Paul M. Bingham

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Paul Montgomery Bingham (born February 25, 1951) is an American molecular biologist and evolutionary biologist, Associate Professor in the Department of Biochemistry and Cell Biology at Stony Brook University [1] and Vice President for Research at Rafael Pharmaceuticals. [2] He is known for his work in molecular biology, and has also published recent articles and a book on human evolution. [3]

Contents

Biography

Bingham received his undergraduate degree at Blackburn College in Carlinville, Illinois, and then completed his PhD in Biochemistry and Molecular Biology at Harvard University in 1980 (thesis advisor, Matthew Meselson) after completing an MS in Microbiology at the University of Illinois (with John W. Drake). [4] He spent two years at the National Institute of Environmental Health Sciences (NIEHS) before joining the faculty of the Department of Biochemistry and Cell Biology and the School of Medicine at Stony Brook University in 1982. [1]

Molecular biology

He was part of a collaborative team that discovered the parasitic DNA sequence element, the P element transposon. [5] This enabled a widely used strategy still used today for retrieving genes from animals. It also shed fundamental new light on how evolution shapes the (self-interested) individual genes that collaborate to build organisms.

With his wife (Zuzana Zachar), he demonstrated that transposon insertion mutations were responsible for most of the alleles used in the development of classical genetics. [6] He also collaborated with Carl Wu and Sarah Elgin (then at Harvard) on fundamental properties of metazoan chromatin structure. [7] In collaboration with Margaret Kidwell, then at Brown University, and Gerry Rubin, then at the Carnegie Institution, he carried out the molecular cloning of the P element transposon in Drosophila. [8] This work revolutionized the retrieval of genes in Drosophila and subsequently contributed to progress in metazoan molecular and developmental genetics. [9] He and his collaborators were the first to propose the use of P element transposon tagging to clone the first metazoan RNA polymerase subunit. [10] This work demonstrated that the P element is a recently invading parasite of the Drosophila genome and gene pool. Thus, P became the first clearly defined metazoan example of this long-suspected phenomenon. [9]

His research group also worked on the nature of metazoan gene regulation [11] and the elucidation of the first case of autoregulation of gene expression at the level of pre-mRNA splicing [12] [13] [14] [15] and of critical features of the nuclear organization of pre-mRNA processing and transport [16] [17] This latter work first clearly established the now-widely accepted model of channeled diffusion for the movement of most pre-mRNAs through the nuclear compartment. [4] [18]

Bingham and Zachar discovered the first-in-class anti-cancer mitochondrial metabolism drug (CPI-613; devimistat), [19] currently in Phase III registrational clinical trials in pancreatic ductal adenocarcinoma and acute myeloid leukemia. [20] This work is now being done in collaboration with Rafael Pharmaceuticals. [19]

Human evolutionary biology

In the mid-1990s, he developed a theory of human uniqueness that proposes a novel explanation of why humans have evolved to be ecologically dominant. The theory has been published in three peer-reviewed journals: The Quarterly Review of Biology , Evolutionary Anthropology and the Journal of Theoretical Biology . [21] [22]

He and co-author Joanne Souza have developed the theory further in a self-published book, Death from a Distance and the Birth of a Humane Universe'. [23] This work builds on W.D. Hamilton's theory of kin selection (Benefit x Relatedness > Cost) and posits that the genus Homo evolved when an ancestral organism developed the ability to effectively manage non-kin conflicts of interests by lowering the cost of coercion between non-kin individuals (Benefit > Cost of Coercion + Cost of Cooperation). [24]

The theory, using precedents established in biological theory, proposes to explain many aspects of human social and sexual behavior. It proposed to account for the evolution of the human species from the advent of its phylogenetic branching from other hominins through physiological and behavioral adaptations until our current civilization. [25] This theory of human uniqueness claims to answer the fundamental scientific challenge posed by Charles Darwin, to explain the descent of man: how did the 'incremental' process of evolution by natural selection suddenly produce an utterly unprecedented kind of animal, humans? It suggests an explanation of human origins, and also of human properties (from speech to political/economic/religious behavior). [26]

