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1.  From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks 
ZooKeys  2012;235-253.
Part diary, part scientific record, biological field notebooks often contain details necessary to understanding the location and environmental conditions existent during collecting events. Despite their clear value for (and recent use in) global change studies, the text-mining outputs from field notebooks have been idiosyncratic to specific research projects, and impossible to discover or re-use. Best practices and workflows for digitization, transcription, extraction, and integration with other sources are nascent or non-existent. In this paper, we demonstrate a workflow to generate structured outputs while also maintaining links to the original texts. The first step in this workflow was to place already digitized and transcribed field notebooks from the University of Colorado Museum of Natural History founder, Junius Henderson, on Wikisource, an open text transcription platform. Next, we created Wikisource templates to document places, dates, and taxa to facilitate annotation and wiki-linking. We then requested help from the public, through social media tools, to take advantage of volunteer efforts and energy. After three notebooks were fully annotated, content was converted into XML and annotations were extracted and cross-walked into Darwin Core compliant record sets. Finally, these recordsets were vetted, to provide valid taxon names, via a process we call “taxonomic referencing.” The result is identification and mobilization of 1,068 observations from three of Henderson’s thirteen notebooks and a publishable Darwin Core record set for use in other analyses. Although challenges remain, this work demonstrates a feasible approach to unlock observations from field notebooks that enhances their discovery and interoperability without losing the narrative context from which those observations are drawn.
“Compose your notes as if you were writing a letter to someone a century in the future.”
Perrine and Patton (2011)
PMCID: PMC3406479  PMID: 22859891
Field notes; notebooks; crowd sourcing; digitization; biodiversity; transcription; text-mining; Darwin Core; Junius Henderson; annotation; taxonomic referencing; natural history; Wikisource; Colorado; species occurrence records
2.  Charles Darwin and the Origin of Life 
When Charles Darwin published The Origin of Species 150 years ago he consciously avoided discussing the origin of life. However, analysis of some other texts written by Darwin, and of the correspondence he exchanged with friends and colleagues demonstrates that he took for granted the possibility of a natural emergence of the first life forms. As shown by notes from the pages he excised from his private notebooks, as early as 1837 Darwin was convinced that “the intimate relation of Life with laws of chemical combination, & the universality of latter render spontaneous generation not improbable”. Like many of his contemporaries, Darwin rejected the idea that putrefaction of preexisting organic compounds could lead to the appearance of organisms. Although he favored the possibility that life could appear by natural processes from simple inorganic compounds, his reluctance to discuss the issue resulted from his recognition that at the time it was possible to undertake the experimental study of the emergence of life.
PMCID: PMC2745620  PMID: 19633921
Darwin; Warm little pond; Origin of life; Spontaneous generation
3.  Reconstructing the Past: A Century of Ideas About Emotion in Psychology 
Emotion review  2009;1(4):316-339.
Within the discipline of psychology, the conventional history outlines the development of two fundamental approaches to the scientific study of emotion—“basic emotion” and “appraisal” traditions. In this article, we outline the development of a third approach to emotion that exists in the psychological literature—the “psychological constructionist” tradition. In the process, we discuss a number of works that have virtually disappeared from the citation trail in psychological discussions of emotion. We also correct some misconceptions about early sources, such as work by Darwin and James. Taken together, these three contributions make for a fuller and more accurate account of ideas about emotion during the century stretching from 1855 to just before 1960.
PMCID: PMC2835158  PMID: 20221412
affect; appraisal; basic emotion; emotion; history; psychological construction
4.  Darwin's goldmine is still open: variation and selection run the world 
The scientific contribution of Darwin, still agonized in many religious circles, has now been recognized and celebrated by scientists from various disciplines. However, in recent years, several evolutionists have criticized Darwin as outdated, arguing that “Darwinism,” assimilated to the “tree of life,” cannot explain microbial evolution, or else was not operating in early life evolution. These critics either confuse “Darwinism” and old versions of “neo-Darwinism” or misunderstand the role of gene transfers in evolution. The core of Darwin explanation of evolution (variation/selection) remains necessary and sufficient to decipher the history of life. The enormous diversity of mechanisms underlying variations has been successfully interpreted by evolutionists in this framework and has considerably enriched the corpus of evolutionary biology without the necessity to kill the father. However, it remains for evolutionists to acknowledge interactions between cells and viruses (unknown for Darwin) as a major driving force in life evolution.
