1
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Dantzer B, Mabry KE, Bernhardt JR, Cox RM, Francis CD, Ghalambor CK, Hoke KL, Jha S, Ketterson E, Levis NA, McCain KM, Patricelli GL, Paull SH, Pinter-Wollman N, Safran RJ, Schwartz TS, Throop HL, Zaman L, Martin LB. Understanding Organisms Using Ecological Observatory Networks. Integr Org Biol 2023; 5:obad036. [PMID: 37867910 PMCID: PMC10586040 DOI: 10.1093/iob/obad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 06/07/2023] [Accepted: 09/21/2023] [Indexed: 10/24/2023] Open
Abstract
Human activities are rapidly changing ecosystems around the world. These changes have widespread implications for the preservation of biodiversity, agricultural productivity, prevalence of zoonotic diseases, and sociopolitical conflict. To understand and improve the predictive capacity for these and other biological phenomena, some scientists are now relying on observatory networks, which are often composed of systems of sensors, teams of field researchers, and databases of abiotic and biotic measurements across multiple temporal and spatial scales. One well-known example is NEON, the US-based National Ecological Observatory Network. Although NEON and similar networks have informed studies of population, community, and ecosystem ecology for years, they have been minimally used by organismal biologists. NEON provides organismal biologists, in particular those interested in NEON's focal taxa, with an unprecedented opportunity to study phenomena such as range expansions, disease epidemics, invasive species colonization, macrophysiology, and other biological processes that fundamentally involve organismal variation. Here, we use NEON as an exemplar of the promise of observatory networks for understanding the causes and consequences of morphological, behavioral, molecular, and physiological variation among individual organisms.
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Affiliation(s)
- B Dantzer
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109,USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109,USA
| | - K E Mabry
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109,USA
- Department of Biology, New Mexico State University, Las Cruces, NM 88003,USA
| | - J R Bernhardt
- Department of Biology, New Mexico State University, Las Cruces, NM 88003,USA
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - R M Cox
- Department of Biology, University of Virginia, Charlottesville, VA 22940,USA
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407,USA
| | - C D Francis
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407,USA
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N‐7491 Trondheim, Norway
| | - C K Ghalambor
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N‐7491 Trondheim, Norway
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - K L Hoke
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - S Jha
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712,USA
| | - E Ketterson
- Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47405,USA
| | - N A Levis
- Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47405,USA
| | - K M McCain
- Global Health and Infectious Disease Research Center, College of Public Health, University of South Florida, Tampa, FL 33612,USA
| | - G L Patricelli
- Department of Evolution and Ecology, University of California, Davis, CA 95616,USA
| | - S H Paull
- Battelle, National Ecological Observatory Network, 1685 38th Street, Boulder, CO 80301, USA
| | - N Pinter-Wollman
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - R J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder 80309,USA
| | - T S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - H L Throop
- School of Earth and Space Exploration and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - L Zaman
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109,USA
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI 48109, USA
| | - L B Martin
- Global Health and Infectious Disease Research Center and Center for Genomics, College of Public Health, University of South Florida, Tampa, FL 33612,USA
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Pinto BJ, Gamble T, Smith CH, Keating SE, Havird JC, Chiari Y. The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly. J Hered 2023; 114:513-520. [PMID: 36869788 PMCID: PMC10445513 DOI: 10.1093/jhered/esad016] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023] Open
Abstract
Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest-quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified 9 of the 19 chromosomal scaffolds were assembled as a near-single contig, whereas the other 10 chromosomes were each scaffolded together from multiple contigs. We qualitatively identified that the percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction of previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000.
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Affiliation(s)
- Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
- Department of Biological Sciences, Marquette University, Milwaukee WI, USA
- Bell Museum of Natural History, University of Minnesota, St Paul, MN, USA
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Shannon E Keating
- Department of Biological Sciences, Marquette University, Milwaukee WI, USA
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, USA
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3
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Pinto BJ, Gamble T, Smith CH, Keating SE, Havird JC, Chiari Y. The revised reference genome of the leopard gecko ( Eublepharis macularius ) provides insight into the considerations of genome phasing and assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.523807. [PMID: 36712019 PMCID: PMC9882329 DOI: 10.1101/2023.01.20.523807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified that 9 of the 19 chromosomes were assembled as single contigs, while the other 10 chromosomes were each scaffolded together from two or more contigs. We qualitatively identified that percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000. The genome version and its associated annotations are also available via this Figshare repository https://doi.org/10.6084/m9.figshare.20069273 .
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Affiliation(s)
- Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
- Bell Museum of Natural History, University of Minnesota, St Paul, MN USA
| | - Chase H. Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Shannon E. Keating
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
| | - Justin C. Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, USA
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4
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Miller AH, Stroud JT, Losos JB. The ecology and evolution of key innovations. Trends Ecol Evol 2023; 38:122-131. [PMID: 36220711 DOI: 10.1016/j.tree.2022.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/05/2022]
Abstract
The idea of 'key innovations' has long been influential in theoretical and empirical approaches to understanding adaptive diversification. Despite originally revolving around traits inducing major ecological shifts, the key innovation concept itself has evolved, conflating lineage diversification with trait-dependent ecological shifts. In this opinion article we synthesize the history of the term, clarify the relationship between key innovations and adaptive radiation, and propose a return to the original concept of key innovations: the evolution of organismal features which permit a species to occupy a previously inaccessible ecological state. Ultimately, we suggest an integrative approach to studying key innovations, necessitating experimental approaches of form and function, natural history studies of resource use, and phylogenetic comparative perspectives.
