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 In  common usage, a miracle is often used to describe highly improbable events such as the “Miracle on the Hudson” when a commercial airliner safely ditched on the Hudson River and all 155 people onboard were saved, the “Miracle on Ice” when the 1980 US hockey team beat the Russians for the gold medal, survival against all odds in the wilderness, and winning the state lottery.  The source of these kinds of miracles can be attributed to skill or chance or both. There is also the possibility that God intervened in some way. In cases of the sudden disappearance of cancer tumors without treatment, the disappearance may be attributed to unknown causes or an act of God.

The Bible and Miracles

Recorded in the Bible are an abundance of miracles attributed to God.   These include events like the six days of creation, Noah’s flood, the parting of the Red Sea, the sun appearing not to move in the sky for almost a day, multiplication of food and the resurrection of the dead.[1]

Materialistic Science Versus Miracles     

Materialistic science is based on the philosophy that everything came about by natural materialistic means without supernatural agency. Materialists have speculated that the first biological cell came together spontaneously by random chance and natural selection.[2]  Then this single cell changed (evolved) into different types of plants and animals over hundreds of millions or billions of years.

Origin of Life – A Test of Miracle (Creation) Versus Materialistic Hypothesizes

All living organisms are composed of one or more biological cells that are the basic structural and functional units of life.  The simplest cell requires (1) a membrane to protect its contents from various outside contaminants while allowing the cell to receive nutrients and excrete wastes, (2) all the information for it to function and reproduce, (3) sufficient types and quantities of biological chemicals, (4) a means of transcribing and converting information and manufacturing all the required biological molecules in functional forms, (5) the ability to transport the manufactured biological molecules to where they are needed, (6) the ability to generate, store and distribute energy needed for the various processes, (7) the ability to destroy improperly constructed polymers harmful to function, (8) the ability to detect and repair critical errors, (9) the ability to dispose of wastes, and (10) the ability to reproduce.  The above list is incomplete but begins to lay out some of the obstacles that must be overcome to produce living organisms.

Many materialists have rejected the first cell as the starting point for life.  Instead, they have started with theoretical self-replicating molecules in Pre-RNA World, RNA World, DNA first, and other such schemes. A major problem with these schemes is that there is no trace of them in the fossil record and there is no way to really prove them. Experiments attempting to make self-replicating RNA have had no real success with one famous study being retracted as it contained major errors and could not be duplicated.[3] Intelligent design scientists have been quick to point out that any experiments of this nature require highly sophisticated lab equipment, strict controls, and intelligence.  So why eliminate intelligence from the equation for the formation of organic life?   Biological cells which are the building blocks of life remain the best starting points for scientifically discovering the origins of life.

Our knowledge about biological cells has greatly increased in the last 50 years and although there is still much more to learn about cells, what is currently known provides an excellent opportunity to test the miracle versus materialistic hypothesizes for the origin of life to find which best fits the facts.   

The hypothesizes can be tested using deductive logic that generally can be stated that if this is true then this must be true.  In the following table, each if hypothesis is given and the then predictions if the hypothesis is true designed accordingly.

Abiogenesis (Origin of Life) and the First Cell(s)

Hypothesizes

Predictions

 

 

Miracle

1.    There is no reasonable possibility of life arising by chance.

2.    All cells are complete and fully functional from the beginning.

3.   Intelligence will be required.

 

Materialistic

1.    All life came about by chance.

2.    The first cell formed slowly in small increments by chemicals only.

 

Natural selection has been eliminated from the materialist predictions for the origin of life. By definition, natural selection is a” process that results in the adaption of an organism to its environment by means of selectively reproducing changes in its genotype, or genetic constitution...”[4] Natural selection only works on living things.[5][6] By itself, natural selection “generates no  new information. It can eliminate genes that already exist, but never create.”[7]  

Test 1 - Biological Proteins Self-Assembly?