According to his theory, the cost to an enforcer of coercing a cheating individual into a cooperative effort, known as the free-rider problem, was lowered when a precursor species to humans developed a way to threaten adult conspecifics from a distance by evolving the ability to throw projectiles with sufficient skill to reliably injure the cheater, especially conjointly with others. [27] This reduced the personal risk to multiple enforcers as formulated by Lanchester's Square Law, when they gang up on a cheater. [28] The theory proposes that this elite throwing ability initially allowed bands of proto-humans improved capacity to repel predators and scavenge their kills in the African savanna. It was later adapted as threat projection towards free-riding conspecifics (cheaters) in non-kin cooperative groups that made the cooperation evolutionarily stable against cheaters who, without coercion by this threat, would otherwise flourish and displace co-operators. [29]

The theory further generalizes to a theory of history, [24] claiming to account for many salient events of the two-million-year course of the human lineage—from the evolution of the genus Homo to the inception of behavioral modernity to the Neolithic Revolution [30] to the rise of the nation-state. [31] [25] [32]

Academic work

In collaboration with Joanne Souza, he has developed a course on the logic and implications of this new theory .

Bingham has served as the Faculty Director of the Freshmen College of Human Development at Stony Brook .

Bingham also serves on the management team of Rafael Pharmaceuticals, a firm developing cancer therapies, as Vice President of Research. He and his collaborator, Prof. Zuzana Zachar, recently received the Maffetone Research Prize from the Carol M. Baldwin Breast Cancer Research Fund for their cancer work. [1] [19]

Publications

Social coercion theory

  • Bingham PM (1999). "Human uniqueness: A general theory". Quarterly Review of Biology. 74 (2): 133–169. doi:10.1086/393069. S2CID   59499229.
  • Bingham PM (2000). "Human evolution and human history: A complete theory". Evolutionary Anthropology. 9 (6): 248–257. doi: 10.1002/1520-6505(2000)9:6<248::AID-EVAN1003>3.0.CO;2-X .
  • Souza J, Bingham PM (2019). "Chapter 7: The New Human Science: Sound, New Evolutionary Theory Gives Us Ultimate Causal Understanding of Human Origins, Behavior, History, Politics, and Economics". In Geher G, Wilson DS, Gallup A, Head H (eds.). Darwin's roadmap to the curriculum: evolutionary studies in higher education. New York, NY. pp. 117–156. doi:10.1093/oso/9780190624965.001.0001. ISBN   978-0-19-062496-5.{{cite book}}: CS1 maint: location missing publisher (link)
  • Souza J, Bingham PM (2014). "Disciplinary unification of the Natural Sciences, the Humanities, and the Social Sciences: Adapted minds and strategic approaches to consilience in the Academy" (PDF). EvoS Journal: The Journal of the Evolutionary Studies Consortium. 6 (1): 51–62.
  • Yumpu.com. "Theoretical Contribution - the EvoS Consortium!". yumpu.com. Retrieved 2021-04-22.
  • Bingham PM, Souza J (2013). "Theory testing in prehistoric North America: fruits of one of the world's great archeological natural laboratories". Evolutionary Anthropology. 22 (3): 145–53. doi:10.1002/evan.21359. PMID   23776052.
  • Bingham PM, Souza J, Blitz JH (May 2013). "Introduction: social complexity and the bow in the prehistoric North American record". Evolutionary Anthropology. 22 (3): 81–8. doi:10.1002/evan.21353. PMID   23776043.
  • Bingham P. "Ultimate causation in evolved human political psychology: implications for public policy" (PDF). APA PsycNet.
  • Bingham PM (2010). "On the evolution of language: implications of a new and general theory of human origins, properties, and history". In Yamakido H, Larson RK, Déprez V (eds.). The Evolution of Human Language: Biolinguistic Perspectives. Approaches to the Evolution of Language. Cambridge: Cambridge University Press. pp. 211–224. doi:10.1017/cbo9780511817755.016. ISBN   978-0-521-51645-7 . Retrieved 2021-04-22.