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Affiliation(s)
- Aryeh H Miller
- Department of Biology, Washington University, St Louis, MO, USA.
| | - James T Stroud
- Department of Biology, Washington University, St Louis, MO, USA.
| | - Jonathan B Losos
- Department of Biology, Washington University, St Louis, MO, USA.
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5
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Woods HA, Moran AL, Atkinson D, Audzijonyte A, Berenbrink M, Borges FO, Burnett KG, Burnett LE, Coates CJ, Collin R, Costa-Paiva EM, Duncan MI, Ern R, Laetz EMJ, Levin LA, Lindmark M, Lucey NM, McCormick LR, Pierson JJ, Rosa R, Roman MR, Sampaio E, Schulte PM, Sperling EA, Walczyńska A, Verberk WCEP. Integrative Approaches to Understanding Organismal Responses to Aquatic Deoxygenation. THE BIOLOGICAL BULLETIN 2022; 243:85-103. [PMID: 36548975 DOI: 10.1086/722899] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
AbstractOxygen bioavailability is declining in aquatic systems worldwide as a result of climate change and other anthropogenic stressors. For aquatic organisms, the consequences are poorly known but are likely to reflect both direct effects of declining oxygen bioavailability and interactions between oxygen and other stressors, including two-warming and acidification-that have received substantial attention in recent decades and that typically accompany oxygen changes. Drawing on the collected papers in this symposium volume ("An Oxygen Perspective on Climate Change"), we outline the causes and consequences of declining oxygen bioavailability. First, we discuss the scope of natural and predicted anthropogenic changes in aquatic oxygen levels. Although modern organisms are the result of long evolutionary histories during which they were exposed to natural oxygen regimes, anthropogenic change is now exposing them to more extreme conditions and novel combinations of low oxygen with other stressors. Second, we identify behavioral and physiological mechanisms that underlie the interactive effects of oxygen with other stressors, and we assess the range of potential organismal responses to oxygen limitation that occur across levels of biological organization and over multiple timescales. We argue that metabolism and energetics provide a powerful and unifying framework for understanding organism-oxygen interactions. Third, we conclude by outlining a set of approaches for maximizing the effectiveness of future work, including focusing on long-term experiments using biologically realistic variation in experimental factors and taking truly cross-disciplinary and integrative approaches to understanding and predicting future effects.
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6
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Danos N, Staab KL, Whitenack LB. The Core Concepts, Competencies, and Grand Challenges of Comparative Vertebrate Anatomy and Morphology. Integr Org Biol 2022; 4:obac019. [PMID: 35919560 PMCID: PMC9338813 DOI: 10.1093/iob/obac019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 05/02/2022] [Accepted: 05/18/2022] [Indexed: 12/02/2022] Open
Abstract
Core concepts offer coherence to the discourse of a scientific discipline and facilitate teaching by identifying large unifying themes that can be tailored to the level of the class and expertise of the instructor. This approach to teaching has been shown to encourage deeper learning that can be integrated across subdisciplines of biology and has been adopted by several other biology subdisciplines. However, Comparative Vertebrate Anatomy, although one of the oldest biological areas of study, has not had its core concepts identified. Here, we present five core concepts and seven competencies (skills) for Comparative Vertebrate Anatomy that came out of an iterative process of engagement with the broader community of vertebrate morphologists over a 3-year period. The core concepts are (A) evolution, (B) structure and function, (C) morphological development, (D) integration, and (E) human anatomy is the result of vertebrate evolution. The core competencies students should gain from the study of comparative vertebrate anatomy are (F) tree thinking, (G) observation, (H) dissection of specimens, (I) depiction of anatomy, (J) appreciation of the importance of natural history collections, (K) science communication, and (L) data integration. We offer a succinct description of each core concept and competency, examples of learning outcomes that could be used to assess teaching effectiveness, and examples of relevant resources for both instructors and students. Additionally, we pose a grand challenge to the community, arguing that the field of Comparative Vertebrate Anatomy needs to acknowledge racism, androcentrism, homophobia, genocide, slavery, and other influences in its history and address their lingering effects in order to move forward as a thriving discipline that is inclusive of all students and scientists and continues to generate unbiased knowledge for the betterment of humanity. Despite the rigorous process used to compile these core concepts and competencies, we anticipate that they will serve as a framework for an ongoing conversation that ensures Comparative Vertebrate Anatomy remains a relevant field in discovery, innovation, and training of future generations of scientists.
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Affiliation(s)
- Nicole Danos
- Biology, University of San Diego, 5998 Alcala Park, San Diego, CA 92210, USA
| | - Katie Lynn Staab
- Biology Department, McDaniel College, 2 College Hill, Westminster, MD 21157, USA
| | - Lisa B Whitenack
- Depts. of Biology and Geology, Allegheny College, 520 N. Main St., Meadville, PA 16335, USA
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7
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Madhavan M, Mustafa S. Systems biology–the transformative approach to integrate sciences across disciplines. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Life science is the study of living organisms, including bacteria, plants, and animals. Given the importance of biology, chemistry, and bioinformatics, we anticipate that this chapter may contribute to a better understanding of the interdisciplinary connections in life science. Research in applied biological sciences has changed the paradigm of basic and applied research. Biology is the study of life and living organisms, whereas science is a dynamic subject that as a result of constant research, new fields are constantly emerging. Some fields come and go, whereas others develop into new, well-recognized entities. Chemistry is the study of composition of matter and its properties, how the substances merge or separate and also how substances interact with energy. Advances in biology and chemistry provide another means to understand the biological system using many interdisciplinary approaches. Bioinformatics is a multidisciplinary or rather transdisciplinary field that encourages the use of computer tools and methodologies for qualitative and quantitative analysis. There are many instances where two fields, biology and chemistry have intersection. In this chapter, we explain how current knowledge in biology, chemistry, and bioinformatics, as well as its various interdisciplinary domains are merged into life sciences and its applications in biological research.
