1
|
de Santis MD. On the nature of evolutionary explanations: a critical appraisal of Walter Bock's approach with a new revised proposal. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2024; 46:3. [PMID: 38190055 PMCID: PMC10774170 DOI: 10.1007/s40656-023-00601-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
Walter Bock was committed to developing a framework for evolutionary biology. Bock repeatedly discussed how evolutionary explanations should be considered within the realm of Hempel's deductive-nomological model of scientific explanations. Explanation in evolution would then consist of functional and evolutionary explanations, and within the latter, an explanation can be of nomological-deductive and historical narrative explanations. Thus, a complete evolutionary explanation should include, first, a deductive functional analysis, and then proceed through nomological and historical evolutionary explanations. However, I will argue that his views on the deductive proprieties of functional analysis and the deductive-nomological parts of evolution fail because of the nature of evolution, which contains a historical element that the logic of deduction and Hempel's converting law model do not compass. Conversely, Bock's historical approach gives a critical consideration of the historical narrative element of evolutionary explanation, which is fundamental to the methodology of the historical nature of evolutionary theory. Herein, I will expand and discuss a modern view of evolutionary explanations of traits that includes the currentacknowledgement of the differences between experimental and the historical sciences, including the token and type event dichotomy, that mutually illuminate each other in order to give us a well confirmed and coherent hypothesis for evolutionary explanations. Within this framework, I will argue that the duality of evolutionary explanations is related to two components of character evolution: origin, with its evolutionary pathways along with the history, and maintenance, the function (mainly a current function) for the character being selected.
Collapse
Affiliation(s)
- Marcelo Domingos de Santis
- Departamento de Entomologia, Museu Nacional, UFRJ, Rio de Janeiro, RJ, Brazil.
- Museum Koenig Bonn, Leibniz-Institut zur Analyse des Bioaffiliationersitatswandels, Adenauerallee 127, 53113, Bonn, Germany.
| |
Collapse
|
2
|
Boto L. Evolutionary change and phylogenetic relationships in light of horizontal gene transfer. J Biosci 2016; 40:465-72. [PMID: 25963270 DOI: 10.1007/s12038-015-9514-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Horizontal gene transfer has, over the past 25 years, become a part of evolutionary thinking. In the present paper I discuss horizontal gene transfer (HGT) in relation to contingency, natural selection, evolutionary change speed and the Tree-of-Life endeavour, with the aim of contributing to the understanding of the role of HGT in evolutionary processes. In addition, the challenges that HGT imposes on the current view of evolution are emphasized.
Collapse
Affiliation(s)
- Luis Boto
- Departamento de Biodiversidad y Biologia Evolutiva, Museo Nacional Ciencias Naturales, CSIC, C/ Jose Gutierrez Abascal 2, 28006, Madrid, Spain,
| |
Collapse
|
3
|
Caetano-Anollés D, Caetano-Anollés G. Ribosomal accretion, apriorism and the phylogenetic method: a response to Petrov and Williams. Front Genet 2015; 6:194. [PMID: 26082795 PMCID: PMC4451634 DOI: 10.3389/fgene.2015.00194] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/14/2015] [Indexed: 12/21/2022] Open
Abstract
Historical (ideographic) and non-historical (nomothetic) studies of ribosomal accretion appear to arrive at diametrically opposite conclusions. Phylogenetic analysis of thousands of RNA molecules and protein structures in hundreds of genomes supports the structural origin of the ribosome in RNA decoding and ribosomal mechanics. Predictions from extant features in a handful of rRNA structural models of the large ribosomal subunit support its origin in protein biosynthesis. In recent correspondence, one of us reported that correcting dismissals of conflicting data and avoiding unwarranted assumptions of the nomothetic method reconciled conclusions. In response, Petrov and Williams dismissed our arguments claiming we did not understand their algorithmic model of ribosomal apical growth. Instead, they controverted the historical approach. Here we show that their objections to the phylogenetic method are unjustified, that their algorithm subjectively guarantees back-in-time molecular deconstructions toward the protein biosynthetic core, and that processes of ribosomal growth are much more complex. We prompt abandoning apriorism, decreasing ad hoc hypotheses and integrating historical and non-historical scientific methods.