Cancer research

Related Research Articles

<span class="mw-page-title-main">Exon</span> A region of a transcribed gene present in the final functional mRNA molecule

An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA splicing, introns are removed and exons are covalently joined to one another as part of generating the mature RNA. Just as the entire set of genes for a species constitutes the genome, the entire set of exons constitutes the exome.

An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word intron is derived from the term intragenic region, i.e., a region inside a gene. The term intron refers to both the DNA sequence within a gene and the corresponding RNA sequence in RNA transcripts. The non-intron sequences that become joined by this RNA processing to form the mature RNA are called exons.

<span class="mw-page-title-main">RNA splicing</span> Process in molecular biology

RNA splicing is a process in molecular biology where a newly-made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). It works by removing all the introns and splicing back together exons. For nuclear-encoded genes, splicing occurs in the nucleus either during or immediately after transcription. For those eukaryotic genes that contain introns, splicing is usually needed to create an mRNA molecule that can be translated into protein. For many eukaryotic introns, splicing occurs in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs). There exist self-splicing introns, that is, ribozymes that can catalyze their own excision from their parent RNA molecule. The process of transcription, splicing and translation is called gene expression, the central dogma of molecular biology.

<span class="mw-page-title-main">Transposable element</span> Semiparasitic DNA sequence

A transposable element is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition often results in duplication of the same genetic material. In the human genome, L1 and Alu elements are two examples. Barbara McClintock's discovery of them earned her a Nobel Prize in 1983. Its importance in personalized medicine is becoming increasingly relevant, as well as gaining more attention in data analytics given the difficulty of analysis in very high dimensional spaces.

Molecular evolution describes how inherited DNA and/or RNA change over evolutionary time, and the consequences of this for proteins and other components of cells and organisms. Molecular evolution is the basis of phylogenetic approaches to describing the tree of life. Molecular evolution overlaps with population genetics, especially on shorter timescales. Topics in molecular evolution include the origins of new genes, the genetic nature of complex traits, the genetic basis of adaptation and speciation, the evolution of development, and patterns and processes underlying genomic changes during evolution.

<span class="mw-page-title-main">Neutral theory of molecular evolution</span> Theory of evolution by changes at the molecular level

The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The theory applies only for evolution at the molecular level, and is compatible with phenotypic evolution being shaped by natural selection as postulated by Charles Darwin.

<span class="mw-page-title-main">Alternative splicing</span> Process by which a gene can code for multiple proteins

Alternative splicing, or alternative RNA splicing, or differential splicing, is an alternative splicing process during gene expression that allows a single gene to produce different splice variants. For example, some exons of a gene may be included within or excluded from the final RNA product of the gene. This means the exons are joined in different combinations, leading to different splice variants. In the case of protein-coding genes, the proteins translated from these splice variants may contain differences in their amino acid sequence and in their biological functions.

<span class="mw-page-title-main">Pseudogene</span> Functionless relative of a gene

Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Most arise as superfluous copies of functional genes, either directly by gene duplication or indirectly by reverse transcription of an mRNA transcript. Pseudogenes are usually identified when genome sequence analysis finds gene-like sequences that lack regulatory sequences needed for transcription or translation, or whose coding sequences are obviously defective due to frameshifts or premature stop codons. Pseudogenes are a type of junk DNA.

Trans-splicing is a special form of RNA processing where exons from two different primary RNA transcripts are joined end to end and ligated. It is usually found in eukaryotes and mediated by the spliceosome, although some bacteria and archaea also have "half-genes" for tRNAs.