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Affiliation(s)
- Maya Madhavan
- Department of Biochemistry , Government College for Women , Thiruvananthapuram , Kerala , India
| | - Sabeena Mustafa
- Department of Biostatistics and Bioinformatics , King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA) , Riyadh , Kingdom of Saudi Arabia
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8
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An Information-theoretic approach to dimensionality reduction in data science. INTERNATIONAL JOURNAL OF DATA SCIENCE AND ANALYTICS 2021. [DOI: 10.1007/s41060-021-00272-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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McEntire KD, Gage M, Gawne R, Hadfield MG, Hulshof C, Johnson MA, Levesque DL, Segura J, Pinter-Wollman N. Understanding Drivers of Variation and Predicting Variability Across Levels of Biological Organization. Integr Comp Biol 2021; 61:2119-2131. [PMID: 34259842 DOI: 10.1093/icb/icab160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 12/27/2022] Open
Abstract
Differences within a biological system are ubiquitous, creating variation in nature. Variation underlies all evolutionary processes and allows persistence and resilience in changing environments; thus, uncovering the drivers of variation is critical. The growing recognition that variation is central to biology presents a timely opportunity for determining unifying principles that drive variation across biological levels of organization. Currently, most studies that consider variation are focused at a single biological level and not integrated into a broader perspective. Here we explain what variation is and how it can be measured. We then discuss the importance of variation in natural systems, and briefly describe the biological research that has focused on variation. We outline some of the barriers and solutions to studying variation and its drivers in biological systems. Finally, we detail the challenges and opportunities that may arise when studying the drivers of variation due to the multi-level nature of biological systems. Examining the drivers of variation will lead to a reintegration of biology. It will further forge interdisciplinary collaborations and open opportunities for training diverse quantitative biologists. We anticipate that these insights will inspire new questions and new analytic tools to study the fundamental questions of what drives variation in biological systems and how variation has shaped life.
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Affiliation(s)
| | | | | | | | | | | | - Danielle L Levesque
- University of Maine College of Natural Sciences Forestry and Agriculture, School of Biology and Ecology
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10
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Beaty MM. Guiding the Facial Rejuvenation Journey: Fulfilling the Complete Role of Surgeon and Aesthetic Practitioner. Facial Plast Surg 2021; 37:140-148. [PMID: 33634448 DOI: 10.1055/s-0041-1723756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The facial plastic surgeon's role today includes more than provision of procedural excellence. To provide excellent quality of care effective planning and guidance for patients through the aesthetic journey is needed. Methods for the delivery of this level of care are presented and discussed.
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Affiliation(s)
- Mark M Beaty
- Department of Facial Plastic Surgery, Beaty Facial Plastic Surgery, Atlanta, Georgia
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11
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Education for a biobased economy: Integrating life and social sciences in flexible short courses accessible from different backgrounds. N Biotechnol 2020; 60:72-75. [PMID: 33039695 DOI: 10.1016/j.nbt.2020.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/17/2020] [Accepted: 10/04/2020] [Indexed: 11/20/2022]
Abstract
To achieve ambitious 21st-century goals and deal with high-level complexity, a bio-based economy is required to cross the boundaries of a single sector and integrate tools, language and knowledge drawn from different disciplines and sub-disciplines. The present contribution highlights how life scientists, social scientists, policymakers and industrial stakeholders should work together to make this technological reversal real and feasible. Importantly, going beyond theoretical and methodological integration, the paper underlines the necessity of developing a new and more flexible educational framework that might facilitate interdisciplinary combination. Specifically, the experience of the summer school "Towards a bio-based economy: science, innovation, economics, education" organized by the University of Milano Bicocca in collaboration with Chalmers University is described. The results reveal the need for high-level education programs likely to promote and guide society towards bio-based innovation.
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12
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Sanger TJ, Rajakumar R. How a growing organismal perspective is adding new depth to integrative studies of morphological evolution. Biol Rev Camb Philos Soc 2019; 94:184-198. [PMID: 30009397 DOI: 10.1111/brv.12442] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 06/11/2018] [Accepted: 06/14/2018] [Indexed: 01/24/2023]
Abstract
Over the past half century, the field of Evolutionary Developmental Biology, or Evo-devo, has integrated diverse fields of biology into a more synthetic understanding of morphological diversity. This has resulted in numerous insights into how development can evolve and reciprocally influence morphological evolution, as well as generated several novel theoretical areas. Although comparative by default, there remains a great gap in our understanding of adaptive morphological diversification and how developmental mechanisms influence the shape and pattern of phenotypic variation. Herein we highlight areas of research that are in the process of filling this void, and areas, if investigated more fully, that will add new insights into the diversification of morphology. At the centre of our discussion is an explicit awareness of organismal biology. Here we discuss an organismal framework that is supported by three distinct pillars. First, there is a need for Evo-devo to adopt a high-resolution phylogenetic approach in the study of morphological variation and its developmental underpinnings. Secondly, we propose that to understand the dynamic nature of morphological evolution, investigators need to give more explicit attention to the processes that generate evolutionarily relevant variation at the population level. Finally, we emphasize the need to address more thoroughly the processes that structure variation at micro- and macroevolutionary scales including modularity, morphological integration, constraint, and plasticity. We illustrate the power of these three pillars using numerous examples from both invertebrates and vertebrates to emphasize that many of these approaches are already present within the field, but have yet to be formally integrated into many research programs. We feel that the most exciting new insights will come where the traditional experimental approaches to Evo-devo are integrated more thoroughly with the principles of this organismal framework.
