3’ end is the end with a hydroxyl group.
[b] The
U for T substitution in mRNA performs an important function as it aids in the breakdown of the messenger RNA after translation.
Picture:
(a) By Zephyris - Own work, CC BY-SA 3.0, via Wikipedia Commons
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[17] Ibid.
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[26] Thomas
[27] “RNA splicing,” Wikipedia, viewed on internet December 29. 2025
[28] Ibid.
[29] “What Happens to mRNA
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[30] Ibid.
[31] “The End of Translation: stop codons looking
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[32] “ribosome.” Britannica, viewed
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[33] Ibid.
[34] From information gathered by copilot.
[35] From information gathered by copilot.
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[41] “DNA Was Created as a Reservoir for the Information
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[42] Oxford American Dictionary, Heald College Edition,
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[44]
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[45] Ibid.
[46] “What is Chirality and Why Does
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[47] Sarfati, J, “Origin of life: the chirality problem,” Creation.com,
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[51] Denton,
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[54] “DNA repair”
[55] Ibid.
[56] Alhmoud,
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[57] Thomas
[58] Lisle
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