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The split gene theory is a theory of the origin of introns, long non-coding sequences in eukaryotic genes between the exons.[1][2][3] The theory holds that the randomness of primordial DNA sequences would only permit small (< 600bp) open reading frames (ORFs), and that important intron structures and regulatory sequences are derived from stop codons. In this introns-first framework, the spliceosomal machinery and the nucleus evolved due to the necessity to join these ORFs (now "exons") into larger proteins, and that intronless bacterial genes are less ancestral than the split eukaryotic genes. The theory originated with Periannan Senapathy.
The theory provides solutions to key questions concerning the split gene architecture, including split eukaryotic genes, exons, introns, splice junctions, and branch points, based on the origin of split genes from random genetic sequences. It also provides possible solutions to the origin of the spliceosomal machinery, the nuclear boundary and the eukaryotic cell.
This theory led to the Shapiro–Senapathy algorithm, which provides the methodology for detecting the splice sites, exons and split genes in eukaryotic DNA, and which is the main method for detecting splice site mutations in genes that cause hundreds of diseases.
Split gene theory requires a separate origin of all eukaryotic species. It also requires that the simpler prokaryotes evolved from eukaryotes. This completely contradicts the scientific consensus about the formation of eukaryotic cells by endosymbiosis of bacteria. In 1994, Senapathy wrote a book about this aspect of his theory - The Independent Birth of Organisms. It proposed that all eukaryotic genomes were formed separately in a primordial pool. Dutch biologist Gert Korthoff criticized the theory by posing various problems that cannot be explained by a theory of independent origins. He pointed out that various eukaryotes need nurturing and called this the 'boot problem', in that even the initial eukaryote needed parental care. Korthoff notes that a large fraction of eukaryotes are parasites. Senapathy's theory would require a coincidence to explain their existence.[4][5] Senapathy's theory cannot explain the strong evidence for common descent (homology, universal genetic code, embryology, fossil record.)[6]
^Senapathy, P. (April 1986). "Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications". Proceedings of the National Academy of Sciences of the United States of America. 83 (7): 2133–2137. Bibcode:1986PNAS...83.2133S. doi:10.1073/pnas.83.7.2133. ISSN 0027-8424. PMC 323245. PMID 3457379.
^Senapathy, P. (February 1982). "Possible evolution of splice-junction signals in eukaryotic genes from stop codons". Proceedings of the National Academy of Sciences of the United States of America. 85 (4): 1129–1133. Bibcode:1988PNAS...85.1129S. doi:10.1073/pnas.85.4.1129. ISSN 0027-8424. PMC 279719. PMID 3422483.
^Senapathy, P. (1995-06-02). "Introns and the origin of protein-coding genes". Science. 268 (5215): 1366–1367, author reply 1367–1369. Bibcode:1995Sci...268.1366S. doi:10.1126/science.7761858. ISSN 0036-8075. PMID 7761858.
^"Independent origin and the facts of life". wasdarwinwrong.com. Retrieved 2021-07-31.
^"Independent Birth of Organisms. Periannan Senapathy. Book review". wasdarwinwrong.com. Retrieved 2021-07-31.
^Theobald, Douglas L. (2012). "29+ Evidences for Macroevolution: The Scientific Case for Common Descent". {{cite journal}}: Cite journal requires |journal= (help)
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