PMCID: PMC3417645  PMID: 22919695
evolutionary synthesis; variation; natural selection; lateral gene transfer; Darwinian threshold; viruses
5.  John Lubbock, science, and the liberal intellectual 
John Lubbock's longest-standing scientific research interest was entomology. Some of his earliest systematic investigations of insect and marine life began under the tutelage of Darwin. Darwin shaped the trajectory of, and the programme for, Lubbock's natural history work. However, to understand John Lubbock's identity as a scientist, he must be located within the context of the Victorian ‘intellectual’. This paper traces Lubbock's entomological work from its early development under Darwin to his later work on insect sensory physiology and comparative psychology. Far from being the death of his scientific career, Lubbock's entry into Parliament marked the pinnacle of his career as a scientific intellectual. He built on his early work on invertebrate anatomy, physiology and taxonomy, and on his archaeological and anthropological research to expound his vision of mental evolution. His research on ‘savages’, on ants, bees and wasps, and on his dog, ‘Van’, permitted him to expatiate upon the psychic unity of all sentient beings, which, in turn, underpinned his overarching educational programme.
PMCID: PMC3928875
Lubbock; entomology; intellectual; mental evolution
6.  From Darwin's Origin of Species toward a theory of natural history 
F1000Prime Reports  2015;7:49.
Darwin is the father of evolutionary theory because he identified evolutionary patterns and, with Natural Selection, he ascertained the exquisitely ecological ultimate processes that lead to evolution. The proximate processes of evolution he proposed, however, predated the discovery of genetics, the backbone of modern evolutionary theory. The later discovery of the laws of inheritance by Mendel and the rediscovery of Mendel in the early 20th century led to two reforms of Darwinism: Neo-Darwinism and the Modern Synthesis (and subsequent refinements). If Darwin's evolutionary thought required much refinement, his ecological insight is still very modern. In the first edition of The Origin of Species, Darwin did not use either the word “evolution” or the word “ecology”. “Ecology” was not coined until after the publication of the Origin. Evolution, for him, was the origin of varieties, then species, which he referred to as well-marked varieties, whereas, instead of using ecology, he used “the economy of nature”. The Origin contains a high proportion of currently accepted ecological principles. Darwin labelled himself a naturalist. His discipline (natural history) was a blend of ecology and evolution in which he investigated both the patterns and the processes that determine the organization of life. Reductionist approaches, however, often keep the two disciplines separated from each other, undermining a full understanding of natural phenomena that might be favored by blending ecology and evolution through the development of a modern Theory of Natural History based on Darwin's vision of the study of life.
PMCID: PMC4447030  PMID: 26097722
7.  Trees and networks before and after Darwin 
Biology Direct  2009;4:43.
It is well-known that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859). Here I attempt to place Darwin's trees in historical context. By the mid-Eighteenth century the Great Chain of Being was increasingly seen to be an inadequate description of order in nature, and by about 1780 it had been largely abandoned without a satisfactory alternative having been agreed upon. In 1750 Donati described aquatic and terrestrial organisms as forming a network, and a few years later Buffon depicted a network of genealogical relationships among breeds of dogs. In 1764 Bonnet asked whether the Chain might actually branch at certain points, and in 1766 Pallas proposed that the gradations among organisms resemble a tree with a compound trunk, perhaps not unlike the tree of animal life later depicted by Eichwald. Other trees were presented by Augier in 1801 and by Lamarck in 1809 and 1815, the latter two assuming a transmutation of species over time. Elaborate networks of affinities among plants and among animals were depicted in the late Eighteenth and very early Nineteenth centuries. In the two decades immediately prior to 1837, so-called affinities and/or analogies among organisms were represented by diverse geometric figures. Series of plant and animal fossils in successive geological strata were represented as trees in a popular textbook from 1840, while in 1858 Bronn presented a system of animals, as evidenced by the fossil record, in a form of a tree. Darwin's 1859 tree and its subsequent elaborations by Haeckel came to be accepted in many but not all areas of biological sciences, while network diagrams were used in others. Beginning in the early 1960s trees were inferred from protein and nucleic acid sequences, but networks were re-introduced in the mid-1990s to represent lateral genetic transfer, increasingly regarded as a fundamental mode of evolution at least for bacteria and archaea. In historical context, then, the Network of Life preceded the Tree of Life and might again supersede it.
