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Title: Nature and Consequences of Biological Reductionism for the Immunological Study of Infectious Diseases

Abstract

Evolution has conserved “economic” systems that perform many functions, faster or better, with less. For example, three to five leukocyte types protect from thousands of pathogens. In order to achieve so much with so little, biological systems combine their limited elements, creating complex structures. Yet, the prevalent research paradigm is reductionist. Focusing on infectious diseases, reductionist and non-reductionist views are here described. Furthermore, the literature indicates that reductionism is associated with information loss and errors, while non-reductionist operations can extract more information from the same data. When designed to capture one-to-many/many-to-one interactions—including the use of arrows that connect pairs of consecutive observations—non-reductionist (spatial–temporal) constructs eliminate data variability from all dimensions, except along one line, while arrows describe the directionality of temporal changes that occur along the line. To validate the patterns detected by non-reductionist operations, reductionist procedures are needed. Integrated (non-reductionist and reductionist) methods can (i) distinguish data subsets that differ immunologically and statistically; (ii) differentiate false-negative from -positive errors; (iii) discriminate disease stages; (iv) capture in vivo, multilevel interactions that consider the patient, the microbe, and antibiotic-mediated responses; and (v) assess dynamics. Integrated methods provide repeatable and biologically interpretable information.

Authors:
 [1];  [2];  [3];  [4];  [1];  [5];  [6];  [2];  [7];  [8];  [9];  [10]; ORCiD logo [11];  [12]
  1. Univ. of New Mexico, Albuquerque, NM (United States)
  2. Kimron Veterinary Inst., Bet Dagan (Israel). National Mastitis Center
  3. US Environmental Protection Agency (EPA), Seattle, WA (United States); Michigan State Univ., East Lansing, MI (United States)
  4. Center for Research and Advanced Studies of the National Polytechnic Inst. (CINVESTAV), Merida (Mexico)
  5. National and Kapodistrian Univ., Athens (Greece)
  6. Univ. of Peloponnese, Sparta (Greece)
  7. Univ. of Milan (Italy)
  8. Univ. of Cyprus, Nicosia (Cyprus)
  9. Univ. of New Mexico, Albuquerque, NM (United States). Dept. of Internal Medicine
  10. Univ. of Cyprus, Nicosia (Cyprus). Dept. of Biological Sciences
  11. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Biosecurity and Public Health
  12. Univ. of Strasbourg (France). National Center of Scientific Research
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1374353
Report Number(s):
LA-UR-17-22486
Journal ID: ISSN 1664-3224
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Frontiers in Immunology
Additional Journal Information:
Journal Volume: 8; Journal ID: ISSN 1664-3224
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; Biological Science; Reductionism, infectious diseases; methods; host–microbe interactions; reductionism; non-reductionism; pattern recognition

Citation Formats

Rivas, Ariel L., Leitner, Gabriel, Jankowski, Mark D., Hoogesteijn, Almira L., Iandiorio, Michelle J., Chatzipanagiotou, Stylianos, Ioannidis, Anastasios, Blum, Shlomo E., Piccinini, Renata, Antoniades, Athos, Fazio, Jane C., Apidianakis, Yiorgos, Fair, Jeanne M., and Van Regenmortel, Marc H. V. Nature and Consequences of Biological Reductionism for the Immunological Study of Infectious Diseases. United States: N. p., 2017. Web. doi:10.3389/fimmu.2017.00612.
Rivas, Ariel L., Leitner, Gabriel, Jankowski, Mark D., Hoogesteijn, Almira L., Iandiorio, Michelle J., Chatzipanagiotou, Stylianos, Ioannidis, Anastasios, Blum, Shlomo E., Piccinini, Renata, Antoniades, Athos, Fazio, Jane C., Apidianakis, Yiorgos, Fair, Jeanne M., & Van Regenmortel, Marc H. V. Nature and Consequences of Biological Reductionism for the Immunological Study of Infectious Diseases. United States. doi:10.3389/fimmu.2017.00612.
Rivas, Ariel L., Leitner, Gabriel, Jankowski, Mark D., Hoogesteijn, Almira L., Iandiorio, Michelle J., Chatzipanagiotou, Stylianos, Ioannidis, Anastasios, Blum, Shlomo E., Piccinini, Renata, Antoniades, Athos, Fazio, Jane C., Apidianakis, Yiorgos, Fair, Jeanne M., and Van Regenmortel, Marc H. V. Wed . "Nature and Consequences of Biological Reductionism for the Immunological Study of Infectious Diseases". United States. doi:10.3389/fimmu.2017.00612. https://www.osti.gov/servlets/purl/1374353.
@article{osti_1374353,
title = {Nature and Consequences of Biological Reductionism for the Immunological Study of Infectious Diseases},
author = {Rivas, Ariel L. and Leitner, Gabriel and Jankowski, Mark D. and Hoogesteijn, Almira L. and Iandiorio, Michelle J. and Chatzipanagiotou, Stylianos and Ioannidis, Anastasios and Blum, Shlomo E. and Piccinini, Renata and Antoniades, Athos and Fazio, Jane C. and Apidianakis, Yiorgos and Fair, Jeanne M. and Van Regenmortel, Marc H. V.},
abstractNote = {Evolution has conserved “economic” systems that perform many functions, faster or better, with less. For example, three to five leukocyte types protect from thousands of pathogens. In order to achieve so much with so little, biological systems combine their limited elements, creating complex structures. Yet, the prevalent research paradigm is reductionist. Focusing on infectious diseases, reductionist and non-reductionist views are here described. Furthermore, the literature indicates that reductionism is associated with information loss and errors, while non-reductionist operations can extract more information from the same data. When designed to capture one-to-many/many-to-one interactions—including the use of arrows that connect pairs of consecutive observations—non-reductionist (spatial–temporal) constructs eliminate data variability from all dimensions, except along one line, while arrows describe the directionality of temporal changes that occur along the line. To validate the patterns detected by non-reductionist operations, reductionist procedures are needed. Integrated (non-reductionist and reductionist) methods can (i) distinguish data subsets that differ immunologically and statistically; (ii) differentiate false-negative from -positive errors; (iii) discriminate disease stages; (iv) capture in vivo, multilevel interactions that consider the patient, the microbe, and antibiotic-mediated responses; and (v) assess dynamics. Integrated methods provide repeatable and biologically interpretable information.},
doi = {10.3389/fimmu.2017.00612},
journal = {Frontiers in Immunology},
number = ,
volume = 8,
place = {United States},
year = {Wed May 31 00:00:00 EDT 2017},
month = {Wed May 31 00:00:00 EDT 2017}
}

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