Periannan Senapathy

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Periannan Senapathy
Born Periannan Senapathy
Chennai, Tamil Nadu, India
Institutions Genome International Corporation
Alma mater National Institutes of Health
University of Wisconsin, Madison
Indian Institute of Science
Known for Genomics
Evolution
Website
Genome International Corporation

Periannan Senapathy is a molecular biologist, geneticist, author and entrepreneur.[1][2] He is the founder, president and chief scientific officer at Genome International Corporation, a biotechnology & bioinformatics firm based in Madison, Wisconsin, which develops next-generation DNA sequencing analysis technologies.[3]

Senapathy is known for his contributions in the biology of RNA splicing and the structure of eukaryotic genes. An algorithm developed by him, known as Shapiro & Senapathy algorithm (S&S) for predicting the splice sites, exons and genes in any animal or plant, has the ability to discover disease-causing mutations in splice junctions in numerous cancers and non-cancer diseases. The Shapiro - Senapathy algorithm has been implemented in many gene-finding and mutation detection tools, and is being used in major research institutions around the world for uncovering mutations in the splicing regions. It is increasingly used in the Next Generation Sequencing era, as it is widely realized that >60% of all mutations causing diseases or adverse drug reactions in humans and other animals occur within the splicing regions of genes. The S&S algorithm has been cited in ~3,000 publications on finding splicing mutations in thousands of diseases including many different forms of cancer.

Senapathy is also known for offering a new theory on the origin and diversity of life on earth, where he proposes that genomes for eukaryotic life forms could have been directly assembled from a common pool of split genes in prebiotic chemistry.[4] He had authored a book, titled Independent Birth of Organisms in 1994,[5][6] where he first proposed this theory. He has also published his scientific findings in journals such as Science (journal), Nucleic Acids Research, PNAS among others, and is the author of several patents in the genomics field.

Biography[edit]

Senapathy has a PhD in molecular biology from the Indian Institute of Science, Bangalore, India. He spent ten years in genome research for the National Institutes of Health's Division of Computer Research and Technology in Bethesda, Maryland,[7] (1980–87) and the Biotechnology Center of the University of Wisconsin, Madison (1987–90).[8][9] Dr. Senapathy founded Genome International in 1992,[10] which owns the domain genome.com.[11]

Notable works[edit]

Senapathy conducted genomics and bioinformatics studies based on the idea that prebiotic genetic sequences must have had random characteristics.[12] He had observed that the reading-frame lengths in a random nucleotide sequence follow an exponential distribution, which is exactly found in eukaryotic genome sequences,[13][14][15] and suggested the split-gene model. In this model, a selective pressure existed in the most primitive unicellular eukaryotes to generate longer coding sequences from random DNA sequences that were populated with in-frame nonsense codons, and intervened between short reading frames, started to be excised by an already existing spliceosome. This model proposes not only that the sequences excised contained random clusters of in-frame nonsense codons[16] but also that the splice junction signal sequences and the branch point sequence originate from nonsense codons.[17][18]

From an evolution perspective, Senapathy's research focused on why eukaryotic genes are split into exons and introns[19][20] and why large genomes such as human and sea urchin contain very long introns and very short exons.[21] Noted evolutionary molecular biologist Colin Blake commented on Senapathy's theory that:[22] "Recent work by Senapathy, when applied to RNA, comprehensively explains the origin of the segregated form of RNA into coding and non-coding regions. It also suggests why a splicing mechanism was developed at the start of primordial evolution. The presence of random sequence was therefore sufficient to create in the primordial ancestor the segregated form of RNA observed in the eukaryotic gene structure.”

