Life Sciences Commons^™

Thinking About Thinking Chickens, Lori Marino

Lori Marino, PhD

This response focuses on three major conceptual threads that run through the peer commentary on my target article: (1) how the use of chickens influences our views of them, (2) whether education is effective, and (3) what components of chicken psychology are most relevant to understanding who chickens are.

The Inconvenient Truth About Thinking Chickens, Lori Marino

Lori Marino, PhD

Original Abstract: Domestic chickens are members of an order, Aves, which has been the focus of a revolution in our understanding of neuroanatomical, cognitive, and social complexity. Some birds are now known to be on a par with many mammals in their intelligence, emotional sophistication, and social interaction. Yet views of chickens have largely remained unrevised in light of this new evidence. In this paper, I examine the data on cognition, emotions, personality, and sociality in chickens, exploring such areas as self-awareness, cognitive bias, social learning and self-control, and comparing their abilities with other birds and other vertebrates, particularly …

Intelligence, Complexity, And Individuality In Sheep, Lori Marino, Debra Merskin

Lori Marino, PhD

Domestic sheep (Ovis aries) are among the earliest animals domesticated for human use. They are consumed worldwide as mutton, hogget, and lamb, kept as wool and milk producers, and used extensively in scientific research. The popular stereotype is that sheep are docile, passive, unintelligent, and timid, but a review of the research on their behavior, affect, cognition, and personality reveals that they are complex, individualistic, and social.

The State Of The Animals Iii: 2005, Deborah J. Salem, Andrew N. Rowan

Andrew N. Rowan, DPhil

In this third, all new, volume in the State of the Animals series, scholars and experts in animal protection examine the challenges facing companion animals, marine mammals, and nonhuman primates and review legal protection for animals here and abroad.

The Animal Research Controversy: Protest, Process & Public Policy, Andrew N. Rowan, Franklin M. Loew, Joan C. Weer

Andrew N. Rowan, DPhil

The controversy today regarding the use of animals in research appears on the surface to be a strongly polarized struggle between the scientific community and the animal protection movement. However, there is a wide range of opinions and philosophies on both sides. Mistrust between the factions has blossomed while communication has withered. Through the 1960s, 1970s and early 1980s, the animal movement grew in numbers and financial resources, and developed much greater public recognition and political clout. The research community paid relatively little attention to the animal movement for much of this period but, alarmed by several public relations coups …

Subsistence Strategies In Traditional Societies Distinguish Gut Microbiomes, Alexandra J. Obregon-Tito, Raul Y. Tito, Jessica Metcalf, Krithivasan Sankaranarayanan, Jose C. Clemente, Luke K. Ursell, Zhenjiang Zech Xu, Will Van Treuren, Rob Knight, Patrick M. Gaffney, Paul Spicer, Paul Lawson, Luis Marin-Reyes, Omar Trujillo-Villarroel, Morris Foster, Emilio Guija-Poma, Luzmila Troncoso-Corzo, Christina Warinner, Andrew T. Ozga, Cecil M. Lewis Jr.

Andrew Ozga

Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional …

Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. Macdonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner

Andrew Ozga

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon …

The Genesis Of Malaria: The Origin Of Mosquitoes And Their Protistan Cargo, Plasmodium Falciparum, Alan L. Gillen, Frank Sherwin

Alan L. Gillen

Malaria is caused by the parasite belonging to the genus Plasmodium; however, creation biologists maintain this organism was not always parasitic. Plasmodium is probably a degenerate form of algae. Mosquitoes, the vector of Plasmodium, were probably designed to be pollinators, not parasite vectors. In this article, we present both the evolutionary and creation explanation for the origin of malaria with a mention to its vector, the mosquito.

The purpose of this article is to provide a reasonable explanation for the genesis of malaria. Microbiology and parasitology research based on the creation paradigm appears to provide some answers to these puzzling …

Critically Evaluating Animal Research, Andrew Knight

Andrew Knight, PhD

No abstract provided.

Orca Behavior And Subsequent Aggression Associated With Oceanarium Confinement, Robert Anderson, Robyn Waayers, Andrew Knight

Andrew Knight, PhD

Based on neuroanatomical indices such as brain size and encephalization quotient, orcas are among the most intelligent animals on Earth. They display a range of complex behaviors indicative of social intelligence, but these are difficult to study in the open ocean where protective laws may apply, or in captivity, where access is constrained for commercial and safety reasons. From 1979 to 1980, however, we were able to interact with juvenile orcas in an unstructured way at San Diego’s SeaWorld facility. We observed in the animals what appeared to be pranks, tests of trust, limited use of tactical deception, emotional self-control, …

Goats Prefer Positive Human Emotional Facial Expressions, Christian Nawroth, Natalia Albuquerque, Carine Savalli, Marie-Sophie Single, Alan G. Mcelligott