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Affiliation(s)
- Thomas J Sanger
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, U.S.A
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13
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Wellmann J. Gluing life together. Computer simulation in the life sciences: an introduction. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2018; 40:70. [PMID: 30467819 PMCID: PMC6267125 DOI: 10.1007/s40656-018-0235-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Over the course of the last three decades, computer simulations have become a major tool of doing science and engaging with the world, not least in an effort to predict and intervene in a future to come. Born in the context of the Second World War and the discipline of physics, simulations have long spread into most diverse fields of enquiry and technological application. This paper introduces a topical collection focussing on simulations in the life sciences. Echoing the current state of tinkering, fast developments, segmentation of knowledge and interdisciplinary collaboration, and in an effort to bridge the science-humanities divide, the contributors to this collection come from multiple disciplinary backgrounds, including information studies, cognitive sciences, philosophy and biology. The ambiguous character of simulations, their cutting across scientific disciplines, analysis and prediction, understanding and doing, gave rise to their success in contemporary life sciences and has been the object of much scientific debate. One of the main aims of this topical collection, by contrast, is to call into question the assumption of an obvious use and easy transfer of methods between fields of knowledge as diverse as, e.g. physics and biology. The collection presents historical case studies from various biological sub-fields. The articles study how simulations are used and the ways they contribute specifically to our understanding of life. Taking up Sergio Sismondo's description of simulations as "compromises" and "glue", they also critically engage with the question of what exactly the life sciences have been gluing together over the last two decades.
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Affiliation(s)
- Janina Wellmann
- mecs - DFG-Kollegforschergruppe, Medienkulturen der Computersimulation, Leuphana Universität Lüneburg, Universitätsallee 1, 21335, Lüneburg, Germany.
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14
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Wellmann J. Model and movement: studying cell movement in early morphogenesis, 1900 to the present. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2018; 40:59. [PMID: 30206717 DOI: 10.1007/s40656-018-0223-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
Morphogenesis is one of the fundamental processes of developing life. Gastrulation, especially, marks a period of major translocations and bustling rearrangements of cells that give rise to the three germ layers. It was also one of the earliest fields in biology where cell movement and behaviour in living specimens were investigated. This article examines scientific attempts to understand gastrulation from the point of view of cells in motion. It argues that the study of morphogenesis in the twentieth century faced a major dilemma, both epistemological and pictorial: representing form and understanding movement are mutually exclusive, as are understanding form and representing movement. The article follows various ways of modelling, imaging, and simulating gastrular processes, from the early twentieth century to present-day systems biology. The first section examines the tactile modelling of shape changes, the second cell cinematography, mainly the pioneering work of the German embryologists Friedrich Kopsch and Ernst Ludwig Gräper in the 1920s but also a series of classic, yet not widely known, studies of the 1960s. The third section deals with the changes that computer simulation and live-cell imaging introduced to the modelling of shape change and the study of cell movement at the turn of the twenty-first century. Although live-cell imaging promises to experiment upon and represent the living body simultaneously, I argue that the new visuals are an obstacle rather than a solution to the puzzle of understanding cell motion.
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Affiliation(s)
- Janina Wellmann
- mecs - DFG-Kollegforschergruppe, Medienkulturen der Computersimulation, Leuphana Universität Lüneburg, Universitätsallee 1, 21335, Lüneburg, Germany.
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15
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Lane PA. The road before us: Have we come to a “fork in the road” in defining complexity? ECOLOGICAL COMPLEXITY 2018. [DOI: 10.1016/j.ecocom.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Di Camillo CG, Gravili C, De Vito D, Pica D, Piraino S, Puce S, Cerrano C. The importance of applying Standardised Integrative Taxonomy when describing marine benthic organisms and collecting ecological data. INVERTEBR SYST 2018. [DOI: 10.1071/is17067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The decline of morphologically based taxonomy is mainly linked to increasing species redundancy, which probably contributed to a worldwide disinterest in taxonomy, and to a reduction of funding for systematic biology and for expertise training. The present trend in the study of biodiversity is integrated taxonomy, which merges morphological and molecular approaches. At the same time, in many cases new molecular techniques have eclipsed the morphological approach. The application of Standardised Integrative Taxonomy, i.e. a rigorous, common method of description based on the integration between ecological and morphological characteristics, may increase the precision, accessibility, exploitability and longevity of the collected data, and favour the renaissance of taxonomy by new investments in biodiversity exploration.