Biological life could not exist without proteins that perform an immense number of essential functions. Their functions include (1) being catalysts, (2) responding to stimuli, (3) providing structure, (4) DNA transcription, (4) DNA replication, (5) signaling, (6) transporting molecules from one place to another, (7) aiding in protein folding, and (8)  DNA repair to name a few.[8][9][10][11][12]  Biological proteins are composed of 20 types of amino acid residues bound together with peptide bonds in long chains.  The functionality of a protein to perform a specific task depends on the sequence of the amino acid residues in the chain that allows it to fold into a specific stable shape so that it can perform a specific function or functions. The first test is whether the amino acids have a realistic chance of self-assembling into the minimal number of functional proteins required for life.

Right Ingredients, Place and Quantities

To form proteins, the right amino acids must be close enough to react and in sufficient quantities. This creates a problem for materialists as not all biological amino acids can be formed under the same conditions.  So how could they all naturally be there in the first place?

Minimum Number and Average Size of Proteins Required for LIfe

What is the least number of protein types required for life?  No one knows for sure. T. aestivum (common wheat) may have the most with 95,000 protein coding genes.[13] Human genomes have at least 20,000 protein coding genes and the number of protein types produced may be much more due to alternative start and top locations. Viruses have the fewest number of protein coding genes (e.g. Influenza A virus with 10 -11) but according to the definition of living, they are not alive as to be alive they must be self-replicating; viruses cannot reproduce without infecting other organisms and using their DNA. The E. coli bacteria has 4,300.[14] The bacteria Carsonella Candidatus ruddii strain BT chromosome has close to the least reported so far with 199 protein coding genes per GenBank: CP024798.1 and 194 protein coding genes per another source. [15][16] Candidatus is endosymbiont with sap feeding psyllids making their true protein needs uncertain.  For the purposes of this test, a generous estimate to the materialist of 175 proteins in the simplest possible cell will be assumed.

The GenBank data for the Candidatus bacteria referenced above indicates the number of amino acid residues per protein for this strain varies from a low of 35 to a high of 1,268 with an average of 274 and a median of 232.  Proteins for human HeLa cells and E. coli have median lengths of 431 and 277 amino acid residues, respectively.[17]  For the purposes of this test, an average of 150 amino acid residues per protein for the simplest possible cell will be assumed; this provides a very generous estimate to the materialistic position.

Useful Amino Acid Residue Sequences

A miniscule number of the possible combinations of amino acid residue sequences will produce useful biological proteins. To be useful, the chain of amino acid residues must fold into stable function ready structures. Based on his experiments with 150-amino acid sequences, molecular biologist Douglas Axe estimated the probability of function ready 150-amino acid sequences to the whole possible number of combinations for 150-amino acid sequences as 1 chance in 1074. [18]

Chirality

Ordinary chemistry produces nearly equal amounts of left and right-handed chiral compounds. [19][20] All 20 types of amino acids, except glycine, used to form biological proteins are chiral and must be of the same handedness or the chain will not form.  Glycine because of its structure will not cause instability in the chain. It has much more conformational flexibility than the other amino acids and this allows it to be placed in restricted areas for other proteins in the chain such as tight bends. [21] All chiral amino acids in biological proteins are left-handed.  The probability of getting only left-handed amino acids in the chain is 50% for each position not filled by glycine. The low probability of all the amino acids, except glycine, having the same handedness creates an enormous problem for the self-assembly of biological proteins. 

Peptide Bonds

Water is a problem for protein formation whether in a primordial soup or in biological cells where it accounts “for 70% or more of the total cell mass.”[22]  Amino acids will not form the long chains required by proteins without peptide bonds and these bonds cannot be expected to be formed in water as they are more than likely to break.[23] Amino acids can make other types of bonds but the resulting molecules form useless globs.[24]

Probability Calculations

So, what are the odds of one functional protein of the assumed 150 amino acid residues forming for the simplest cell by chance?  Stephen Meyers in his 2009 book, Signature in the Cell, makes that calculation utilizing the probabilities for peptide bonds at 1/2150-1 which is approximately 1/1045, same handedness at 1/2150 (the nonhandedness of glycine is possibly neglected for simplicity) which is also approximately 1/1045, and functional proteins with 150 amino acid residues by Axe of 1/1074.  He calculates the odds at no better than 1 chance in 1045x1045x1074which equals 1 chance in 10164.[25] There is an extremely small probability of just one functional

protein of 150 amino residues self-assembling, however,175 are needed.