Alan G. McElligott, PhD

Domestication has shaped the physiology and the behaviour of animals to better adapt to human environments. Therefore, human facial expressions may be highly informative for animals domesticated for working closely with people, such as dogs and horses. However, it is not known whether other animals, and particularly those domesticated primarily for production, such as goats, are capable of perceiving human emotional cues. In this study, we investigated whether goats can distinguish human facial expressions when simultaneously shown two images of an unfamiliar human with different emotional valences (positive/ happy or negative/angry). Both images were vertically attached to a wall on …

Goats Prefer Positive Human Emotional Facial Expressions, Christian Nawroth, Natalia Albuquerque, Carine Savalli, Marie-Sophie Single, Alan G. Mcelligott

Christian Nawroth, PhD

Domestication has shaped the physiology and the behaviour of animals to better adapt to human environments. Therefore, human facial expressions may be highly informative for animals domesticated for working closely with people, such as dogs and horses. However, it is not known whether other animals, and particularly those domesticated primarily for production, such as goats, are capable of perceiving human emotional cues. In this study, we investigated whether goats can distinguish human facial expressions when simultaneously shown two images of an unfamiliar human with different emotional valences (positive/ happy or negative/angry). Both images were vertically attached to a wall on …

Final Thesis For Submission.Pdf, Nisha Patel

Nisha Patel

Mode And Rate Of Evolution Of Haemosporidian Mitochondrial Genomes: Timing The Radiation Of Avian Parasites, Patricia Parker, M Andreína Pacheco, Nubia E. Matta, Gediminas Valkiūnas, Beatriz Mello, Craig E. Stanley Jr, Miguel Lentino, Maria Alexandra Garcia-Amado, Michael Cranfield, Sergei L Kosakovsky Pond, Ananias A. Escalante

Patricia Parker

Clusters Of Alpha Satellite On Human Chromosome 21 Are Dispersed Far Onto The Short Arm And Lack Ancient Layers, William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, Jeffrey Doering

Catherine Putonti

Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the …

Crystal Structure Of Apobec3a Bound To Single-Stranded Dna Reveals Structural Basis For Cytidine Deamination And Specificity, Takahide Kouno, Tania V. Silvas, Brendan J. Hilbert, Shivender Shandilya, Markus-Frederik Bohn, Brian A. Kelch, William E. Royer, Mohan Somasundaran, Nese Kurt Yilmaz, Hiroshi Matsuo, Celia A. Schiffer

Celia A. Schiffer

Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 A. This structure not only visualizes the active site …

A Genetic Signature Of The Evolution Of Loss Of Flight In The Galapagos Cormorant, Patricia Parker, Alejandro Burga, Weiguang Wang, Eyal Ben-David, Paul C. Wolf, Andrew M. Ramey, Claudio Verdugo, Karen Lyons, Leonid Kruglyak

Patricia Parker

High-Level Systematics And Phylogeny Of The Extant Scorpions (Scorpiones: Orthosterni), Michael E. Soleglad, Victor Fet

Victor Fet

A number of authors (e. g. Birula, 1917a, 1917b; Mello-Leitão, 1945; Stockwell, 1989) addressed above-level systematics of extant scorpions, and accepted the grouping of scorpion families in several superfamilies. At the same time, Kjellesvig-Waering (1986) classified all extant scorpions under the same superfamily, Scorpionoidea. Sissom (1990) and Fet et al. (2000) did not list any superfamilies, considering the systematic situation above family (and often at the family level as well) unresolved. Most recently, Lourenço (2000a) listed six superfamilies, largely following the unpublished but important study of Stockwell (1989). The goal of this paper is to address scorpion systematics and phylogeny …

Intrinsic Axonal Growth And The Drive For Regeneration, Kevin O'Donovan

Kevin O'Donovan

No abstract provided.

Microhabitat Use Affects Brain Size And Structure In Intertidal Gobies, Gemma E. White, Culum Brown

Culum Brown, PhD

The ecological cognition hypothesis poses that the brains and behaviours of individuals are largely shaped by the environments in which they live and the associated challenges they must overcome during their lives. Here we examine the effect of environmental complexity on relative brain size in 4 species of intertidal gobies from differing habitats. Two species were rock pool specialists that lived on spatially complex rocky shores, while the remainder lived on dynamic, but structurally simple, sandy shores. We found that rock pool-dwelling species had relatively larger brains and telencephalons in particular, while sand-dwelling species had a larger optic tectum and …

Variation In Brain Morphology Of Intertidal Gobies: A Comparison Of Methodologies Used To Quantitatively Assess Brain Volumes In Fish, Gemma E. White, Culum Brown

Culum Brown, PhD

When correlating brain size and structure with behavioural and environmental characteristics, a range of techniques can be utilised. This study used gobiid fishes to quantitatively compare brain volumes obtained via three different methods; these included the commonly used techniques of histology and approximating brain volume to an idealised ellipsoid, and the recently established technique of X-ray micro-computed tomography (micro-CT). It was found that all three methods differed significantly from one another in their volume estimates for most brain lobes. The ellipsoid method was prone to over- or under-estimation of lobe size, histology caused shrinkage in the telencephalon, and although micro-CT …