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17
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Investigating the biodiversity of ciliates in the ‘Age of Integration’. Eur J Protistol 2017; 61:314-322. [DOI: 10.1016/j.ejop.2017.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 01/10/2023]
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18
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Wellmann J. Animating embryos: the in toto representation of life. BRITISH JOURNAL FOR THE HISTORY OF SCIENCE 2017; 50:521-535. [PMID: 28923124 DOI: 10.1017/s0007087417000656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
With the recent advent of systems biology, developmental biology is taking a new turn. Attempts to create a 'digital embryo' are prominent among systems approaches. At the heart of these systems-based endeavours, variously described as 'in vivo imaging', 'live imaging' or 'in toto representation', are visualization techniques that allow researchers to image whole, live embryos at cellular resolution over time. Ultimately, the aim of the visualizations is to build a computer model of embryogenesis. This article examines the role of such visualization techniques in the building of a computational model, focusing, in particular, on the cinematographic character of these representations. It asks how the animated representation of development may change the biological understanding of embryogenesis. By situating the animations of the digital embryo within the iconography of developmental biology, it brings to light the inextricably entwined, yet shifting, borders between the animated, the living and the computational.
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Affiliation(s)
- Janina Wellmann
- *Institute for Advanced Study on Media Cultures of Computer Simulation,Leuphana University Lüneburg,Wallstr.3,21335 Lüneburg,Germany.
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Lira ME, Gardner SM. Structure-function relations in physiology education: Where's the mechanism? ADVANCES IN PHYSIOLOGY EDUCATION 2017; 41:270-278. [PMID: 28442480 DOI: 10.1152/advan.00175.2016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/27/2017] [Accepted: 03/16/2017] [Indexed: 06/07/2023]
Abstract
Physiology demands systems thinking: reasoning within and between levels of biological organization and across different organ systems. Many physiological mechanisms explain how structures and their properties interact at one level of organization to produce emergent functions at a higher level of organization. Current physiology principles, such as structure-function relations, selectively neglect mechanisms by not mentioning this term explicitly. We explored how students characterized mechanisms and functions to shed light on how students make sense of these terms. Students characterized mechanisms as 1) processes that occur at levels of organization lower than that of functions; and 2) as detailed events with many steps involved. We also found that students produced more variability in how they characterized functions compared with mechanisms: students characterized functions in relation to multiple levels of organization and multiple definitions. We interpret these results as evidence that students see mechanisms as holding a more narrow definition than used in the biological sciences, and that students struggle to coordinate and distinguish mechanisms from functions due to cognitive processes germane to learning in many domains. We offer the instructional suggestion that we scaffold student learning by affording students opportunities to relate and also distinguish between these terms so central to understanding physiology.
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Affiliation(s)
- Matthew E Lira
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Stephanie M Gardner
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
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Pitchers WR, Constantinou SJ, Losilla M, Gallant JR. Electric fish genomics: Progress, prospects, and new tools for neuroethology. ACTA ACUST UNITED AC 2016; 110:259-272. [PMID: 27769923 DOI: 10.1016/j.jphysparis.2016.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/06/2016] [Accepted: 10/16/2016] [Indexed: 01/01/2023]
Abstract
Electric fish have served as a model system in biology since the 18th century, providing deep insight into the nature of bioelectrogenesis, the molecular structure of the synapse, and brain circuitry underlying complex behavior. Neuroethologists have collected extensive phenotypic data that span biological levels of analysis from molecules to ecosystems. This phenotypic data, together with genomic resources obtained over the past decades, have motivated new and exciting hypotheses that position the weakly electric fish model to address fundamental 21st century biological questions. This review article considers the molecular data collected for weakly electric fish over the past three decades, and the insights that data of this nature has motivated. For readers relatively new to molecular genetics techniques, we also provide a table of terminology aimed at clarifying the numerous acronyms and techniques that accompany this field. Next, we pose a research agenda for expanding genomic resources for electric fish research over the next 10years. We conclude by considering some of the exciting research prospects for neuroethology that electric fish genomics may offer over the coming decades, if the electric fish community is successful in these endeavors.
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Affiliation(s)
- William R Pitchers
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA.
| | - Savvas J Constantinou
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA
| | - Mauricio Losilla
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA
| | - Jason R Gallant
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA.
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Efstathiou S. Is it possible to give scientific solutions to Grand Challenges? On the idea of grand challenges for life science research. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 56:48-61. [PMID: 26698954 DOI: 10.1016/j.shpsc.2015.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 06/05/2023]
Abstract
This paper argues that challenges that are grand in scope such as "lifelong health and wellbeing", "climate action", or "food security" cannot be addressed through scientific research only. Indeed scientific research could inhibit addressing such challenges if scientific analysis constrains the multiple possible understandings of these challenges into already available scientific categories and concepts without translating between these and everyday concerns. This argument builds on work in philosophy of science and race to postulate a process through which non-scientific notions become part of science. My aim is to make this process available to scrutiny: what I call founding everyday ideas in science is both culturally and epistemologically conditioned. Founding transforms a common idea into one or more scientifically relevant ones, which can be articulated into descriptively thicker and evaluatively deflated terms and enable operationalisation and measurement. The risk of founding however is that it can invisibilise or exclude from realms of scientific scrutiny interpretations that are deemed irrelevant, uninteresting or nonsensical in the domain in question-but which may remain salient for addressing grand-in-scope challenges. The paper considers concepts of "wellbeing" in development economics versus in gerontology to illustrate this process.
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Affiliation(s)
- Sophia Efstathiou
- Norwegian University of Science and Technology, Department of Philosophy and Religious Studies, NTNU Dragvoll, 7491 Trondheim, Norway.
