Senapathy algorithm undermines his own theory of independent birth of organisms from the primordial pond

In his Wikipedia article Periannan Senapathy, paragraph 'Origin of split genes from random DNA sequences', he explains why eukaryotic genes have a split structure or an exon - intron structure. His explanation is: genes and genomes with this structure originated from random DNA sequences in the Primordial Pond. 

The structure of a split gene: exon-intron
Exons (blue) are the protein coding parts of a gene,
introns are the non-coding parts which are removed,
the combined exons produce the protein

The problem with this explanation is: if a hypothetical gene has a random sequence than everything from begin to end is random including the supposed 'exon-intron' boundaries. Since a gene is a continuous sequence of the bases A, T, C, G, how do you know where an exon ends and an intron starts? Introns have to be recognized somehow in order to get removed. In all animals and plants with split genes (eukaryotes) recognition is achieved by special splice site recognition sequences which are located at the beginning and end of each intron. In fact those sites define introns. And by implication they define beginning and end of exons too (see illustration). Without those special sites, exons and introns cannot be distinguished. In Senapathy's scenario of independent birth of all plants and animals, both exons and introns are by definition random sequences anyway. My point is that these boundaries are specific and therefore non-random [1], [2]. Consequently, there is no way that these non-random splice sites occur in random DNA. Impossible. 

Think about this: human genes contain on average 8 introns, that is 16 splice sites per gene. Since humans have about 25,000 genes, there are about 400,000 splice sites. A few could occur by chance, but not 400,000. 

My argument can be summarized in one sentence: 

• Either a sequence is random, and then there can be no well defined splice recognition sites, and thus no exons and introns 
• or there are splice recognition sites, and exons and introns, but then the sequence is not random anymore. 

I discovered additional evidence in Senapathy (1987) [2]: 

"A sequence of eight nucleotides is highly conserved at the boundary between an exon and an intron (...) The boundary between an intron and an exon also exhibits a highly conserved sequence of 4 nucleotides, preceded by a pyrimidine-rich region." 

So, he knows that these are non-random sequences. The rest could have been random, but not those specific sequences. He should have concluded that the exon-intron structure of eukaryotic genes cannot arise from random DNA. The same holds for genomes. And the same holds for the organisms themselves. The inescapable and final conclusion is that the origin of eukaryotes (all plants and animals) cannot be explained by random DNA. Sorry, there is no escape from this conclusion. Unfortunately,  Senapathy failed to explain the origin of life. His Primordial Pond will not be and can not be the birthplace of eukaryotes, plants and animals. Under the most favourable conditions his Primordial Pond will only contain dead and meaningless random DNA molecules. If he is lucky, it will produce a lot of dead and meaningless random DNA. But nothing more. It is a primordial soup and it stays that way forever because there is no evolution in his scenario. His primordial pond will not bring forth life.

Ironically, the very existence of his Shapiro–Senapathy algorithm undermines his own theory of Independent birth of organisms from random DNA sequences.

 

Notes

1. "A splice site defines the boundary between a coding exon and a non-coding intron in eukaryotic genes." quote from wikipedia article: Shapiro–Senapathy algorithm (This page was last edited on 28 July 2025, at 14:35 (UTC).) 
2. M. B. Shapiro, P. Senapathy (1987) RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression, Nucleic Acids Res 1987. This publication appeared 7 years before his 1994 book.

 Sources

• Wikipedia article Periannan Senapathy (last edited 16 July 2025)
• Wikipedia article Shapiro–Senapathy algorithm (last edited 28 July 2025)
• Wikipedia article Split gene theory (these three Wikipedia articles are written by Senapathy supporters or by himself and give the false impression of being mainstream science and omitting any criticism)
• Gert Korthof What's Wrong with Independent Birth of Organisms? (this is my criticism of Senapathy's theory)
• Periannan Senapathy (1994) 'Independent Birth of Organisms. A New Theory That Distinct Organisms Arose Independently From The Primordial Pond Showing That Evolutionary Theories Are Fundamentally Incorrect'. (now more than 30 years old, the book is still available at amazon).