Bioinformatics-Understanding DNA

Lessons from Bioinformatics and Functional Genomics, 3rd ed. Johnathan Pevsner (Wiley, 2015)

CharlesDarwin knew nothing of information science, nothing of cellular biology, nothing of molecular genetics and molecular biology, and nothing of the physics and chemistry required to understand biochemistry. Darwin’s knowledge of anatomy and physiology is suspect since he was a medical school dropout. Yet Darwin presented a theory for the creation of life based on the shape, or morphology, of species. What Darwin did not know, and could not know, is that biology is DNA, and DNA is information. That sounds simple enough, yet DNA is so historically complex that even an elementary understanding of the amount and nature of information stored in DNA requires the use of computer databases and the new sciences of bioinformatics and genomics. This article is divided into four sections: I Definitions and Introduction of Bioinformatics and Genomics, II Brief Synopsis of Molecular Genetics, III Nature of Mutations, and IV Conclusion.

I Definitions and Introduction of Bioinformatics and Genomics

Defining bioinformatics and genomics is not a simple task. (Simplistically, bioinformatics is the sequencing of DNA nucleotide by nucleotide, and genomics refers to ultimate gene function.) The experts, of course, have more precise and useful definitions. There are three useful definitions of bioinformatics. First, according to the National Institutes of Health, bioinformatics is “research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral, or health data, including those to acquire, store, organize, analyze, or visualize such data.”[1]Second, computational bioinformatics is defined as, “the development and application of data-analytical and theoretical methods, mathematical modeling, and computational simulation techniques to the study of biological, behavioral and social systems.”[2]And third from the National Human Genome Research Institute, “Bioinformatics is the branch of biology that is concerned with the acquisition storage, display, and analysis of the information found in nucleic acid and protein sequence data.”[3]

Similarly, genomics is a complex science. A genome is the collection of DNA that comprises an organism. According to Pevsner, “Functional genomics is the genome-wide study of the function of DNA (including genes and nongenic elements) as well as the nucleic acid and protein products encoded by DNA.”[4]These definitions illustrate the informational nature of biology that manifests as anatomy and physiology.

In 1958 Francis Crick formulated the central dogma of molecular biology that states biological information travels in one direction—DNA is transcribed into RNA then translated into protein. Information cannot travel backwards from protein to RNA to DNA.[5]Genomics has been characterized in several ways but the most important of these is from a functional perspective in which, “the most challenging and fundamental problem in modern biology is to understand the relationship between genotype and phenotype.”[6](Genotype is the genetic constitution of an organism, and phenotype is an organism’s physical appearance, i.e. anatomy and physiology.)[7]And it is here that Darwin’s theory of evolution by the natural selection of random mutations fails. Remember, Darwin based his theory on nothing more than the morphology—shape—of species.

II Brief Synopsis of Molecular Genetics

Knowing the sequence of a genome is incredibly complex but that is not enough. Understanding what information, the genome possesses is what we know as biology. Transferring information from genotype to phenotype occurs through the creation of amino acids which are linearly sequenced in a physicochemical manner that produces specific three-dimensional structures. This three-dimensional structure determines a proteins capacity to function. Countless proteins are the molecular machines that create the anatomy and function as the physiology of the human body.

Protein structure is defined at several levels. Primary structure is the linear sequence of amino acids that produce a polypeptide chain. Secondary structure is the arrangement of primary amino acids into motifs such as helices, sheets, coils or loops. Tertiary structure is the three-dimensional arrangement created by packing secondary structure elements into globular domains. And lastly, quaternary structure is the arrangement of tertiary structures into more functionally complex molecular machinery.[8]But complexity creates its own problem and possesses an inherent disadvantage. One question that relates to DNA’s extreme complexity is, how much mutation can the extraordinarily complex DNA tolerate and not lose function or cause disease? Kimura notes that, “the rate of amino acid substitution averages approximately one change per 28 X 106 years for proteins of 100 residues,”[9]and that “most observed DNA substitutions must be neutral or nearly neutral.”[10]

Another problem for Darwinists, besides mutation tolerance, is the availability of time. The numbers provided by Kimura do not support the time available for one species to mutate into another, or improve a species as highly complex as a human.