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De Grandis G. Practical integration: The art of balancing values, institutions and knowledge - lessons from the History of British Public Health and Town Planning. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 56:92-105. [PMID: 26598466 DOI: 10.1016/j.shpsc.2015.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
The paper uses two historical examples, public health (1840-1880) and town planning (1945-1975) in Britain, to analyse the challenges faced by goal-driven research, an increasingly important trend in science policy, as exemplified by the prominence of calls for addressing Grand Challenges. Two key points are argued. (1) Given that the aim of research addressing social or global problems is to contribute to improving things, this research should include all the steps necessary to bring science and technology to fruition. This need is captured by the idea of practical integration, which brings this type of research under the umbrella of collective practical reason rather than under the aegis of science. Achieving practical integration is difficult for many reasons: the complexity of social needs, the plurality of values at stake, the limitation of our knowledge, the elusive nature of the skills needed to deal with uncertainty, incomplete information and asymmetries of power. Nevertheless, drawing from the lessons of the case studies, it is argued that (2) practical integration needs a proper balance between values, institutions and knowledge: i.e. a combination of mutual support and mutual limitation. Pursuing such a balance provides a flexible strategy for approximating practical integration.
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Affiliation(s)
- Giovanni De Grandis
- Norwegian University of Science and Technology, Department of Philosophy and Religious Studies, NTNU Dragvoll, 7491 Trondheim, Norway.
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De Grandis G, Efstathiou S. Introduction-Grand Challenges and small steps. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 56:39-47. [PMID: 26705674 DOI: 10.1016/j.shpsc.2015.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This collection addresses two different audiences: 1) historians and philosophers of the life sciences reflecting on collaborations across disciplines, especially as regards defining and addressing Grand Challenges; 2) researchers and other stakeholders involved in cross-disciplinary collaborations aimed at tackling Grand Challenges in the life and medical sciences. The essays collected here offer ideas and resources both for the study and for the practice of goal-driven cross-disciplinary research in the life and medical sciences. We organise this introduction in three sections. The first section provides some background and context. The second motivates our take on this topic and then outlines the central ideas of each paper. The third section highlights the specificity and significance of this approach by considering: a) how this collection departs from existing literature on inter- and trans-disciplinarity, b) what is characteristic about this approach, and c) what role this suggests for the history and philosophy of the life sciences in addressing Grand Challenges.
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Affiliation(s)
- Giovanni De Grandis
- Norwegian University of Science and Technology, Department of Philosophy and Religious Studies, NTNU Dragvoll, 7491 Trondheim, Norway.
| | - Sophia Efstathiou
- Norwegian University of Science and Technology, Department of Philosophy and Religious Studies, NTNU Dragvoll, 7491 Trondheim, Norway.
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Shamchuk AL, MacMillan HA. Crossing boundaries and building bridges: integrative zoology. CAN J ZOOL 2015. [DOI: 10.1139/cjz-2015-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The invited papers in this special issue highlight contributions to the symposium with the same title, held at Genomes to Biomes: the First Joint Meeting of the Canadian Society for Ecology and Evolution, the Canadian Society of Zoologists, and the Society of Canadian Limnologists. Today, leading researchers cross boundaries between layers of biological organization and traditional areas of expertise, and increasingly reach beyond their historical role in society to serve as public educators and science advocates. This series includes reviews of the integrative study of animals ranging from the very small (the world’s southernmost insect) to the very large (rorqual whales), a review on using ancient DNA to elucidate the physiology of long-extinct animals, and research articles that take us from the proteomic response of honey bees to Israeli acute paralysis virus (IAPV) infection to the geographic spread of a harmful invasive earthworm in the boreal forest.
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Affiliation(s)
- Angela L. Shamchuk
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Heath A. MacMillan
- Zoophysiology, Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
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Brock PM, Murdock CC, Martin LB. The history of ecoimmunology and its integration with disease ecology. Integr Comp Biol 2014; 54:353-62. [PMID: 24838746 DOI: 10.1093/icb/icu046] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ecoimmunology is an example of how fruitful integrative approaches to biology can be. Since its emergence, ecoimmunology has sparked constructive debate on a wide range of topics, from the molecular mechanics of immune responses to the role of immunity in shaping the evolution of life histories. To complement the symposium Methods and Mechanisms in Ecoimmunology and commemorate the inception of the Division of Ecoimmunology and Disease Ecology within the Society for Integrative and Comparative Biology, we appraise the origins of ecoimmunology, with a focus on its continuing and valuable integration with disease ecology. Arguably, the greatest contribution of ecoimmunology to wider biology has been the establishment of immunity as an integral part of organismal biology, one that may be regulated to maximize fitness in the context of costs, constraints, and complex interactions. We discuss historical impediments and ongoing progress in ecoimmunology, in particular the thorny issue of what ecoimmunologists should, should not, or cannot measure, and what novel contributions ecoimmunologists have made to the understanding of host-parasite interactions. Finally, we highlight some areas to which ecoimmunology is likely to contribute in the near future.
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Affiliation(s)
- Patrick M Brock
- *Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Center for Infectious Disease Dynamics, Penn State University, PA, USA; Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Courtney C Murdock
- *Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Center for Infectious Disease Dynamics, Penn State University, PA, USA; Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Lynn B Martin
- *Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Center for Infectious Disease Dynamics, Penn State University, PA, USA; Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
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Integrating Ecology and Evolution: Niche Construction and Ecological Engineering. HISTORY, PHILOSOPHY AND THEORY OF THE LIFE SCIENCES 2014. [DOI: 10.1007/978-94-007-7067-6_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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Hunt F, Thornsbury S. Facilitating Transdisciplinary Research in an Evolving Approach to Science. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/jss.2014.24038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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O'Malley MA. When integration fails: Prokaryote phylogeny and the tree of life. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:551-62. [PMID: 23137776 DOI: 10.1016/j.shpsc.2012.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today's literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history (often called 'universal phylogeny'). Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a 'meta-heuristic' in the normative commitments guiding scientific practice.
