From the First Functional Cells to the Cells of Common Ancestry

K Production
4 days ago
7 min read

Updated: 10 hours ago

The first cells have divided and are in competition. Natural selection selects the winners and the losers. Chemical evolution has come to an end. It is here that Ernst Mayr’s definition comes into play:

Evolution is best understood as the genetic turnover of the individuals of every population from generation to generation.1

The population is all the cells of the First Cell Species. Each cell represented one of the individuals of this population. These cells replicated, lived, and died. The genome of the First Cell Species coded for somewhere between 151 to 387 functional protein-coding genes.2 Some of these genes mutated and caused a genetic turnover in the population.

Immortality

The First Cells Species mutated into the Cells of Common Ancestry Species. The genome of this second species contained about 500 genes, which are called immortal because they are found in all three biological domains: Prokaryotes, archaebacteria, and eukaryotes.3 Immortal genes code for the enzymes involved in metabolism and reproduction.

A minimal genome of 151 genes would need to generate 349 genes to reach the 500 genes of the cells of common ancestry. A minimal bacterial genome of 387 genes would have to generate 113 genes to do the same. Also, genes would have to increase in size to code for proteins and enzymes that averaged 300 to 400 amino acid residuals.4

Experiment Number Two

The question for the second thought experiment is as follows:

What is the maximum overall probability for the first functional cells to evolve into the cells of common ancestry within an unplanned evolution?

The thought experiment will generate one number─the maximum overall probability.

The maximum overall probability will be used to answer the second question:

Does an unplanned evolution have the potential to generate 113 to 349 new genes for the cells of common ancestry?

Potential

The potential within an unplanned evolution equals the total number of heritable genetic mutations that can be generated.

This last sentence is the key element in validating the hypothesis. Therefore, the sentence bares repeating: The potential within an unplanned evolution equals the total number of heritable genetic mutations that can be generated.

The number of heritable genetic mutations can be calculated by finding:

◦ The number of organisms generated per year,

◦ The number of years available for evolution, and

◦ The mutation rate per organism.

Population

Assume that the first functional cells replicated at the same rate as bacteria do today. With this assumption, the first functional cells produced 1.7x10³⁰ new cells each year.5

Time

The first functional cells evolved into the cells of common ancestry within three billion years. However, three billion years will be given for this evolutionary event.

Mutation Rate

Assume that the first functional cells had a mutation rate of less than one mutation per replication. This mutation rate is up to 5,000 times greater than the mutation rate of bacteria today.6

Running The Second Experiment

With 1.7x10³⁰ new cells replicated each year for a period of three billion years, the total population existent over the three billion years would have been fewer than 10⁴⁰ organisms.7

With fewer than 10⁴⁰ organisms having less than one genetic mutation per replication, the total evolutionary potential contributed by all cells over three billion years would be fewer than 10⁴⁰ heritable genetic mutations.8

Overall Probability

The probability of generating a new gene coding for an enzyme is equal to the probability of generating the enzyme. Thus, the probability of generating a gene coding for a cytochrome c enzyme is the same probability as generating the enzyme, which is 2 chances in 10⁶⁵ tries.9

The overall probability of generating a cytochrome c gene with fewer than 10⁴⁰genetic mutations is less than two chances in 10²⁵ or less than one chance in 5 trillion trillion.10

Drum Roll

Again, the gene for cytochrome c is only a representative of the 113 to 349 new genes found in the cells of common ancestry. The genes within these cells coded for structural proteins and enzymes averaging 300 to 400 amino acid residuals. The likelihood of generating any gene coding for an enzyme of 101 amino acid residuals would be less than one chance in 5 trillion trillion. While the generation of smaller genes would be more likely, average-sized genes would be far less likely.

Therefore, the second question can be answered:

Does an unplanned evolution have the potential to generate 113 to 349 genes for the cells of common ancestry?

Again, the conclusion is negative.

With fewer than 10⁴⁰ heritable genetic mutations, the evolution of the first functional cells into the cells of common ancestry could not happen within an unplanned evolution.

Nature used all the evolutionary potential present in all organisms existent over three billion years and came up empty handed. Thus, an unplanned evolution does not have the potential to generate the genes required to evolve the first functional cells into the cells of common ancestry.

Pulling Back The Curtain

By the time the cells of common ancestry came into existence, the genome contained all immortal genes, including the genes coding for the enzymes of the citric acid cycle.

The citric acid cycle is made up of discrete metabolic steps, each requiring a complex enzyme. The following is an ordered list of each component of the enzymes and the number of amino acid residuals in each component:

1. Pyruvate dehydrogenase complex is composed of E1 component subunit alpha with 390 amino acid residuals,11 E1 component subunit beta with 359 amino acid residuals,12 E2 with 647 amino acid residuals,13 and E3 with 509 amino acid residuals. The pyruvate dehydrogenase complex contains a total of 1,905 amino acid residuals.

2. Citrate synthetase is composed of 466 amino acid residuals.14

3. Aconitate hydrolase is composed of 780 amino acid residuals.15

4. Isocitrate dehydrogenase is composed of 452 amino acid residuals.16

5. 2-oxoglutarate dehydrogenase is composed of 1,023 amino acid residuals.17

6. Succinate-CoA ligase subunit alpha contains 333 amino acid residuals,18 and Succinate-CoA ligase subunit beta contains 432 amino acid residuals.19 The succinate-CoA complex contains a total of 765 amino acid residuals.