Animal Pleasure And Its Moral Significance, Jonathan Balcombe

Jonathan Balcombe, PhD

This paper presents arguments for, and evidence in support of, the important role of pleasure in animals’ lives, and outlines its considerable significance to humankind’s relationship to other animals. In the realms of animal sentience, almost all scholarly discussion revolves around its negative aspects: pain, stress, distress, and suffering. By contrast, the positive aspects of sentience – rewards and pleasures – have been rarely broached by scientists. Yet, evolutionary principles predict that animals, like humans, are motivated to seek rewards, and not merely to avoid pain and suffering. Natural selection favours behaviours that enhance survival and procreation. In the conscious, …

Evaluation Of The Utility Of Deciduous Molar Morphological Variation In Great Ape Phylogenetic Analysis, Anna M. Hardin, Scott S. Legge

Scott Legge

Non-metric dental traits are well- established tools for anthropologists investigating population affiliation and movement in humans. Nonetheless, similar traits in the great apes have received considerably less attention. The present study provides data on non-metric trait variability in the deciduous molars of great apes from museum context. Twenty-eight traits are observed in the upper and lower deciduous molars in specimens of Pan troglodytes, Pan paniscus, Gorilla gorilla, and Gorilla beringei. These groups are compared based on trait frequencies and mean measures of divergence. This study demonstrates the variability of non-metric traits in the deciduous molars of chimpanzees and gorillas. These …

Evolutionary Biology For The 21st Century, Robert Ricklefs, Jonathan B. Losos, Stevan J. Arnold, Gill Bejerano, E. D. Brodie Iii, David Hibbett, Hopi E. Hoekstra, David P. Mindell, Antonia Monteiro, Craig Moritz, H. Allen Orr, Dmitri A. Petrov, Susanne S. Renner, Pamela S. Soltis, Thomas L. Turner

Robert Ricklefs

No abstract provided.

Shrews, Rats, And A Polecat In "The Pardoner's Tale", Sandy Feinstein, Neal Woodman

Neal Woodman

No abstract provided.

How Culture Makes Us Human: Primate Social Evolution And The Formation Of Human Societies, Dwight W. Read

Dwight W Read

Evaluation Of The Minimum Energy Hypothesis And Other Potential Optimality Criteria For Human Running, Ross H. Miller, Brian R. Umberger, Joseph Hamill, Graham E. Caldwell

Joseph Hamill

A popular hypothesis for human running is that gait mechanics and muscular activity are optimized in order to minimize the cost of transport (CoT). Humans running at any particular speed appear to naturally select a stride length that maintains a low CoT when compared with other possible stride lengths. However, it is unknown if the nervous system prioritizes the CoT itself for minimization, or if some other quantity is minimized and a low CoT is a consequential effect. To address this question, we generated predictive computer simulations of running using an anatomically inspired musculoskeletal model and compared the results with …

Molecular Cloning And Characterization Of The Porcine Fto Promoter And Coding Regions.Pdf, Jinming Huang, Yunzhou Yang, Gang Liu, Jibin Zhang, Xinxing Dong, Ying Bai, Meiying Fang

Jibin Zhang

Evolution Of The Cd163 Family And Its Relationship To The Bovine Gamma Delta T Cell Co-Receptor Wc1, Carolyn T. A. Herzig, Ray W. Walters, Cynthia L. Baldwin, Janice T. Telfer

Janice C. Telfer

Background

The scavenger receptor cysteine rich (SRCR) domain is an ancient and conserved protein domain. CD163 and WC1 molecules are classed together as group B SRCR superfamily members, along with Spα, CD5 and CD6, all of which are expressed by immune system cells. There are three known types of CD163 molecules in mammals, CD163A (M130, coded for by CD163), CD163b (M160, coded for by CD163L1) and CD163c-α (CD163L1 or SCART), while their nearest relative, WC1, is encoded by a multigene family so far identified in the artiodactyl species of cattle, sheep, and pigs. Results

We annotated the bovine genome and …

Evolution Of The Cd163 Family And Its Relationship To The Bovine Gamma Delta T Cell Co-Receptor Wc1, Carolyn Ta Herzig, Ray W. Waters, Cynthia Baldwin, Janice C. Telfer

Cynthia Baldwin

Background: The scavenger receptor cysteine rich (SRCR) domain is an ancient and conserved protein domain. CD163 and WC1 molecules are classed together as group B SRCR superfamily members, along with Spα, CD5 and CD6, all of which are expressed by immune system cells. There are three known types of CD163 molecules in mammals, CD163A (M130, coded for by CD163), CD163b (M160, coded for by CD163L1) and CD163c-α (CD163L1 or SCART), while their nearest relative, WC1, is encoded by a multigene family so far identified in the artiodactyl species of cattle, sheep, and pigs. Results: We annotated the bovine genome and …