Collapse
Affiliation(s)
- Derek Caetano-Anollés
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Gustavo Caetano-Anollés
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| |
Collapse
|
4
|
Kim KM, Nasir A, Hwang K, Caetano-Anollés G. A tree of cellular life inferred from a genomic census of molecular functions. J Mol Evol 2014; 79:240-62. [PMID: 25128982 DOI: 10.1007/s00239-014-9637-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
Abstract
Phylogenomics aims to describe evolutionary relatedness between organisms by analyzing genomic data. The common practice is to produce phylogenomic trees from molecular information in the sequence, order, and content of genes in genomes. These phylogenies describe the evolution of life and become valuable tools for taxonomy. The recent availability of structural and functional data for hundreds of genomes now offers the opportunity to study evolution using more deep, conserved, and reliable sets of molecular features. Here, we reconstruct trees of life from the functions of proteins. We start by inferring rooted phylogenomic trees and networks of organisms directly from Gene Ontology annotations. Phylogenies and networks yield novel insights into the emergence and evolution of cellular life. The ancestor of Archaea originated earlier than the ancestors of Bacteria and Eukarya and was thermophilic. In contrast, basal bacterial lineages were non-thermophilic. A close relationship between Plants and Metazoa was also identified that disagrees with the traditional Fungi-Metazoa grouping. While measures of evolutionary reticulation were minimum in Eukarya and maximum in Bacteria, the massive role of horizontal gene transfer in microbes did not materialize in phylogenomic networks. Phylogenies and networks also showed that the best reconstructions were recovered when problematic taxa (i.e., parasitic/symbiotic organisms) and horizontally transferred characters were excluded from analysis. Our results indicate that functionomic data represent a useful addition to the set of molecular characters used for tree reconstruction and that trees of cellular life carry in deep branches considerable predictive power to explain the evolution of living organisms.
Collapse
Affiliation(s)
- Kyung Mo Kim
- Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
| | | | | | | |
Collapse
|
5
|
Caetano-Anollés G, Nasir A, Zhou K, Caetano-Anollés D, Mittenthal JE, Sun FJ, Kim KM. Archaea: the first domain of diversified life. ARCHAEA (VANCOUVER, B.C.) 2014; 2014:590214. [PMID: 24987307 PMCID: PMC4060292 DOI: 10.1155/2014/590214] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 02/15/2014] [Accepted: 03/25/2014] [Indexed: 01/23/2023]
Abstract
The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.
Collapse
Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Arshan Nasir
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kaiyue Zhou
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Derek Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jay E. Mittenthal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Feng-Jie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
| | - Kyung Mo Kim
- Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
| |
Collapse
|
6
|
Kim KM, Nasir A, Caetano-Anollés G. The importance of using realistic evolutionary models for retrodicting proteomes. Biochimie 2014; 99:129-37. [DOI: 10.1016/j.biochi.2013.11.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/22/2013] [Indexed: 01/16/2023]
|
7
|
Lienau EK, Blazar JM, Wang C, Brown EW, Stones R, Musser S, Allard MW. Phylogenomic analysis identifies gene gains that define Salmonella enterica subspecies I. PLoS One 2013; 8:e76821. [PMID: 24204679 PMCID: PMC3810377 DOI: 10.1371/journal.pone.0076821] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 09/04/2013] [Indexed: 11/29/2022] Open
Abstract
Comparative methods for analyzing whole genome sequence (WGS) data enable us to assess the genetic information available for reconstructing the evolutionary history of pathogens. We used the comparative approach to determine diagnostic genes for Salmonella enterica subspecies I. S. enterica subsp. I strains are known to infect warm-blooded organisms regularly while its close relatives tend to infect only cold-blooded organisms. We found 71 genes gained by the common ancestor of Salmonella enterica subspecies I and not subsequently lost by any member of this subspecies sequenced to date. These genes included many putative functional phenotypes. Twenty-seven of these genes are found only in Salmonella enterica subspecies I; we designed primers to test these genes for use as diagnostic sequence targets and data mined the NCBI Sequence Read Archive (SRA) database for draft genomes which carried these genes. We found that the sequence specificity and variability of these amplicons can be used to detect and discriminate among 317 different serovars and strains of Salmonella enterica subspecies I.
Collapse
Affiliation(s)
- E. Kurt Lienau
- Office of the Center Director, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
- Evolution Industries LLC, Frederick, Maryland, United States of America
| | - Jeffrey M. Blazar
- Office of the Center Director, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Charles Wang
- Office of the Center Director, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Eric W. Brown
- Office of the Center Director, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Robert Stones
- The Food and Environment Research Agency, Sand Hutton, York, United Kingdom
| | - Steven Musser
- Office of the Center Director, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Marc W. Allard
- Office of the Center Director, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| |
Collapse
|
8
|
Sterling EJ, Gómez A, Porzecanski AL. A systemic view of biodiversity and its conservation: Processes, interrelationships, and human culture. Bioessays 2010; 32:1090-8. [DOI: 10.1002/bies.201000049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|