This article was reviewed by Eric Bapteste, Patrick Forterre and Dan Graur.
PMCID: PMC2793248  PMID: 19917100
8.  Darwin's Galápagos finches in modern biology 
One of the classic examples of adaptive radiation under natural selection is the evolution of 15 closely related species of Darwin's finches (Passeriformes), whose primary diversity lies in the size and shape of their beaks. Since Charles Darwin and other members of the Beagle expedition collected these birds on the Galápagos Islands in 1835 and introduced them to science, they have been the subjects of intense research. Many biology textbooks use Darwin's finches to illustrate a variety of topics of evolutionary theory, such as speciation, natural selection and niche partitioning. Today, as this Theme Issue illustrates, Darwin's finches continue to be a very valuable source of biological discovery. Certain advantages of studying this group allow further breakthroughs in our understanding of changes in recent island biodiversity, mechanisms of speciation and hybridization, evolution of cognitive behaviours, principles of beak/jaw biomechanics as well as the underlying developmental genetic mechanisms in generating morphological diversity. Our objective was to bring together some of the key workers in the field of ecology and evolutionary biology who study Darwin's finches or whose studies were inspired by research on Darwin's finches. Insights provided by papers collected in this Theme Issue will be of interest to a wide audience.
PMCID: PMC2830240  PMID: 20194163
Darwin's finches; evolution; speciation; adaptive radiation
9.  Whale Shark (Rhincodon typus) Seasonal Presence, Residence Time and Habitat Use at Darwin Island, Galapagos Marine Reserve 
PLoS ONE  2014;9(12):e115946.
The life history of the whale shark (Rhincodon typus), including its reproductive ecology, still remains largely unknown. Here, we present results from the first whale shark population study around Darwin Island, Galapagos Marine Reserve. Following a diversified approach we characterized seasonal occurrence, population structure and size, and described habitat use of whale sharks based on fine scale movements around the island. Whale shark presence at Darwin Island was negatively correlated with Sea Surface Temperature (SST), with highest abundance corresponding to a cool season between July and December over six years of monitoring. From 2011 to 2013 we photo-identified 82 whale sharks ranging from 4 to 13.1 m Total Length (TL). Size distribution was bimodal, with a great majority (91.5%) of adult female individuals averaging 11.35 m±0.12 m (TL±SE), all but one showing signs of a potential pregnancy. Population dynamics models for apparently pregnant sharks estimated the presence of 3.76±0.90 (mean ± SE) sharks in the study area per day with an individual residence time of 2.09±0.51 (mean ± SE) days. Movement patterns analysis of four apparently pregnant individuals tracked with acoustic tags at Darwin Island revealed an intense use of Darwin's Arch, where no feeding or specific behavior has been recorded, together with periodic excursions around the island's vicinity. Sharks showed a preference for intermediate depths (20–30 m) with occasional dives mostly to mid-water, remaining the majority of their time at water temperatures between 24–25°C. All of our results point to Darwin Island as an important stopover in a migration, possibly with reproductive purposes, rather than an aggregation site. Current studies carried out in this area to investigate regional scale movement patterns may provide essential information about possible pupping grounds for this enigmatic species.
PMCID: PMC4281130  PMID: 25551553
10.  The teacher taught? What Charles Darwin owed to John Lubbock 
The period around the publication of John Lubbock's Origin of civilisation in 1870 and Charles Darwin's Descent of man and selection in relation to sex the following year is key to a re-evaluation of the relationship between the two men, usually characterized as that of pupil and master. It is in the making of Descent that Lubbock's role as a scientific collaborator is most easily discerned, a role best understood within the social and political context of the time. Lubbock made Darwin—both the man and his science—acceptable and respectable. Less obvious is Darwin's conscious cultivation of Lubbock's patronage in both his private and public life, and Lubbock's equally conscious bestowal, culminating in his role in Darwin's burial in Westminster Abbey.