The chance of producing the assumed 175 functional proteins of 150 amino acids long is 1/10164 times itself 175 times which is 1 in 1028,700. The chance of just forming these 175 proteins are extremely close to impossible even with billions of years to accomplish it. Also, proteins have a relatively short mean lifetime before they degrade, therefore, it is necessary to constantly repair or replace them. With the chance scenario time is not on its side as the longer the time, the more times the proteins need to be reformed. The chance self-assembly of two complete sets of 175 proteins is 1/1028,700 times itself which equals 1 in 10 57,400 (i.e. 1 chance in 1 followed by 57,400 zeros).

These large numbers need to be put in perspective. The makers of the film Origin attempted that with very generous estimates for the materialists. They first estimated the amount of the various elements available to make amino acids on the earth and in its atmosphere.  Then they calculated the number of 150-amino-acid chain sets with 20 different amino acids available per position that could be formed at 1041.  “We then calculated the self-assembly rate of 150-amino-acid chains at one chain per second. In the assumed 4.6-billion-year age of the earth, we could expect the construction of at least 1.45 x 1058 chains. That is far short of the 10164 chains that would have to self-assemble (on average) to expect one useful protein.”[26] 

Chance fails.  As the first proteins did not self-assemble by chance, how then were they assembled?

Test 2 - Prebiotic Soup and Cell Membrane

In the past, materialists have promoted the idea that life may have evolved in a warm pond of prebiotic soup as proposed by Darwin and others.  Today, this idea has generally been discarded in the scientific community. First, there is no evidence in the oldest rocks on earth of the existence of a prebiotic soup. Second, the oldest rocks indicate an oxidizing atmosphere that would quickly destroy the molecules (proteins, DNA, RNA) required for life. This means biological life could not have developed outside some protective environment.    

To provide the necessary protection, materialists have more recently speculated on bubbles, lipid membranes, and underwater hydrothermal vents.  Bubbles and lipid membranes are unsatisfactory because they do not provide pathways for needed materials to enter or wastes to be excreted. Underwater hydrothermal vents fail for a number of reasons including “the presence of water, which prevents” many needed reactions (e.g. polymer formation) and “the heat in deep sea vents would speed up the breakdown of any lucky chemical formation.”[27] With these speculative ideas eliminated, this leaves materialists with a conundrum:  the types of protective membranes found on all types of biological cells today.

 

 

 

 

 

 

 

 

 

 

The protective membrane of a cell is itself quite complex and is made up of “different lipid chains combined with phosphates” and also contains a “wide variety of proteins and carbohydrate molecules for signaling and the import of a wide variety of compounds for cell function and metabolism.”[28] How could such a cell membrane have been formed?  The cell membrane and the cell contents provide a catch - 22 scenario.  For the membrane is required to protect the cells contents that will quickly be destroyed without it and the membrane is formed by its extremely complex contents (DNA, RNA, proteins, biological machines, energy ATP).  One cannot exist without the other.  All had to be there at the same time in the beginning – a prediction of the miracle hypothesis.  

Test 3 - Biological Protein Assembly Process

All biological cells have DNA molecules containing all the information necessary for the cell to function and reproduce.  DNA, except during replication, is in a double stranded helix with nucleotides paired in rungs like a ladder.  Each nucleotide includes (1) one of four nitrogenous bases that scientists have designated by the letters C,G, A and T that are paired in the “rungs” with C to G only and A to T only, (2) a sugar called deoxyribose and (3) a phosphate group. A sequence of nucleotides that encode for a protein or an RNA is called a gene.  Protein coding genes are made up of a series of many codons. Each codon consists of a series of three nucleotides (e.g. CTA, GAT, CGA, etc.) that specify (code for) one of the twenty types of amino acids used to build a protein.  As protein chains generally vary from about 50 up to 1000s of amino acid residues, the number of codons for these chains will vary accordingly.