<span class="mw-page-title-main">Canalisation (genetics)</span> Measure of the ability of a population to produce the same phenotype

Canalisation is a measure of the ability of a population to produce the same phenotype regardless of variability of its environment or genotype. It is a form of evolutionary robustness. The term was coined in 1942 by C. H. Waddington to capture the fact that "developmental reactions, as they occur in organisms submitted to natural selection...are adjusted so as to bring about one definite end-result regardless of minor variations in conditions during the course of the reaction". He used this word rather than robustness to consider that biological systems are not robust in quite the same way as, for example, engineered systems.

Exon shuffling is a molecular mechanism for the formation of new genes. It is a process through which two or more exons from different genes can be brought together ectopically, or the same exon can be duplicated, to create a new exon-intron structure. There are different mechanisms through which exon shuffling occurs: transposon mediated exon shuffling, crossover during sexual recombination of parental genomes and illegitimate recombination.

Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules expressed in animal cells. piRNAs form RNA-protein complexes through interactions with piwi-subfamily Argonaute proteins. These piRNA complexes are mostly involved in the epigenetic and post-transcriptional silencing of transposable elements and other spurious or repeat-derived transcripts, but can also be involved in the regulation of other genetic elements in germ line cells.

mir-2 microRNA precursor

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RNA-based evolution is a theory that posits that RNA is not merely an intermediate between Watson and Crick model of the DNA molecule and proteins, but rather a far more dynamic and independent role-player in determining phenotype. By regulating the transcription in DNA sequences, the stability of RNA, and the capability of messenger RNA to be translated, RNA processing events allow for a diverse array of proteins to be synthesized from a single gene. Since RNA processing is heritable, it is subject to natural selection suggested by Darwin and contributes to the evolution and diversity of most eukaryotic organisms.

Vasa is an RNA binding protein with an ATP-dependent RNA helicase that is a member of the DEAD box family of proteins. The vasa gene is essential for germ cell development and was first identified in Drosophila melanogaster, but has since been found to be conserved in a variety of vertebrates and invertebrates including humans. The Vasa protein is found primarily in germ cells in embryos and adults, where it is involved in germ cell determination and function, as well as in multipotent stem cells, where its exact function is unknown.

<span class="mw-page-title-main">DM domain</span> Protein family

In molecular biology the DM domain is a protein domain first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in C. elegans and mammalian proteins. In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription.

<span class="mw-page-title-main">SWAP protein domain</span>

In molecular biology, the protein domain SWAP is derived from the term Suppressor-of-White-APricot, a splicing regulator from the model organism Drosophila melanogaster. The protein domain is found in regulators that control splicing. It is found in splicing regulatory proteins. When a gene is expressed the DNA must be transcribed into messenger RNA (mRNA). However, it sometimes contains intervening or interrupting sequences named introns. mRNA splicing helps to remove these sequences, leaving a more favourable sequence. mRNA splicing is an essential event in the post-transcriptional modification process of gene expression. SWAP helps to control this process in all cells except gametes.

The gene Maelstrom, Mael, creates a protein, which was first located in Drosophila melanogaster in the nuage perinuclear structure and has functionality analogous to the spindle, spn, gene class. Its mammalian homolog is MAEL.

<i>De novo</i> gene birth Evolution of novel genes from non-genic DNA sequence

De novo gene birth is the process by which new genes evolve from non-coding DNA. De novo genes represent a subset of novel genes, and may be protein-coding or instead act as RNA genes. The processes that govern de novo gene birth are not well understood, although several models exist that describe possible mechanisms by which de novo gene birth may occur.

The G-value paradox arises from the lack of correlation between the number of protein-coding genes among eukaryotes and their relative biological complexity. The microscopic nematode Caenorhabditis elegans, for example, is composed of only a thousand cells but has about the same number of genes as a human. Researchers suggest resolution of the paradox may lie in mechanisms such as alternative splicing and complex gene regulation that make the genes of humans and other complex eukaryotes relatively more productive.