PMCID: PMC3928872
John Lubbock; Charles Darwin; scientific collaboration
11.  LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory 
PLoS ONE  2013;8(7):e67460.
The electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research.
Methodology/Principal Findings
We chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system.
LabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment.
PMCID: PMC3720848  PMID: 23935832
12.  A Cross-species Comparison of Facial Morphology and Movement in Humans and Chimpanzees Using the Facial Action Coding System (FACS) 
Journal of nonverbal behavior  2007;31(1):1-20.
A comparative perspective has remained central to the study of human facial expressions since Darwin’s [(1872/1998). The expression of the emotions in man and animals (3rd ed.). New York: Oxford University Press] insightful observations on the presence and significance of cross-species continuities and species-unique phenomena. However, cross-species comparisons are often difficult to draw due to methodological limitations. We report the application of a common methodology, the Facial Action Coding System (FACS) to examine facial movement across two species of hominoids, namely humans and chimpanzees. FACS [Ekman & Friesen (1978). Facial action coding system. CA: Consulting Psychology Press] has been employed to identify the repertoire of human facial movements. We demonstrate that FACS can be applied to other species, but highlight that any modifications must be based on both underlying anatomy and detailed observational analysis of movements. Here we describe the ChimpFACS and use it to compare the repertoire of facial movement in chimpanzees and humans. While the underlying mimetic musculature shows minimal differences, important differences in facial morphology impact upon the identification and detection of related surface appearance changes across these two species.
PMCID: PMC3008553  PMID: 21188285
Comparative anatomy; Chimpanzees; Facial action coding system (FACS); Facial morphology
13.  From Down House to Avebury: John Lubbock, prehistory and human evolution through the eyes of his collection 
When Sir John Lubbock died in May 1913, his estate included a seemingly eclectic assortment of prehistoric stone tools and ethnographic artefacts displayed on the walls of his home at High Elms and hidden away in storage. However, detailed analysis of the history of this collection reveals a fascinating story of a man inspired by Darwin and like-minded evolutionary thinkers, who became one of the most important intellectuals in Victorian Britain to examine the controversial subject of human evolution. Six acquisitions are used in this article to explore how Lubbock began as Darwin's friend and scientific apprentice and became an international champion for the study of prehistory and the protection of prehistoric ancient monuments.
PMCID: PMC3928870
John Lubbock; history of archaeology; history of science; Darwin; human evolution; ancient monuments protection
14.  The ‘root-brain’ hypothesis of Charles and Francis Darwin 
Plant Signaling & Behavior  2009;4(12):1121-1127.
This year celebrates the 200th aniversary of the birth of Charles Darwin, best known for his theory of evolution summarized in On the Origin of Species. Less well known is that, in the second half of his life, Darwin’s major scientific focus turned towards plants. He wrote several books on plants, the next-to-last of which, The Power of Movement of Plants, published together with his son Francis, opened plants to a new view. Here we amplify the final sentence of this book in which the Darwins proposed that: “It is hardly an exaggeration to say that the tip of the radicle thus endowed [with sensitivity] and having the power of directing the movements of the adjoining parts, acts like the brain of one of the lower animals; the brain being seated within the anterior end of the body, receiving impressions from the sense-organs, and directing the several movements.” This sentence conveys two important messages: first, that the root apex may be considered to be a ‘brain-like’ organ endowed with a sensitivity which controls its navigation through soil; second, that the root apex represents the anterior end of the plant body. In this article, we discuss both these statements.
PMCID: PMC2819436  PMID: 20514226
auxin; cognition; plant neurobiology; plant tropisms; roots; sensory biology; signaling
15.  The Cells that Fill the Bill 
Journal of Dental Research  2009;88(1):12-21.
Avian embryos, which have been studied scientifically since Aristotle, continue to persevere as invaluable research tools, especially for our understanding of the development and evolution of the craniofacial skeleton. Whether the topic is beak shape in Darwin’s finches or signaling interactions that underlie bone and tooth formation, birds offer advantages for craniofacial biology that uniquely complement the strengths of other vertebrate model systems, such as fish, frogs, and mice. Several papers published during the past few years have helped pinpoint molecular and cellular mechanisms that pattern the face and jaws through experiments that could only have been done together with our feathered friends. Ultimately, such knowledge will be essential for devising novel clinical approaches to treat and/or prevent diseases, injuries, and birth defects that affect the human craniofacial skeleton. Here we review recent insights plucked from avians on key developmental processes that generate craniofacial diversity.