The DNA is transcribed by RNA polymerase (RNAP) that is a mechanically complex nano-machine formed from many proteins. The RNAP surrounds the segment of the DNA to be transcribed and proceeds quickly along the DNA unwinding the strands and copying the DNA sequence into RNA. The RNAP also corrects errors in the DNA while proceeding. DNA molecules are very fragile. Gyrase, a protein enzyme, proceeds in front of the RNAP to reduce topological strain while the DNA is being unwound.   

After the RNA sequence of amino acid residues for a specific protein is transcribed, it is known as a messenger RNA (mRNA) or pre-messenger RNA (pmRNA).  If it is a pmRNA, a spliceosome is assembled to cut out any introns present. Introns are noncoding regions in the RNA transcript or DNA that encodes it; they allow alternative splicing of genes and regulating of gene expression.  Spliceosomes are large molecular machines composed of nuclear RNAs and about 80 proteins.[29] After the introns are removed, the pmRNA becomes a mRNA.

The mRNA is then taken to a ribosome, a complex macromolecular machine for translation to a protein.  Ribosomes are composed of ribosomal RNA (rRNA) and a variety of ribosomal proteins.  During translation, transfer RNA (tRNA) select the specified amino acids, convey them to the ribosome and place them in the sequence coded into the mRNA. The completed amino acid residue sequence for the protein is functionally useless or harmful unless it is properly folded into the right shape.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Proteins will usually fold automatically to the right shape but they are very unstable. Chaperones watch over the proteins, help correct any misfolding and transport them. Also, proteins may be transported to a complex macromolecular machine called a chaperonin, a type of chaperone, where there are favorable conditions to facilitate correct folding.  Chaperones are proteins that are coded in the DNA.

Here again there is a conundrum: the first biologically functional proteins cannot be made from the information in the DNA without functional proteins that already exist and are coded in the DNA including but not limited to the proteins in RNA polymerase, gyrase, spliceosomes if introns are present, and ribosomes. Small incremental steps as required by evolution do not work.  The process of producing the first functional biological proteins from the information in the DNA is irreducibly complex – a miracle.

Test 4 - DNA for Proteins Formed by Chance?

DNA contains far more information than protein coding genes as will be discussed in Test 5.  As in Test 1, the probability calculations will be for a minimally complex cell with 175 functional proteins of 150 amino acid residues.

Genetic Code

In DNA, each amino acid is specified in the genetic code by three nucleotides with each nucleotide as previous stated having one of four nucleobases C, G, A, or T. The number of nucleotides to specify a modest length protein of 150 amino acid residues is 150 times 3 or 450 all in proper sequence. (An insertion of an extra nucleotide or deletion of a nucleotide will cause a misreading of all the nucleotides that follow in that gene. All twenty biological proteins, except Methionine, are coded from two to six multiple ways reducing the probability of errors.)

Useful Amino Acid Residue Sequences

Working with DNA does not change Axe’s estimated ratio of function ready 150 amino acid residue sequences to the whole possible number of combinations for 150 amino acid residue sequences. That remains as 1 chance in 1074.[30] 

Chirality

Chirality (handedness) remains a major problem as DNA formation requires 100% of the nucleotides to be the same handedness.  All nucleotides are right-handed. The problem is multiplied as each amino acid has a codon (three nucleotides) required to specify it.  For 150 amino acids, the probability of single handedness is 1 chance in 2 150x3 or approximately 1 chance in10135.

Bonding

DNA (like RNA) nucleotides are joined in a chain by a covalent bond between the sugar of one nucleotide to the phosphate of the next nucleotide. These complex bonds pose a problem for DNA and RNA polymerization.  Assuming the probability of each of these bonds forming as 50%, then for 150 times 3 nucleotides, the probability is one chance in 2450+1 or approximately 1 chance in 10135.

