Biochromatics is the study of how organisms produce and utilize color, encompassing both the underlying
mechanisms and the ecological and evolutionary significance of coloration. This course introduces students to the
diverse strategies organisms ose to create color, including pigment-based and structural mechanisms, as well as
dynamic changes in coloration.
Students will explore key topics such as the biochemical pathways of pigment synthesis, the physics of structural
colors, and the interactions between color and the environment. The course also examines the roles of coloration
in communication, camouflage, mate selection and other biological functions.
Combining perspectives from biology, chemistry and physics, this interdisciplinary course provides a
comprehensive understanding of the science of color in nature and its broader applications. It is suitable for
students interested in natural sciences and those seeking to understand the intricate processes that shape the
visual diversity of life.
Last update: Joseph Jacques, Mgr., Ph.D. (14.05.2025)
Course completion requirements
Essay
For the essay, students will read a recent scientific paper related to biochromatics and write a two-page A4 analysis. The essay should summarize the paper's main findings, discuss methods, and assess its implications in the context of biological coloration. This assignment will help students engage with current research and improve their scientific writing.
Exam
During the oral exam, students will first discuss their essay. Afterward, I will ask one question related to the topics covered in the lessons. Students will need to demonstrate their understanding by answering the question and connecting the course concepts to the content of the paper, methods and results discussed earlier.
Last update: Joseph Jacques, Mgr., Ph.D. (14.05.2025)
Syllabus
Lesson 1: Introduction to Biochromatics
Overview of biological coloration: pigments and structural colors
Evolutionary significance and functions of color
Lesson 2: Pigments in the Natural World
Types of pigments: melanins, carotenids, psittacofulvins, pterins and others
Biochemistry and distribution across taxa
Lesson 3: Biochemical Pathways of Pigment Production
Enzymes and genetic pathways involved in pigment synthesis
Case studies: Melanin pathway and psittacofulvin synthesis in parrots
Lesson 4: Structural Colors - Physics in Biology
Mechanisms of light scattering, diffraction and interference
Examples: Irridescence in butterflies and non-iridescent blues in birds
Lesson 5: Structural Colors - Nanostructures and Beyond
Photonic crystals and multilayer reflectors
Case studies: Morpho butterflies and lizards
Lesson 6: Dynamic Coloration and Color Change
Cromatophores, iridophores and leucophores
Mechanisms in cephalopods, chameleons and fish
Lesson 7: Combined Mechanisms - Pigments and Structures
How pigments and nanostructures interact to produce complex colors
Examples: Green coloration, violet
Lesson 8: Color Vision and Perception in Organisms
How animals perceive and interpret colors
Influence of vision on the evolution of coloration strategies
Metamerism
Lesson 9: Ecological Roles of Coloration
Camouflage, mimicry, warning coloration and mating signals
Case studies: Aposematism in poison dart frogs, mimicry in butterflies
Lesson 10: Evolutionary Perspectives in Coloration
Natural and sexual selection in the evolution of color traits
Adaptive radiations and convergent evolution
Lesson 11: Coloration in Plants and Microorganisms
Pigments in flowers, fruits and microorganisms
Ecological and biochemical roles
Lesson 12: Applications and Biomimicry
How human technologies mimic natural coloration
Future directions in the study of biochromatics
Last update: Joseph Jacques, Mgr., Ph.D. (14.05.2025)
Learning outcomes
Learning Outcomes
Upon successful completion of this course, the student will be able to:
Define and correctly use key concepts related to biological coloration, including pigment-based coloration, structural coloration, dynamic coloration, and color perception.
Identify and classify major types of biological pigments (e.g. melanins, carotenoids, psittacofulvins, pterins) and describe their distribution across major taxonomic groups.
Explain the biochemical pathways underlying pigment synthesis, including the role of enzymes and genetic regulation, using selected model systems as examples.
Describe and interpret the physical principles behind structural colors, including light scattering, interference, and diffraction, and relate these principles to biological nanostructures.
Analyze how pigments and structural mechanisms interact to produce complex coloration patterns in organisms.
Compare static and dynamic coloration mechanisms and explain the cellular, physiological, and ecological bases of color change in selected organisms.
Explain how color perception differs among organisms and discuss the implications of these differences for the evolution of coloration (e.g. metamerism, sensory bias).
Analyze and discuss the ecological functions of coloration, including camouflage, mimicry, aposematism, communication, and mate choice, using concrete biological examples.
Evaluate coloration traits from an evolutionary perspective, including the roles of natural selection, sexual selection, convergence, and constraint.
Summarize and interpret coloration mechanisms in plants and microorganisms and compare them with those found in animals.
Critically analyze a recent scientific paper in biochromatics by:
summarizing its main findings,
describing and assessing the methods used,
discussing its implications for understanding biological coloration.
Integrate knowledge from biology, chemistry, and physics to formulate coherent explanations of how color is produced, perceived, and used in living systems.
Communicate course-related concepts clearly and accurately in oral form, and defend interpretations and conclusions using evidence from the scientific literature.
Last update: Brejcha Jindřich, Mgr., Ph.D. (30.01.2026)