PMCID: PMC3317957  PMID: 19131312
neural crest cells; craniofacial; development; experimental embryology; chimeras; evolutionary biology
16.  Modularity, comparative cognition and human uniqueness 
Darwin's claim ‘that the difference in mind between man and the higher animals … is certainly one of degree and not of kind’ is at the core of the comparative study of cognition. Recent research provides unprecedented support for Darwin's claim as well as new reasons to question it, stimulating new theories of human cognitive uniqueness. This article compares and evaluates approaches to such theories. Some prominent theories propose sweeping domain-general characterizations of the difference in cognitive capabilities and/or mechanisms between adult humans and other animals. Dual-process theories for some cognitive domains propose that adult human cognition shares simple basic processes with that of other animals while additionally including slower-developing and more explicit uniquely human processes. These theories are consistent with a modular account of cognition and the ‘core knowledge’ account of children's cognitive development. A complementary proposal is that human infants have unique social and/or cognitive adaptations for uniquely human learning. A view of human cognitive architecture as a mosaic of unique and species-general modular and domain-general processes together with a focus on uniquely human developmental mechanisms is consistent with modern evolutionary-developmental biology and suggests new questions for comparative research.
PMCID: PMC3427548  PMID: 22927578
cognitive evolution; human uniqueness; modularity; dual process theories
17.  Variation under domestication in plants: 1859 and today 
Charles Darwin began The Origin of Species with a chapter entitled variation under domestication, which encapsulated decades of his research on a diverse array of animal and plant domesticated species. Variation in these species compared with that in their wild relatives, their origins and their selection by humans, formed a paradigm for his theory of the evolutionary origin of species by means of natural selection. This chapter, its subsequent expansion into a two-volume monograph, together with the rediscovery of Mendel's laws, later became the foundation of scientific plant breeding. In the period up to the present, several advances in genetics (such as artificial mutation, polyploidy, adaptation and genetic markers) have amplified the discipline with concepts and questions, the seeds of which are in Darwin's original words. Today, we are witnessing a flowering of genomic research into the process of domestication itself, particularly the specific major and minor genes involved. In one striking way, our view of domestic diversity contrasts with that in Darwin's writing. He stressed the abundance of diversity and the diversifying power of artificial selection, whereas we are concerned about dwindling genetic diversity that attends modern agriculture and development. In this context, it is paramount to strive for a deeper understanding of how farmer selection including both deliberate selection and unconscious selection, might generate and retain diversity. This knowledge is essential for devising in situ conservation measures.
PMCID: PMC2935096  PMID: 20643742
crop diversity; genomics; landraces; farmer selection; mutual evolution
18.  Epigenetics and the Evolution of Darwin’s Finches 
Genome Biology and Evolution  2014;6(8):1972-1989.
The prevailing theory for the molecular basis of evolution involves genetic mutations that ultimately generate the heritable phenotypic variation on which natural selection acts. However, epigenetic transgenerational inheritance of phenotypic variation may also play an important role in evolutionary change. A growing number of studies have demonstrated the presence of epigenetic inheritance in a variety of different organisms that can persist for hundreds of generations. The possibility that epigenetic changes can accumulate over longer periods of evolutionary time has seldom been tested empirically. This study was designed to compare epigenetic changes among several closely related species of Darwin’s finches, a well-known example of adaptive radiation. Erythrocyte DNA was obtained from five species of sympatric Darwin’s finches that vary in phylogenetic relatedness. Genome-wide alterations in genetic mutations using copy number variation (CNV) were compared with epigenetic alterations associated with differential DNA methylation regions (epimutations). Epimutations were more common than genetic CNV mutations among the five species; furthermore, the number of epimutations increased monotonically with phylogenetic distance. Interestingly, the number of genetic CNV mutations did not consistently increase with phylogenetic distance. The number, chromosomal locations, regional clustering, and lack of overlap of epimutations and genetic mutations suggest that epigenetic changes are distinct and that they correlate with the evolutionary history of Darwin’s finches. The potential functional significance of the epimutations was explored by comparing their locations on the genome to the location of evolutionarily important genes and cellular pathways in birds. Specific epimutations were associated with genes related to the bone morphogenic protein, toll receptor, and melanogenesis signaling pathways. Species-specific epimutations were significantly overrepresented in these pathways. As environmental factors are known to result in heritable changes in the epigenome, it is possible that epigenetic changes contribute to the molecular basis of the evolution of Darwin’s finches.