Senapathy's research focuses on how all of life's complexity originated directly from the primordial pond, without a need for the origin of the primitive bacterium-like microbe that had to evolve into all organisms on earth through laborious genetic mutations.[23][24][25]

Independent Birth of Organisms[edit]

Senapathy published a book titled Independent Birth of Organisms in 1994, which proposes that all organisms on earth had originated independently from a chemical pond, thus rejecting common descent[26][27] The book was a result of his 12 years research in molecular biology.[28]

Andrew Petto, an anthropologist of University of Wisconsin reviewed Senapathy's book saying that Senapathy has some very interesting views about the origins of life, such as his interpretation of the primordial soup theory and that these ideas should be taken seriously by the reader.[29]

Recent literature findings from comparative genomics are showing overwhelmingly that the earliest organisms could have been highly complex and eukaryotic and could have contained complex proteins,[30][31][32][33][34][35][36][37] which is predicted by Senapathy’s theory.

Gert Korthof, an evolutionary biologist, reviewed Senapathy’s book in detail.[38] Although Korthof rejects Senapathy’s theory, he states that it would not be fair to disprove his theory using current biological knowledge or dogmatically use the theory of evolution to refute his views. In addition, Gert Korthof shows how even theories of the origin of life are fundamentally flawed, such as those in The Origin of Membrane Biogenetics,[39] and its commentary.[40] He also brings out many other errors in the conventional origin of life models, such as the impossible origin of the minimalistic ribosomal RNA sequences which is the foundation for the origin of life, and how the authors try erroneously to overcome this difficulty.[41]

Selected publications[edit]

See also[edit]

References[edit]