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Affiliation(s)
- Maureen A O'Malley
- Department of Philosophy, University of Sydney, Quadrangle A14, NSW 2006, Australia.
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29
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21st Century Biology: An Interdisciplinary Approach of Biology, Technology, Engineering and Mathematics Education. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.sbspro.2013.10.732] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Kültz D, Clayton DF, Robinson GE, Albertson C, Carey HV, Cummings ME, Dewar K, Edwards SV, Hofmann HA, Gross LJ, Kingsolver JG, Meaney MJ, Schlinger BA, Shingleton AW, Sokolowski MB, Somero GN, Stanzione DC, Todgham AE. New Frontiers for Organismal Biology. Bioscience 2013. [DOI: 10.1525/bio.2013.63.6.8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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31
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Structuring institutional analysis for urban ecosystems: A key to sustainable urban forest management. Urban Ecosyst 2013. [DOI: 10.1007/s11252-013-0286-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
Integrative Biology (IB) uses experimental or computational quantitative technologies to characterize biological systems at the molecular, cellular, tissue and population levels. IB typically involves the integration of the data, knowledge and capabilities across disciplinary boundaries in order to solve complex problems. We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration that brings jargons, terminologies and taxonomies from various disciplines into a unified network of ontologies; (iii) knowledge integration that integrates disparate knowledge elements from multiple sources; (iv) service integration that build applications out of services provided by different vendors. We argue that IB can benefit significantly from the integration solutions enabled by Semantic Web (SW) technologies. The SW enables scientists to share content beyond the boundaries of applications and websites, resulting into a web of data that is meaningful and understandable to any computers. In this review, we provide insight into how SW technologies can be used to build open, standardized and interoperable solutions for interdisciplinary integration on a global basis. We present a rich set of case studies in system biology, integrative neuroscience, bio-pharmaceutics and translational medicine, to highlight the technical features and benefits of SW applications in IB.
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Affiliation(s)
- Huajun Chen
- College of Computer Science, Zhejiang University, Hangzhou, 310027, P.R. China.
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Eronen JT, Polly PD, Fred M, Damuth J, Frank DC, Mosbrugger V, Scheidegger C, Stenseth NC, Fortelius M. Ecometrics: the traits that bind the past and present together. Integr Zool 2012; 5:88-101. [PMID: 21392327 DOI: 10.1111/j.1749-4877.2010.00192.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We outline here an approach for understanding the biology of climate change, one that integrates data at multiple spatial and temporal scales. Taxon-free trait analysis, or "ecometrics," is based on the idea that the distribution in a community of ecomorphological traits such as tooth structure, limb proportions, body mass, leaf shape, incubation temperature, claw shape, any aspect of anatomy or physiology can be measured across some subset of the organisms in a community. Regardless of temporal or spatial scale, traits are the means by which organisms interact with their environment, biotic and abiotic. Ecometrics measures these interactions by focusing on traits which are easily measurable, whose structure is closely related to their function, and whose function interacts directly with local environment. Ecometric trait distributions are thus a comparatively universal metric for exploring systems dynamics at all scales. The main challenge now is to move beyond investigating how future climate change will affect the distribution of organisms and how it will impact ecosystem services and to shift the perspective to ask how biotic systems interact with changing climate in general, and how climate change affects the interactions within and between the components of the whole biotic-physical system. We believe that it is possible to provide believable, quantitative answers to these questions. Because of this we have initiated an IUBS program iCCB (integrative Climate Change Biology).
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Affiliation(s)
- Jussi T Eronen
- Department of Geosciences and Geography, Helsinki University, FinlandDepartment of Geological Sciences, Indiana University, USAARONIA Research Institute at Åbo Akademi University and Novia, University of Applied Sciences, Coastal Zone Research Team, Ekenäs, FinlandDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USASwiss Federal Research Institute WSL, Birmensdorf, SwitzerlandSenckenberg Natural History Museum and Research Institute, Frankfurt, GermanyCentre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
| | - P David Polly
- Department of Geosciences and Geography, Helsinki University, FinlandDepartment of Geological Sciences, Indiana University, USAARONIA Research Institute at Åbo Akademi University and Novia, University of Applied Sciences, Coastal Zone Research Team, Ekenäs, FinlandDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USASwiss Federal Research Institute WSL, Birmensdorf, SwitzerlandSenckenberg Natural History Museum and Research Institute, Frankfurt, GermanyCentre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
| | - Marianne Fred
- Department of Geosciences and Geography, Helsinki University, FinlandDepartment of Geological Sciences, Indiana University, USAARONIA Research Institute at Åbo Akademi University and Novia, University of Applied Sciences, Coastal Zone Research Team, Ekenäs, FinlandDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USASwiss Federal Research Institute WSL, Birmensdorf, SwitzerlandSenckenberg Natural History Museum and Research Institute, Frankfurt, GermanyCentre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
| | - John Damuth
- Department of Geosciences and Geography, Helsinki University, FinlandDepartment of Geological Sciences, Indiana University, USAARONIA Research Institute at Åbo Akademi University and Novia, University of Applied Sciences, Coastal Zone Research Team, Ekenäs, FinlandDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USASwiss Federal Research Institute WSL, Birmensdorf, SwitzerlandSenckenberg Natural History Museum and Research Institute, Frankfurt, GermanyCentre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
