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Credulity Is the Soil for Darwin’s Tree

tree and a man
Photo credit: Gilly Stewart via Unsplash.

Researchers from the Institute of Molecular Evolution at Heinrich Heine University Düsseldorf (HHU) could teach a class on how to look confident when faced with impossible odds that make winning the Powerball lottery every time look ordinary. The secret is to restrict one’s explanations for life to unguided natural events. 

Once that decision has been made, everything else flows deductively from it. Natural miracles become everyday occurrences. A vision becomes fixed in the believer’s imagination: molecules arranging themselves at hydrothermal vents or in ponds struck by lightning, the emergence of a first protocell, a universal common ancestor, and miracle after miracle to the tips of all the branches in Darwin’s tree — including us. Credulity is the soil in which Darwin’s tree grows best. Researchers can simply assume that whatever miracles evolution needs naturalism will provide: indeed, has provided. 

After All, We’re Here, Aren’t We?

The HHU researchers worked to identify the requirements for the next stage after LUCA (the last universal common ancestor) to find LBCA (the last bacterial common ancestor). Since bacteria are the most numerous of the microbes, they felt that comparing genomes of anaerobes (the ones that do not rely on oxygen for respiration), they could keep it simple. They realize that oxygenic respiration adds much more complexity to an organism’s genome.

What did the ancestor of all bacteria look like, where did it live and what did it feed on? A team of researchers from the Institute of Molecular Evolution at Heinrich Heine University Düsseldorf (HHU) has now found answers to these questions by analysing biochemical metabolic networks and evolutionary trees. In the journal Communications Biology, they report on how they can now even infer the shape of the first bacterium. [Emphasis added.]

Their confidence extends to the shape of LBCA:

“We can infer with confidence that LBCA was most likely rod-shaped”, says Xavier. “If it was similar to Clostridia, it is possible that LBCA was able to sporulate.” This hypothesis was recently laid out by other researchers “and is highly compatible with our results”, says Xavier. Forming spores would allow early cells to survive the inhospitable environment of the early Earth.

Need sporulation? No problem. Coming right up from the Darwin Supply House. The bacteria needed it, didn’t they?

Cloudy Thinking

Readers might overlook the only diagram provided because of its fine print, but it is the key to seeing confidence in credulity. It’s a cloud diagram of the metabolic networks required by the LCBA. The network is grouped into three sub-clouds: Hydride transfer, Carbon, and Energy/ Protein synthesis. The caption reads,

The metabolic network of the last bacterial common ancestor, LBCA. The small circles are metabolites or compounds; the diamonds are reactions. Arrows indicate the flow of compounds to and from reactions. Three large functional modules of the network are highlighted as large regions.

The team evaluated 1,046 anaereobic genomes and found 146 protein families conserved in all bacteria. While that comprises the minimum core of genes needed, it wasn’t enough.

To complete LBCA’s biochemistry, just nine further genes had to be added for the reconstructed metabolic network to include all essential and universal metabolites. To be fully independent and self-generated, LBCA’s network would still require further genes inherited from the last universal common ancestor, LUCA, and nutrients from the environment.

The diagram shows nearly 200 ingredients with lines connecting them. Look at some of them: all the amino acids are conveniently left-handed. A few simple compounds like ammonia and several alcohols are listed. Several more are the well-known energy compounds used by cells, including NAD, GDP, and ATP. Many of the rest are complex proteins or ribozymes, including transfer RNAs, acetyl coenzyme-A, and the aminoacyl-tRNA synthetases. 

Consider just the relatively small thioredoxin enzyme, ubiquitous in all life as an antioxidant. It has 12,000 atomic mass units (12kD). In E. coli, it has 108 amino acid residues, all left-handed. The probability is astronomically small that those amino acids would link up in the right sequence, and that is for just one enzyme! There are dozens more required. They cannot just exist independently, either; they must link up with the right molecules in the network to perform their functions. The credulity required to believe this happened is already mounting.

A “Simple” Bacterium

The paper in Communications Biology by Joana C. Xavier et al., “The metabolic network of the last bacterial common ancestor,” lists some of the capabilities this “simple” bacterium would have needed:

  • The acetyl coenzyme A pathway
  • Glucogenesis (sugar manufacturing process to build the cell wall)
  • Numerous RNA modifications
  • Multifunctional enzymes
  • A nearly complete trunk gluconeogenetic pathway with pyruvate kinase (PK), enolase, phosphoglycerate kinase (PGK), glyceraldehyde 3-phosphate dehydrogenase, and triosephosphate isomerase
  • Four other kinases in addition to PK and PGK, two involved in cofactor metabolism and two in phosphorylating ribonucleotides to nucleoside diphosphates
  • Two enzymes involved in cell division, FtsH and FtsY, which however also fulfill a number of other functions in the cell including protein degradation and assembly and correct targeting of proteins and ribosomes to the membrane
  • 57 universally essential prokaryotic metabolites
  • The 20 amino acids, four DNA bases, four RNA bases
  • 8 universal cofactors
  • Glycerol 3-phosphate as a lipid precursor
  • Nine genes—seven aminoacyl tRNA synthetases (aaRS), ADP: thiamine diphosphate phosphotransferase and d-ribulose 5-phosphate, d-glyceraldehyde 3-phosphate pyridoxal 5′-phosphate-lyase

…and more. See how simple it is? The authors treat this list as eminently achievable by natural processes. What are they thinking? If waiting for just one relatively small enzyme to emerge by chance exceeds the age of the universe, getting all of them together is beyond miraculous. It is so unbelievable, a new word is needed to describe someone who thinks it could happen: perhaps mega-credulous.

The analyses so far suggest that the 146 protein families conserved in all groups of anaerobic bacteria were present in LBCA, not only due to their ubiquitous and nearly universal nature (Supplementary Fig. 1) but also because they form a functional unit: a highly connected, nearly complete core metabolic network.

It must have happened somehow.

After All, We’re Here

Notice they are talking about 146 protein families, not just individual proteins. For instance, “The acetyl CoA pathway requires approximately 10 enzymes, roughly as many organic cofactors, and more than 500 kDa of combined subunit molecular mass to catalyze the conversion of H2 and CO2 to formate, acetate, and pyruvate in acetogens and methanogens,” says William Martin in Frontiers in Microbiology. That’s just one pathway. Martin thinks it began at hydrothermal vents, but that requires mega-credulity itself.

All these ingredients not only had to form at the same time and in the same place, but they had to get programmed in genes, implying a complete working set of transcription and translation machinery. All the amino acids and sugars had to be homochiral. They all had to assemble inside membranes. All the ingredients had to link up and support one another for functional ends, and each function had to support the whole organism. 

It is difficult to fathom the credulity necessary to believe the evolutionary story. Sadly, the only thing exceeding the level of credulity is the mega-confidence they have that it happened.

Those are the consequences of starting with the assumption of naturalism. Some of the evolutionary biologists accuse theists or Darwin skeptics of appealing to miracles. It’s time to laugh that hypocritical argument out of court.