PMCID: PMC4159007  PMID: 25062919
epimutations; DNA methylation; copy number variation; phylogeny; adaptive radiation; BMP; toll; melanogenesis
19.  Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence 
BMC Genomics  2013;14:95.
A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2–3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris.
13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin’s finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins.
These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin’s finches.
PMCID: PMC3575239  PMID: 23402223
Genomics; Evolution; Darwin’s finches; Large ground finch; Geospiza magnirostris
20.  Computation of emotions in man and machines 
The importance of emotional expression as part of human communication has been understood since Aristotle, and the subject has been explored scientifically since Charles Darwin and others in the nineteenth century. Advances in computer technology now allow machines to recognize and express emotions, paving the way for improved human–computer and human–human communications.
Recent advances in psychology have greatly improved our understanding of the role of affect in communication, perception, decision-making, attention and memory. At the same time, advances in technology mean that it is becoming possible for machines to sense, analyse and express emotions. We can now consider how these advances relate to each other and how they can be brought together to influence future research in perception, attention, learning, memory, communication, decision-making and other applications.
The computation of emotions includes both recognition and synthesis, using channels such as facial expressions, non-verbal aspects of speech, posture, gestures, physiology, brain imaging and general behaviour. The combination of new results in psychology with new techniques of computation is leading to new technologies with applications in commerce, education, entertainment, security, therapy and everyday life. However, there are important issues of privacy and personal expression that must also be considered.
PMCID: PMC2781898  PMID: 19884138
psychology; emotions; human–computer interactions; affective computing
21.  On the temporality of creative insight: a psychological and phenomenological perspective 
Frontiers in Psychology  2014;5:1184.
Research into creative insight has had a strong emphasis on the psychological processes underlying problem-solving situations as a standard model for the empirical study of this phenomenon. Although this model has produced significant advances in our scientific understanding of the nature of insight, we believe that a full comprehension of insight requires complementing cognitive and neuroscientific studies with a descriptive, first-person, phenomenological approach into how creative insight is experienced. Here we propose to take such first-person perspective while paying special attention to the temporal aspects of this experience. When this first-person perspective is taken into account, a dynamic past–future interplay can be identified at the core of the experience of creative insight, a structure that is compatible with both biological and biographical evidences. We believe this approach could complement and help bring together biological and psychological perspectives. Furthermore, we argue that because of its spontaneous but recurrent nature, creative insight could represent a relevant target for the phenomenological investigation of the flow of experience itself.
PMCID: PMC4201093  PMID: 25368595
creativity; insight; flow of experience; temporality; socio-cultural approach
22.  Charles Darwin’s Mitochondria 
Genetics  2013;194(1):21-25.
Charles Darwin’s long-term illness has been the subject of much speculation. His numerous symptoms have led to conclusions that his illness was essentially psychogenic in nature. These diagnoses have never been fully convincing, however, particularly in regard to the proposed underlying psychological background causes of the illness. Similarly, two proposed somatic causes of illness, Chagas disease and arsenic poisoning, lack credibility and appear inconsistent with the lifetime history of the illness. Other physical explanations are simply too incomplete to explain the range of symptoms. Here, a very different sort of explanation will be offered. We now know that mitochondrial mutations producing impaired mitochondrial function may result in a wide range of differing symptoms, including symptoms thought to be primarily psychological. Examination of Darwin’s maternal family history supports the contention that his illness was mitochondrial in nature; his mother and one maternal uncle had strange illnesses and the youngest maternal sibling died of an infirmity with symptoms characteristic of mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS syndrome), a condition rooted in mitochondrial dysfunction. Darwin’s own symptoms are described here and are in accord with the hypothesis that he had the mtDNA mutation commonly associated with the MELAS syndrome.