  1. ^ Kamath, M. V. The United States and India, 1776–1996. Indian Council for Cultural Relations, 1998, p. 311.
  2. ^ Independent Birth of Organisms on Amazon
  3. ^ Genome International Corporation
  4. ^ "A long explanation for introns", New Scientist, June 26, 1986.
  5. ^ Biology digest, Volume 15, Plexus Pub., 1988, p. 107
  6. ^ Review of Independent Birth of Organisms, Nucleic acids research, Volume 23, Issues 1–3, Information Retrieval Limited., 1995, p. 312
  7. ^ "A long explanation for introns", New Scientist, June 26, 1986.
  8. ^ "Exon, introns, and evolution", New Scientist, March 31, 1988.
  9. ^ Review of Senapathys theory in Nucleic acids research, Volume 23, Issues 1–3, Information Retrieval Limited., 1995
  10. ^ [1]
  11. ^ Genome International Corporation
  12. ^ "Exons, introns and evolution", New Scientist, March 31, 1988.
  13. ^ Senapathy, P. (1988). "Possible evolution of splice-junction signals in eukaryotic genes from stop codons". Proc Natl Acad Sci U S A. 85 (4): 1129–33. PMC 279719Freely accessible. PMID 3422483. doi:10.1073/pnas.85.4.1129. 
  14. ^ Senapathy, P. (1986). "Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications". Proc Natl Acad Sci U S A. 83 (7): 2133–7. PMC 323245Freely accessible. PMID 3457379. doi:10.1073/pnas.83.7.2133. 
  15. ^ Regulapati, R.; Bhasi, A.; Singh, C.K.; Senapathy, P. (2008). "Origination of the Split Structure of Spliceosomal Genes from Random Genetic Sequences". PLoS ONE. 3: 10. PMC 2565106Freely accessible. PMID 18941625. doi:10.1371/journal.pone.0003456. 
  16. ^ Senapathy, P. (1986). "Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications". Proc Natl Acad Sci U S A. 83 (7): 2133–7. PMC 323245Freely accessible. PMID 3457379. doi:10.1073/pnas.83.7.2133. 
  17. ^ Francesco, Catania; et al. (September–October 2009). "Endogenous Mechanisms for the Origins of Spliceosomal Introns". Journal of Heredity. 100 (5): 591–596. PMC 2877546Freely accessible. PMID 19635762. doi:10.1093/jhered/esp062. 
  18. ^ Senapathy, P. (1988). "Possible evolution of splice-junction signals in eukaryotic genes from stop codons". Proc Natl Acad Sci U S A. 85 (4): 1129–33. PMC 279719Freely accessible. PMID 3422483. doi:10.1073/pnas.85.4.1129. 
  19. ^ Senapathy, P. (1986). "Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications". Proc Natl Acad Sci U S A. 83 (7): 2133–7. PMC 323245Freely accessible. PMID 3457379. doi:10.1073/pnas.83.7.2133. 
  20. ^ Senapathy, P. (1995). "Introns and the origin of protein-coding genes". Science. 268 (5215): 1366–7. PMID 7761858. doi:10.1126/science.7761858. 
  21. ^ Regulapati, R.; Bhasi, A.; Singh, C.K.; Senapathy, P. (2008). "Origination of the Split Structure of Spliceosomal Genes from Random Genetic Sequences". PLoS ONE. 3: 10. PMC 2565106Freely accessible. PMID 18941625. doi:10.1371/journal.pone.0003456. 
  22. ^ Holland, S.K.; Blake, C.C.F. (1990). "Proteins, Exons, and Molecular Evolution, in Intervening Sequences in Evolution and Development". Oxford University Press: 32. 
  23. ^ "Origin of biological information", Nature Precedings, December 13, 2010.
  24. ^ "Exons, introns and evolution", New Scientist, March 31, 1988.
  25. ^ "A long explanation for introns", New Scientist, June 26, 1986.
  26. ^ Biology digest, Volume 15, Plexus Pub., 1988, p. 107
  27. ^ Review of Independent Birth of Organisms, Nucleic acids research, Volume 23, Issues 1–3, Information Retrieval Limited., 1995, p. 312
  28. ^ The United States and India, 1776–1996 Indian Council for Cultural Relations, 1998, p. 311.
  29. ^ Independent Birth of Organisms reviewed by Andrew J. Petto, Department of Anthropology, University of Wisconsin, National Center for Science Education, Issue 37, Winter 1995 Online Edition
  30. ^ C. G. Kurland, B. Canbäck, O. G. Berg, "The origins of modern proteomes" Biochimie89, 1454-1463 (2007)"
  31. ^ G. Caetano-Anollés, D. Caetano-Anollés, "An evolutionarily structural universe of protein architecture." Genome research13, 1563-1571 (2003).
  32. ^ N. Glansdorff, Y. Xu, B. Labedan, "The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner." Biology direct3, 56-125 (2008).
  33. ^ C. G. Kurland, L. J. Collins, D. Penny, "Genomics and the Irreducible Nature of Eukaryote Cells" Science312, 1011-1014 (2006).
  34. ^ L. Collins, D. Penny,"Complex Spliceosomal Organization Ancestral to Extant Eukaryotes" ,Molecular biology and evolution22, 1053-1066 (2005).
  35. ^ A. M. Poole, D. C. Jeffares, D. Penny, "The path from the RNA world" Journal of molecular evolution 46, 1-17 (1998).
  36. ^ D. Penny, L. J. Collins, T. K. Daly, S. J. Cox, "The relative ages of eukaryotes and akaryotes". Journal of molecular evolution 79, 228-239 (2014); published online EpubDec (10.1007/s00239-014-9643-y).
  37. ^ J. A. Fuerst, E. Sagulenko, "Keys to eukaryality: planctomycetes and ancestral evolution of cellular complexity". Frontiers in microbiology3, (2012).
  38. ^ Korthof, Gert (7 Oct 2015). "What's Wrong with Independent Birth of Organisms? An investigation into the origin of life". Retrieved May 2016.  Check date values in: |access-date= (help)
  39. ^ Ed Yong (2012) "How life emerged from deep-sea rocks", Nature, 20 December 2012 (free access)
  40. ^ E. Young, "How life emerged from deep-sea rocks", Nature, 012, Doi:10.1038/nature.2012.12109
  41. ^ Koonin's 'dirty' secret and his extraordinary solution to the improbable Origin of Life. A "review" by GertKorthoff on The Logic of Chance’ by Eugene Koonin

External links[edit]