III Nature of Mutations

Evolutionary biologists try their best to apply Darwin’s simplistic theory, created well before any knowledge of molecular biology or DNA existed, to the structure of DNA. But their attempts fail. Evolutionary biologists inappropriately use homology, or similarity, as a cause and effect. Pevsner quotes Margaret Dayhoff who applies current knowledge of biology to Darwinism, “An accepted point mutation in a protein is a replacement of one amino acid by another; accepted by natural selection. . . To be accepted, the new amino acid usually must function in a way similar to the old one . . .”[11]Dayhoff is correct in locating the site of random mutations to amino acids or nucleotides which produce amino acids. Interestingly she requires that the new amino acid must function in a way similar to the amino acid which is being replaced. But the more similar amino acids are, the less change occurs in the organism and the longer it takes for organisms to evolve. (For a discussion of how little time actually exists for evolution of human beings to occur, please see my discussion of the Mitochondrial Eve Unit found in The Collapse of Darwinism, page 29.) Knowing that changes are slowed due to the requirement of mutated amino acids functioning similarly to the replaced amino acids, makes a mutation rate of 2.8 X 107 years for proteins of 100 residues wholly incompatible with Darwin’s theory.

Further complicating the situation forDarwinists is the inconvenient reality that mutations are either negative, neutral or beneficial. In his final chapter, Pevsner describes DNA variation and disease, “Mutations affect all parts of the human genome. There are limitless opportunities for maladaptive mutations to occur, and there are many mechanisms by which mutations can cause disease.”[12]Pevsner discusses several data bases for bioinformatics and genomics that relate mutations to disease. The Human Genome Mutation Database (HGMD) project lists approximately 115,000 mutation entries for public release and 164,000 entries for commercial release. (Search of the database as of 11/15/2018 reveals the numbers have increased to 157,114 and 240,269 respectively.)[13]The OMIM database contains entries for over 22,000 human diseases and relevant genes.[14]What is not stated, and is profoundly significant, is the fact that there is no database with even one entry containing a mutation that leads to a beneficial change in phenotype. Pevsner provides even more evidence that defeats Darwin’s theory, “While the genetic basis of over a thousand single-gene disorders has been found, it is far more difficult to identify the genetic causes of common human diseases that involve multiple genes. Part of the challenge is that a large number of genes may each make only small contribution to the disease risk.”[15]

IV Conclusion

            In summary, the concept that the astronomically complex anatomy and physiology of human beings is created by the natural selection of random mutations defies logic and requires the reader to suspend reason. The fact that Darwin knew nothing of DNA, molecular biology, biochemistry and information science relegates his 1800’s theory of evolution to the dust bin of archaic scientific theories along with spontaneous generation and the geocentric theory of our solar system.

            Kimura tells us that amino acid substitutions averages one change every 2.8 million years for proteins of 100 residues. However, we know that the Cambrian explosion occurred 540 million years ago. Applying simple math tells us that only 192.8 amino acid substitutions may have occurred from the time aquatic creatures swam in the earth’s ancient oceans until humans began to walk on land. Logic tells us that amino acid substitutions cannot be a mechanism for Darwinian evolution.

            The human genome contains approximately 3 billion base pairs. It is amazing that this huge human genome has been sequenced. But knowing the sequence is not the same as knowing how every base pair functions. Pevsner makes us aware of the numerous databases and research that are attempting to discover how DNA produces three-dimensional proteins which function as machines. He makes it very clear there is much work to be done. Pevsner describes the many databases of hundreds-of-thousands of mutations, and thousands of diseases that result from mutations. It is enlightening that no author, scientist, professor or Nobel Laureate can identify one nucleotide mutation that caused an improved phenotype manifesting as improved anatomy and physiology.

            Bioinformatics and functional genomics demonstrate that DNA is astronomically complex and mutations are neutral or harmful. To date, the scientific evidence proves that evolution by the natural selection of random mutations cannot be the mechanism by which humans were created.

[1]Jonathan Pevsner, Bioinformatics andFunctional Genomics, 3rd ed. (Sussex: Wiley, 2015), 3.


[3] Id.

[4] Id., 635.

[5] Id., 433.

[6] Id., 636.

[7] Id., 1087.

[8] Id., 591.

[9] Id., 258.

[10] Id.

[11] Id., 69. Pevsner quoting Margaret Dayhoff (1978, p. 345).

[12] Id., 1012.

[13]Human Genome Mutation Database, Accessed on 11/15/2018.

[14] Id., 1036.

[15] Id., 1047.

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