7. Succinate dehydrogenase is composed of several subunits, the flavoprotein subunit contains 664 amino acid residuals,20, the iron-sulphur subunit contains 280 amino acid residuals,21, and the cytochrome b small subunit contains 159 amino acid residuals.22 The succinate dehydrogenase complex contains a total of 1,103 amino acid residuals.

8. Fumarate hydratase is composed of 510 amino acid residuals.23

9. Malate dehydrogenase is composed of 338 amino acid residuals.24

10. Pyruvate carboxylase is composed of 1,178 amino acid residuals.25

An unplanned evolution that does not have the potential to generate the representative enzyme, cytochrome c, does not have the potential to generate the enzymes for the citric acid cycle.

“The Chicken or The Egg” Conundrum

In the citric acid cycle, the enzyme, aconitate hydrolase, reversibly isomerizes citrate to isocitrate. This reaction provides no immediate benefit to the cell. The enzyme, isocitrate dehydrogenase, oxidizes isocitrate plus NAD+ to α-ketoglutarate plus NADH plus H+. The generation of NADH is equivalent to 2.5 molecules of ATP, the “gasoline” of the cell. Only the second step is immediately beneficial and would be selected for by natural selection.

Aconitate hydrolase provides no immediate benefit to the cell and would not be selected for unless isocitrate dehydrogenase was present to metabolize isocitrate. However, isocitrate dehydrogenase provides no immediate benefit to the cell unless aconitate hydrolase is present to generate isocitrate. Therefore, in the evolutionary scheme, which came first, the enzyme, aconitate hydrolase, or the enzyme, isocitrate dehydrogenase?

A second conundrum occurs between the enzymes fumarate hydratase and malate dehydrogenase. Fumarate hydratase combines fumarate with H₂O to form L-malate. The enzyme, malate dehydrogenase, combines L-malate plus NAD+ to form oxaloacetate plus NADH plus H+. Again, NADH is equivalent to 2.5 molecules of ATP, which is a selective benefit in natural selection.

If the enzyme, fumarate hydratase, is not present to form L-malate, no selective pressure exists to generate malate dehydrogenase. If the enzyme, malate dehydrogenase, is not present, no selective pressure exists to select fumarate hydratase. Which enzyme came first, fumarate hydratase or malate dehydrogenase?

The probability of the simultaneous unplanned generation of two successive metabolic enzymes or their genes approaches zero.

An unplanned Darwinian Evolution has a vast deficit, by many orders of magnitude, of DNA mutations to search sequence space.

Since an unplanned evolution does not have the potential to generate the cells of common ancestry from the first functional cells, a planner and a plan were required. Evolution did not give rise to the planner.

Endnotes

1. E. Mayr, What Evolution Is, (New York: Basic Books, 2001), 76.

2. J. Glass, et. al., “Essential genes of a minimal bacterium,” Proceedings of the National Academy of Sciences, 103, no. 2, (January 10, 2006), 429.

A. Forster & G. Church, “Towards synthesis of a minimal cell,” Molecular Systems Biology, (2006), 3. doi:10.1038/msb4100090.

3. S. Carroll, The Making of the Fittest, New York: W.W. Norton & Co., 2006), 79.

4. Ibid, 74.

5. W. Whitman, D. Coleman, and W. Wiebe, “Prokaryotes: The unseen majority,” Proc. Nat. Acad. Sci., 95, June 1998, Table 7, 6581.

6. Ibid, 6582: “Assuming a prokaryotic mutation rate of 4 x 10^-7 mutations per gene per DNA replication, ...”.

K. Jacobs & D. Grogan, “Rates of spontaneous mutation in an archaeon from geothermal environments,” Journal of Bacteriology, 179, no. 10 (1997), 3298-3303.

4 x 10^-7 mutations per gene per DNA replication x 5x10² genes = 2x10^-4 mutations per replication

1 mutation per replication = y x 2x10^-4 mutations per replication

y = 1 mutation per replication/2x10^-4 mutations per replication = 5,000

7. 1.7x10³⁰ organisms/year x 3x10⁹ years = <10⁴⁰ organisms.

8. <10⁴⁰ organisms x 1 mutations/organism = <10⁴⁰ mutations

9. H. P. Yockey, “A calculation of the probability of spontaneous biogenesis by information theory.” J. Theor. Bio., 67 (1977), 387.

J. Reidhaar-Olson and R. Sauer, “Functionally Acceptable Substitutions in Two α-Helical Regions of λ Repressor.” Proteins: Structure, Function, and Genetics, 7 (1990), 315.

D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology 2004 Aug 27; 341 (5): 1295-1315.

10. 2 chances in 10⁶⁵ tries x <10⁴⁰ heritable genetic mutations or tries = 2 chances in 10²⁵

11. http://www.uniprot.org/uniprot/P08559

12. http://www.uniprot.org/uniprot/P11177

13. http://www.uniprot.org/uniprot/P10515

14. https://www.uniprot.org/uniprot/075390

15. http://www.uniprot.org/uniprot/Q99798

16. http://www.uniprot.org/uniprot/P48735

17. http://www.uniprot.org/uniprot/Q02218

18. http://www.uniprot.org/uniprot/B2R8A1

19. http://www.uniprot.org/uniprot/Q96I99

20. http://www.uniprot.org/uniprot/P31040

21. http://www.uniprot.org/uniprot/P21912