PMCID: PMC3632469  PMID: 23633139
23.  Ecoimmunity in Darwin's Finches: Invasive Parasites Trigger Acquired Immunity in the Medium Ground Finch (Geospiza fortis) 
PLoS ONE  2010;5(1):e8605.
Invasive parasites are a major threat to island populations of animals. Darwin's finches of the Galápagos Islands are under attack by introduced pox virus (Poxvirus avium) and nest flies (Philornis downsi). We developed assays for parasite-specific antibody responses in Darwin's finches (Geospiza fortis), to test for relationships between adaptive immune responses to novel parasites and spatial-temporal variation in the occurrence of parasite pressure among G. fortis populations.
Methodology/Principal Findings
We developed enzyme-linked immunosorbent assays (ELISAs) for the presence of antibodies in the serum of Darwin's finches specific to pox virus or Philornis proteins. We compared antibody levels between bird populations with and without evidence of pox infection (visible lesions), and among birds sampled before nesting (prior to nest-fly exposure) versus during nesting (with fly exposure). Birds from the Pox-positive population had higher levels of pox-binding antibodies. Philornis-binding antibody levels were higher in birds sampled during nesting. Female birds, which occupy the nest, had higher Philornis-binding antibody levels than males. The study was limited by an inability to confirm pox exposure independent of obvious lesions. However, the lasting effects of pox infection (e.g., scarring and lost digits) were expected to be reliable indicators of prior pox infection.
This is the first demonstration, to our knowledge, of parasite-specific antibody responses to multiple classes of parasites in a wild population of birds. Darwin's finches initiated acquired immune responses to novel parasites. Our study has vital implications for invasion biology and ecological immunology. The adaptive immune response of Darwin's finches may help combat the negative effects of parasitism. Alternatively, the physiological cost of mounting such a response could outweigh any benefits, accelerating population decline. Tests of the fitness implications of parasite-specific immune responses in Darwin's finches are urgently needed.
PMCID: PMC2799526  PMID: 20066052
24.  Reduced inclination of cervical spine in a novel notebook screen system - implications for rehabilitation 
Professional working at computer notebooks is associated with high requirements on the body posture in the seated position. By the high continuous static muscle stress resulting from this position at notebooks, professionals frequently working at notebooks for long hours are exposed to an increased risk of musculoskeletal complaints. Especially in subjects with back pain, new notebooks should be evaluated with a focus on rehabilitative issues.
In a field study a new notebook design with adjustable screen was analyzed and compared to standard notebook position.
There are highly significant differences in the visual axis of individuals who are seated in the novel notebook position in comparison to the standard position. Also, differences are present between further alternative notebook positions. Testing of gender and glasses did not reveal influences.
This study demonstrates that notebooks with adjustable screen may be used to improve the posture. Future studies may focus on patients with musculoskeletal diseases.
PMCID: PMC3253038  PMID: 22118159
25.  Relationships between Depression and High Intellectual Potential 
This paper proposes to analyse the relationships between depression and high intellectual potential through a multidisciplinary and original approach. Based on their respective experience in psychology and child psychiatry, the authors will focus their analysis on creative potential. First, relationships between creativity (literary, artistic, or scientific creativity) and melancholy (“melancholy” comes from the Greek words for “black” (“melas”) and “bile” (“khole”)) will be examined from antiquity to modern times. Aristotle introduced a quantitative factor, asserting that levels of melancholy and black bile are positively correlated; however, under a given threshold of black bile, it can give rise to an exceptional being. Second, the case study of Blaise Pascal (scientific and philosophical creativity associated with major depressive episodes from childhood) will be presented and discussed. This case study sheds light on the paradoxical role of depression in the overinvestment in intellectual and creative spheres as well as on the impact of traumatic events on high intellectual potential. Third, observations will be reported based on a study conducted on 100 children with high intellectual potential (6–12 years old). Finally, based on these different levels of analysis, it appears that heterogeneity of mental functioning in children with high intellectual potential is at the center of the creative process and it has related psychological vulnerability.
PMCID: PMC3356869  PMID: 22645671

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