Created: September 9, 2015
Revised:Synopsis Sept 2017  

The Creation Narrative of Science and the Bible
 

Dr. David C. Bossard

Dr. David C. Bossard
Biographical Information

The Central Dogma of Molecular BiologyM.40
The Common genetic processing used by every living cell

The Central Dogma of molecular biology is the machinery that exists in every living cell. Its function is to transcribe digital genetic content contained in DNA to form proteins, which build all of the specialized molecules that carry out a cell's metabolism. The most remarkable fact is that the basic operations of the Central Dogma are virtually the same for every species, from the simplest microbe to humansM.41.

The first surprise is that all of life, every living species, uses digital coding to specify everything that defines and is characteristic of that physical species. It involves many complex innovations that, as far as is known, must all work together before anything can be called "living". The following table is a partial list of the necessary innovations.

It is estimated that every living cell, however simple, requires the DNA to include at least 150 genes requiring 250,000 base pairs to set up and implement the central dogma, in addition to whatever genes are needed to do the regular cell functions.M.42  In my view, given the size of this DNA molecule and the list of specialized molecules just to carry out the Central Dogma, it is utterly incredible to assert that this all came about by undirected natural processes.

COMPONENTS OF THE CENTRAL DOGMA

Innovation

Function


Adenosine tri-phosphate (ATP)


The universal "battery" storage to power most cell metabolism in every known living species. In particular it powers the Central Dogma. Not known to occur naturally.


ATP Synthase and ATPase
See Box on Photosynthesis


ATP Synthase is a proton motor molecule which adds a 3rd phosphate to ADP to form ATP. ATpase performs the opposite function, releasing energy. These processes are "widely used in all known forms of life." "Essentially the same structure and activity of ATP synthase enzymes are present in all kingdoms of life."M.43

DNA

The repository of a cell's genetic coding, the genes. A spiral ladder structure in which the rungs are nucleotides.


Nucleotides: A (adenine), C (cytosine), G (guanine), and T (thymine)M.44
The "rungs" (= base pairs (bp)) in DNA consisting of pairs A-T and G-C. Codons are three nucleotide pairs that specify for a particular amino acid (or "start" and "stop" markers) in gene transcription.

Genes (250 to thousands, depending on species complexity)

Specify for proteins or RNA regulatory  molecules. Average gene size about 1000 bp.


DNA Polymerase

Duplicates the DNA molecule. Essential for cell reproduction. This is the most basic (but only one of many) step in the remarkable ability of all living species to "reproduce after its kind".


RNA transcription factor
RNA Polymerase (RNAP)


Factors bind to DNA and Polymerases transcribe  genes to form messenger RNA (mRNA) for a particular gene. Found in all living species. Factors control gene expression by the RNAP.


Amino Acids: 21 varieties

All proteins are chains of left-handed amino acids. A few of the simpler ones have been observed in outer space, probably formed by random assembly.


Ribosomes
"The smartest living nanomachine"

A complex (2-part) molecular motor that removes amino acids from tRNA to build protein chains from mRNA. Ribosome biogenesis involves the coordinated function of over 200 proteins and ribosomal RNA (rRNA) in its synthesis. This is true for all species, however simple or complex. The ribosomes include a built-in error correction mechanism to reduce errors.M.45

Transfer RNA (tRNA)


Each codon triplet requires its own t-shaped tRNA molecule that associates a codon triplet at one end to a particular amino acid attached to the opposite end. The complete set of tRNAs defines the "codon table", which is essentially the same for all species of life. Every species manufactures its own tRNA taking about 150-250 genes to specify the codon table (506 tRNA genes in humans and 36 in Mycoplasma genitalium).


Chaperone Proteins

Form a mature protein by folding and/or modifying the amino acid chain. Many proteins require a specially-designed chaperone. This is the subject area of the Levinthal Paradox (below).


Cellular Proof-reading

Error-checking of all molecular reproduction. This is the subject of the Eigen Paradox (below)M.46.

Notes to table

Is this molecule known to exist in inorganic form (e.g. found in outer space (Y or N)? Is there a known way to build this molecule using natural processes (a plausible natural scheme done outside of a laboratory) (Y or N)?


* A few of the simpler amino acids have been observed in outer space.


[*fn]M.40 The word "dogma" was originally used as an ironic epithet by Francis Crick in 1956. See his article, Central Dogma of Molecular Biology (1970 - PDF). As used conventionally, there is a narrow and a broad meaning to "central dogma." The narrow meaning is just the claim that DNA->RNA->proteins (but not the reverse). Here we use the broad meaning—the full panoply of machinery that produces proteins from DNA.

 [*fn]M.41 This fact is unexpected because many aspects of the central dogma appear to be contingent, that is, they appear to be somewhat arbitrary features that could easily have been quite different: such things as the exclusive use of  left-handed amino acids, the specific associations of cordons to particular amino acids, etc. This universal use of the same contingencies in all species leads to the (reasonable) conclusion that the scheme was "invented" only once—it is exceedingly improbable that the same scheme could have arisen by happenstance more than once.


[*fn]M.42 See Size Limits above.The DNA for even the smallest microorganism requires over a half-million C and a million N atoms, and this doesn't take into account any of the molecules required to build and carry out the cell's purpose. Almost all C and N used in a living cell have to have been fixed by specific (and slow!) molecular machines either by the cell itself or found in its food and produced by another living cell at some time in  the past. Very few bacterial species can generate their own N, and these species are unable to carry on the full range of cell functions, because of the extreme sensitivity to the presence of Oxygen.

[*fn]M.43 The quotes are from Wikipedia articles on ATPase and  ATP Synthase.

[*fn]M.44 In 2011 NASA suggested that meteorites may have A and G formed in outer space.

[*fn]M.45 See The Smartest Living Nanomachine, (pdf), Los Alamos Science and Technology Magazine, August 2008.

[*fn]M.46 Wikipedia, Error Threshold calls this "one of the most intractable puzzles in the study of the origins of life." The paradox is this: "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."

M.47 [*fn]M.47 Note for M.47

M.48 [*fn]M.48 Note for M.48

M.49 [*fn]M.49 Note for M.49



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