Probability Calculations

Usingthe probabilities for functional proteins, same handedness, and covalent bonds, the estimated chance of DNA specifying one functional protein of 150 amino acid residues is no better than 1 chance in 1074x10135x10135 equaling 1 chance in 10344.  The chance of specifying 175 different proteins of 150 amino acid residues is 1 in 10344 times itself 175 times or 1 in 1060,200.  The chance of DNA specifying these 175 different proteins are extremely close to impossible even with billions of years to accomplish it. So, if not chance then what is the source of the first cell?

Test 5 – Intelligence

Junk DNA?

Materialists based on one theory of evolution had estimated that 95% of the human genome was nonfunctional junk.[31]  The Human Genome Project (HGP), an international research project, with the goal of mapping and understanding all the genes in the human DNA was started in 1990 and completed in 2003. It found that of the over 3 billion base pairs in the human genome only about 2% coded for proteins.  But what about rest of the genome?

 In 2007, ENCODE, Encyclopedia of DNA Elements, a public research project was commenced with the goal of identifying all functional elements in the human genome.  In 2012, the ENCODE project scientists reported that “(t)he vast majority (80.4%) of the human genome participates in at least one biochemical RNA and/or chromatin associated event in at least one cell type.”[32] (There is no reason to assume that the remaining 19.6% does not have functions under certain circumstances or at different stages of human development.) “What we learned from ENCODE is how complicated the human genome is, and the incredible choreography that is going on with the immense number of switches that are choreographing how genes are used.” Eric Green, director of the National Human Genome Research Institute (NHGRI).[33]  

Complex Information System

“DNA is by far the most compact information storage  system in the universe.”[34] All living organisms whether single or multi-celled have DNA that provides the information needed for life. The coded information in the DNA provides instructions for making every component of the cell including membranes, portals, transport structures, machines for all kinds of functions (e.g. energy production, transcription, transportation, translation, protection, repair, demolition, waste disposal, reproduction) and instructions specifying when and how much of a molecule is produced (e.g. proteins, RNA) and restricting variations in certain critical genes to name a few.  DNA amounts to a super complex   program required for life that is orders of magnitudes more complicated than any computer program today.   Computer programs do not just happen but are programmed by intelligent individuals. In like manner, it is therefore logical that DNA was programmed by a super intelligent supernatural being.   

Conclusions

Origin of life speculations starting with molecules coming together and making nonliving cells that somehow self-replicate and get incrementally more complicated over time until they become alive are fruitless as they depend on chance and natural selection.  The probability of the first living cell forming by chance is extremely close to impossible and natural selection works only on living things.   

All the predictions of the miracle hypothesis are demonstrated to be true, as follows:

1.    There is no reasonable probability of life arising by chance. (Tests 1 and 4 together verify this is true)

2.    All cells are complete and fully functional from the beginning. (Tests 2 and 3 verify this is true)

3.    Intelligence will be required. (Test 5 verifies this is true)

All the predictions of the materialist hypothesis are demonstrated to be false, as follows:

1.    All life came about by chance. (Tests 1 and 4 together prove this is false)

2.    The first cell formed slowly in small increments by chemicals only. (Tests 2 and 3 prove this is false)

These results confirm the “Law of Biogenesis: Life comes only from life.”[35]  

 

_______________________

[1] Genesis 1:1-27, Genesis 7, Exodus 14:21, Joshua 10:13, Matthew 4:13-21, John 11:43-44

[2] Peacock, Richard, The Probability of Life, evolution, frequently asked questions, viewed January 11, 2020,  evolutionfaq.com/articles/probability-life

[3] Tomkins, Jeffrey, ‘RNA World’ Paper Retracted, January 15, 2018, Institute for Creation Research, icr.org/article/rna-world-paper-retracted

[4]Natural selection, Encyclopedia Britannica, January 3, 2020, britannica.com/science/natural-selection