| | - David C Frank
- Department of Geosciences and Geography, Helsinki University, FinlandDepartment of Geological Sciences, Indiana University, USAARONIA Research Institute at Åbo Akademi University and Novia, University of Applied Sciences, Coastal Zone Research Team, Ekenäs, FinlandDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USASwiss Federal Research Institute WSL, Birmensdorf, SwitzerlandSenckenberg Natural History Museum and Research Institute, Frankfurt, GermanyCentre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
| | - Volker Mosbrugger
- Department of Geosciences and Geography, Helsinki University, FinlandDepartment of Geological Sciences, Indiana University, USAARONIA Research Institute at Åbo Akademi University and Novia, University of Applied Sciences, Coastal Zone Research Team, Ekenäs, FinlandDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USASwiss Federal Research Institute WSL, Birmensdorf, SwitzerlandSenckenberg Natural History Museum and Research Institute, Frankfurt, GermanyCentre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
| | - Christoph Scheidegger
- Department of Geosciences and Geography, Helsinki University, FinlandDepartment of Geological Sciences, Indiana University, USAARONIA Research Institute at Åbo Akademi University and Novia, University of Applied Sciences, Coastal Zone Research Team, Ekenäs, FinlandDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USASwiss Federal Research Institute WSL, Birmensdorf, SwitzerlandSenckenberg Natural History Museum and Research Institute, Frankfurt, GermanyCentre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
| | - Nils Chr Stenseth
- Department of Geosciences and Geography, Helsinki University, FinlandDepartment of Geological Sciences, Indiana University, USAARONIA Research Institute at Åbo Akademi University and Novia, University of Applied Sciences, Coastal Zone Research Team, Ekenäs, FinlandDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USASwiss Federal Research Institute WSL, Birmensdorf, SwitzerlandSenckenberg Natural History Museum and Research Institute, Frankfurt, GermanyCentre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
| | - Mikael Fortelius
- Department of Geosciences and Geography, Helsinki University, FinlandDepartment of Geological Sciences, Indiana University, USAARONIA Research Institute at Åbo Akademi University and Novia, University of Applied Sciences, Coastal Zone Research Team, Ekenäs, FinlandDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USASwiss Federal Research Institute WSL, Birmensdorf, SwitzerlandSenckenberg Natural History Museum and Research Institute, Frankfurt, GermanyCentre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
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Polly PD, Eronen JT, Fred M, Dietl GP, Mosbrugger V, Scheidegger C, Frank DC, Damuth J, Stenseth NC, Fortelius M. History matters: ecometrics and integrative climate change biology. Proc Biol Sci 2011; 278:1131-40. [PMID: 21227966 PMCID: PMC3049084 DOI: 10.1098/rspb.2010.2233] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Climate change research is increasingly focusing on the dynamics among species, ecosystems and climates. Better data about the historical behaviours of these dynamics are urgently needed. Such data are already available from ecology, archaeology, palaeontology and geology, but their integration into climate change research is hampered by differences in their temporal and geographical scales. One productive way to unite data across scales is the study of functional morphological traits, which can form a common denominator for studying interactions between species and climate across taxa, across ecosystems, across space and through time—an approach we call ‘ecometrics’. The sampling methods that have become established in palaeontology to standardize over different scales can be synthesized with tools from community ecology and climate change biology to improve our understanding of the dynamics among species, ecosystems, climates and earth systems over time. Developing these approaches into an integrative climate change biology will help enrich our understanding of the changes our modern world is undergoing.
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Affiliation(s)
- P David Polly
- Department of Geological Sciences, Indiana University, Bloomington, IN 47405, USA.
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Robinson GE, Banks JA, Padilla DK, Burggren WW, Cohen CS, Delwiche CF, Funk V, Hoekstra HE, Jarvis ED, Johnson L, Martindale MQ, del Rio CM, Medina M, Salt DE, Sinha S, Specht C, Strange K, Strassmann JE, Swalla BJ, Tomanek L. Empowering 21st Century Biology. Bioscience 2010. [DOI: 10.1525/bio.2010.60.11.8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Sih A, Stamps J, Yang LH, McElreath R, Ramenofsky M. Behavior as a key component of integrative biology in a human-altered world. Integr Comp Biol 2010; 50:934-44. [PMID: 21558249 DOI: 10.1093/icb/icq148] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A major grand challenge in biology is to understand the interactions between an organism and its environment. Behavior resides in the central core of this association as it affects and is affected by development, physiology, ecological dynamics, environmental choice, and evolution. We present this central role of behavior in a diagram illustrating the multifaceted program emphasizing the necessity for understanding this nexus and to fully appreciate the organism in its environment given the ongoing changes affected by contemporary human induced, rapid environmental change (HIREC). We call for the consideration of educational and research focuses to concentrate on the interdisciplinary role that behavior plays in the integration of biological processes.
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Affiliation(s)
- Andrew Sih
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
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Schwenk K, Padilla DK, Bakken GS, Full RJ. Grand challenges in organismal biology. Integr Comp Biol 2009; 49:7-14. [DOI: 10.1093/icb/icp034] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Moslemi JM, Capps KA, Johnson MS, Maul J, McIntyre PB, Melvin AM, Vadas TM, Vallano DM, Watkins JM, Weiss M. Training Tomorrow's Environmental Problem Solvers: An Integrative Approach to Graduate Education. Bioscience 2009. [DOI: 10.1525/bio.2009.59.6.10] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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