References

  1. 1 2 3 "Biochemistry faculty profile". SUNY Stonybrook. Retrieved 18 March 2017.
  2. ↑ "Paul Bingham, Ph.D.Vice President of Research". Rafael Pharmaceuticals. Archived from the original on 23 February 2021. Retrieved 23 February 2021.
  3. ↑ "Paul Bingham". World Science Festival. Retrieved 2021-04-22.
  4. 1 2 "Paul Bingham | SUNY: Stony Brook University - Academia.edu". sbsuny.academia.edu. Retrieved 2021-04-22.
  5. ↑ "2012-13 ALLELE Series". ALLELE Seminar Series. Retrieved 2021-04-22.
  6. ↑ Zachar Z, Bingham PM (September 1982). "Regulation of white locus expression: the structure of mutant alleles at the white locus of Drosophila melanogaster". Cell. 30 (2): 529–41. doi:10.1016/0092-8674(82)90250-1. PMID   6291773. S2CID   25146339.
  7. ↑ Wu C, Bingham PM, Livak KJ, Holmgren R, Elgin SC (April 1979). "The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence". Cell. 16 (4): 797–806. doi:10.1016/0092-8674(79)90095-3. PMID   455449. S2CID   10025372.
  8. ↑ Bingham PM, Kidwell MG, Rubin GM (July 1982). "The molecular basis of P-M hybrid dysgenesis: the role of the P element, a P-strain-specific transposon family". Cell. 29 (3): 995–1004. doi:10.1016/0092-8674(82)90463-9. PMID   6295641. S2CID   18723067.
  9. 1 2 Rabinow L, Birchler JA (1989-03-01). "A dosage-sensitive modifier of retrotransposon-induced alleles of the Drosophila white locus". The EMBO Journal. 8 (3): 879–889. doi: 10.1002/j.1460-2075.1989.tb03449.x . ISSN   1460-2075. PMC   400888 . PMID   2542025.
  10. ↑ Searles LL, Jokerst RS, Bingham PM, Voelker RA, Greenleaf AL (December 1982). "Molecular cloning of sequences from a Drosophila RNA polymerase II locus by P element transposon tagging". Cell. 31 (3 Pt 2): 585–92. doi:10.1016/0092-8674(82)90314-2. PMID   6297774. S2CID   1985358.
  11. ↑ Zachar Z, Bingham PM (1989). Suppressible Insertion-Induced Mutations in Drosophila. Progress in Nucleic Acid Research and Molecular Biology. Vol. 36. pp. 87–98. doi:10.1016/S0079-6603(08)60163-4. ISBN   978-0-12-540036-7. PMID   2544017.
  12. ↑ Chou TB, Zachar Z, Bingham PM (December 1987). "Developmental expression of a regulatory gene is programmed at the level of splicing". The EMBO Journal. 6 (13): 4095–104. doi:10.1002/j.1460-2075.1987.tb02755.x. PMC   553892 . PMID   2832151.
  13. ↑ Zachar Z, Chou TB, Bingham PM (December 1987). "Evidence that a regulatory gene autoregulates splicing of its transcript". The EMBO Journal. 6 (13): 4105–11. doi:10.1002/j.1460-2075.1987.tb02756.x. PMC   553893 . PMID   3443103.
  14. ↑ Bingham PM, Chou TB, Mims I, Zachar Z (May 1988). "On/off regulation of gene expression at the level of splicing". Trends in Genetics. 4 (5): 134–8. doi:10.1016/0168-9525(88)90136-9. PMID   2853467.
  15. ↑ Spikes DA, Kramer J, Bingham PM, Van Doren K (October 1994). "SWAP pre-mRNA splicing regulators are a novel, ancient protein family sharing a highly conserved sequence motif with the prp21 family of constitutive splicing proteins". Nucleic Acids Research. 22 (21): 4510–9. doi:10.1093/nar/22.21.4510. PMC   308487 . PMID   7971282.