[5] Origin, Unlocking the Mystery of Life, DVD, Illustra Media

[6] Catchpoole, David, Sarfati, Jonathan, Batten, Don, Natural selection cannot explain the origin of life, Creation, November 12, 2009, creation.com/ns-origin-of-life

[7] Catchpoole, David, Isn’t it obvious? Natural selection can eliminate, but never create!”, Creation Magazine 39(1):38-41, January 2017

[8] Protein, Wikipedia, en.wikipedia.org/wiki/Protein

[9] Protein folding, Wikiipedia, en.wikipedia.org/wiki/Protein_folding

[10] RNA polymerase, Wikipedia, en.wikipedia.org/wiki/RNA_polymerse

[11] RNA polymerase, PDB-101,pdb101.rcsb.org/motm/40

[12] Membrane protein, Wikipedia, en.wikipedia.org/wiki/Membrane_protein 

[13] How Many Genes are in a Genome? book. bionumbers.org/how-many-genes-are-in-a-genome/

[14] Ibid.

[15] Genome sequence of “Candidatus Carsonella rudii” strain BT,GenBank: CP024798.1

[16] Katsir L, Zhepu R, Piasezky, Jiang J, Sela N, Freilich S, Bahar O. 2018.Genome sequence of “Candidatus Carsonella rudii” strain BT from the psyllid Bactericera trigonica. doi.org/10.1128/genomeA.01466-17

[17] Cell Biology by the Numbers, How Big is the “Average” Protein? book.bionumbers.org/how-big-is-the-average-protein/

[18] Meyer, Stephen C., Signature in the Cell,(New York: HarperCollins Publishers, 2009), 210

[19] Sarfati, Jonathan, Origin of life: the chirality problem, Journal of Creation (formerly TJ) 12(3):263-266, (first published December 1998; updated in 2010)

[20] Batton, Don, Origin of Life: An Explanation of what is needed for abiogenesis (or biopoiesis), last amended July 3, 2019, creation.com/origin-of-life

[21] Betts, M.J., Russell, R.B.,Amino acid properties and consequences of substitutions. In Bioinformatics for Geneticists, Barnes, M.R., Gray, I.C.eds. (Wiley, 2003)

[22] Cooper, G. M.,The Molecular Composition of Cells,  ncbi.nlm.nih.gov/books/NBK9879/

[23] The Mathematics of Origin, Mathematical Basis for Probability Calculations Used in Origin, Illustra Media, viewed January 2, 2020, originthefilm.com/mathematics.php)

[24] Ibid.

[25] Meyer, 212

[26] Ibid. The Mathematics of Origin

[27] Batton, Ibid

[28] Morris III, Henry, Tomkins, Jeffrey, et al., Creation Basics & Beyond, (Dallas, Texas: Institute of Creation Research, 2013), 191

[29] Spliceosome, Wikipedia, viewed January 13, 2020,en.wikipedia.org/wiki/Spliceosome

[30] Meyer, 210

[31] Tomkins, Jeffrey, 95% of Human Genome Can't Evolve, October 25, 2018, Institute for Creation Research, icr.org/article/ninety-five-percent-of-human-genome-cant-evolve

[32] ENCODE, Wikipedia, viewed January 9, 2020,en.wikipedia.org/wiki/ENCODE

[33] Park, Alice, Junk DNA-Not So Useless After All, Time.com, September 6, 2012, healthland.time.com/2012/09/06/junk-dna-not-so-useless-after-all/

[34] Sarfati, Jonathan, DNA: marvelous messages or mostly mess? Creation 25(2):26-31, March 2003

[35] Dewitt, David A, The Origin of Life: A Problem for Evolution, undated, creation.com/the-origin-of-life-a-problem-for-evolution

Cell Membrane
DNA
Blausen.com staff (2014)
Ribosome
Newly born protein
Amino acids
Small subunit
mRNA
Large subunit
tRNA
Protein Myoglobin 
(a representation of its 3-D structure)