  16. ↑ Li H, Bingham PM (October 1991). "Arginine/serine-rich domains of the su(wa) and tra RNA processing regulators target proteins to a subnuclear compartment implicated in splicing". Cell. 67 (2): 335–42. doi:10.1016/0092-8674(91)90185-2. PMID   1655279. S2CID   20307555.
  17. ↑ Zachar Z, Kramer J, Mims IP, Bingham PM (May 1993). "Evidence for channeled diffusion of pre-mRNAs during nuclear RNA transport in metazoans". The Journal of Cell Biology. 121 (4): 729–42. doi:10.1083/jcb.121.4.729. PMC   2119787 . PMID   8491768.
  18. ↑ Kramer J, Zachar Z, Bingham PM (February 1994). "Nuclear pre-mRNA metabolism: channels and tracks". Trends in Cell Biology. 4 (2): 35–7. doi:10.1016/0962-8924(94)90001-9. PMID   14731863.
  19. 1 2 3 "Executive Management Team". Rafael Pharmaceuticals. Retrieved 2021-04-22.
  20. ↑ "Rafael cornerstone starts phase III pancreatic trial; CPI-613 in AML study, too". www.bioworld.com. Retrieved 2021-04-22.
  21. ↑ Okada D, Bingham PM (July 2008). "Human uniqueness-self-interest and social cooperation". Journal of Theoretical Biology. 253 (2): 261–70. Bibcode:2008JThBi.253..261O. doi:10.1016/j.jtbi.2008.02.041. PMID   18462758.
  22. ↑ Bingham PM (1999). "Human uniqueness: A general theory". Quarterly Review of Biology. 74 (2): 133–169. doi:10.1086/393069. S2CID   59499229.
  23. ↑ Bingham PM, Souza J (2009). Death from a Distance and the Birth of a Humane Universe. South Carolina, USA: BookSurge. ISBN   978-1-4392-5412-7.
  24. 1 2 Bingham PM, Souza J (2013). "Theory testing in prehistoric North America: fruits of one of the world's great archeological natural laboratories". Evolutionary Anthropology. 22 (3): 145–53. doi:10.1002/evan.21359. PMID   23776052.
  25. 1 2 Bingham PM (1999-12-01). "Becoming Human: Evolution and Human Uniqueness. Ian Tattersall". The Quarterly Review of Biology. 74 (4): 499. doi:10.1086/394207. ISSN   0033-5770.
  26. ↑ Sterelny K (2012). The evolved apprentice: how evolution made humans unique. Cambridge, Mass.: The MIT Press. ISBN   978-0-262-52666-1.
  27. ↑ Boyd R, Gintis H, Bowles S (April 2010). "Coordinated punishment of defectors sustains cooperation and can proliferate when rare". Science. 328 (5978): 617–20. Bibcode:2010Sci...328..617B. doi:10.1126/science.1183665. PMID   20431013.
  28. ↑ Johnson DD, MacKay NJ (March 2015). "Fight the power: Lanchester's laws of combat in human evolution". Evolution and Human Behavior. 36 (2): 152–63. Bibcode:2015EHumB..36..152J. doi:10.1016/j.evolhumbehav.2014.11.001.
  29. ↑ niallmck1 (24 January 2021). "Self-Interested or Super-Cooperators? Human Nature from an Evolutionary Perspective". The Weekend University. Retrieved 2021-04-22.{{cite web}}: CS1 maint: numeric names: authors list (link)
  30. ↑ Bingham PM, Souza J, Blitz JH (May 2013). "Introduction: social complexity and the bow in the prehistoric North American record". Evolutionary Anthropology. 22 (3): 81–8. doi:10.1002/evan.21353. PMID   23776043.
  31. ↑ Poe M, Bingham P, Souza J (2010-04-30). "P. Bingham and J. Souza, "Death From a Distance and the Birth of a Humane Universe"". New Books Network.
  32. ↑ Bingham PM (2000). "Human evolution and human history: A complete theory". Evolutionary Anthropology. 9 (6): 248–257. doi: 10.1002/1520-6505(2000)9:6<248::AID-EVAN1003>3.0.CO;2-X .
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