General Study Syllabus for Biology

Biology, with specialisations listed below

Swedish title: Biologi med nedan uppräknade inriktningar

TNBIOL02, TNBIOL05, TNBIOL08, TNBIOL09, TNBIOL10, TNBIOL11, TNBIOL13, TNBIOL17, TNBIOL18, TNBIOL21, TNBIOL22, TNBIOL23, TNBIOL24, TNBIOL25, TNBIOL26, TNBIOL27, TNBIOL28

Subject-specific parts (*) in Swedish adopted by the Faculty Board (the Doctoral Education Board) on 2008-07-02. Revision on 2008-07-02, 2012-11-21, 2013-05-15, 2018-02-06 and 2022-08-24. Translations approved 2010-08-10, 2013-05-15, 2019-11-06 and 2022-08-24.

Faculty-common parts approved by the Faculty Board of Science and Technology on 2022-04-26. Revision on 2023-02-07.

The faculty-common parts go into force on 1 July 2022. The Faculty-common parts also apply to those who started their doctoral education prior to 1 July 2022, except if this would have a negative impact on the conditions for doctoral students.

Subject description *

Doctoral education in biology is offered at the Evolutionary Biology Centre (EBC, Department of Ecology and Genetics and Department of Organismal Biology) and Uppsala Biomedical Centre (BMC, Department of Cell and Molecular Biology). There are a variety of specialisations in biology. The programs are called Biology with specialisation in xxx. Further information on what research is being carried out can be obtained through discussion with researchers within the various programs and through information on the website. For programs at EBC please refer to www.ieg.uu.se and www.iob.uu.se and for programs in biology at BMC please refer to www.icm.uu.se.

Below, the specialisations are described, and it is stated at which institution the teaching is given:

Ecological Botany, ekologisk botanik (EBC, Department of Ecology and Genetics) TNBIOL02. In ecological botany processes that influence the occurrence and evolution of plants are studied. The topic includes studies of how interactions with the surrounding environment affect the growth and reproduction of individual plants, the size and evolution of populations as well as the composition and change of the plant cover over time. The research also covers applications in conservation biology.

Evolutionary Genetics, Evolutionär genetik (EBC, Department of Ecology and Genetics) TNBIOL05. This specialisation includes genome and molecular evolution, evolution of genetic systems and bioinformatics. It also includes biodiversity, conservation genetics, evolutionary biology and molecular ecology. The subject area is connected to several biological sub-disciplines, for example, classical genetics, evolutionary ecology, molecular biology and functional genomics.

Comparative physiology, Jämförande fysiologi (EBC, Department of Organismal Biology) TNBIOL08. Comparative physiology encompasses physiological, biochemical and molecular studies on adaptations in different environments by a range of organisms. Studies are performed on whole organisms as well as on tissues or cells and molecules, often by employing molecular, cell biological and proteomic techniques. An important issue is how physiological processes such as for example immune reactions have developed and changed during the course of evolution.

Limnology, Limnologi (EBC, Department of Ecology and Genetics) TNBIOL09. Limnology is a discipline within ecology, focusing on inland water ecosystems, including communities, populations, and biogeochemical processes. Microorganisms as well as larger organisms are studied. The issues addressed are of significance for the understanding of aquatic ecosystems, but they also have general ecological and evolutionary implications. Limnology encompasses basic scientific problems as well as research of interest for the management and protection of the environment.

Microbiology, Mikrobiologi (EBC, Department of Ecology and Genetics) TNBIOL10. (No new admissions, see instead Molecular Life Sciences TNNOBI00). Microbiology is a subspecialty within biology which focuses on the study of microorganisms. The field covers molecular biology, molecular genetics, physiology, population biology, and ecology. The current research is primarily experimental and concentrated primarily on the first three fields.

Molecular Biotechnology, Molekylär bioteknik (BMC, Department of Cell and Molecular Biology) TNBIOL11. (No new admissions, see instead Molecular Life Sciences TNNOBI00). Molecular biotechnology is a cross-disciplinary subject which focuses on biotechnology and biological basic research at the molecular level.

Molecular Evolution, Molekylär evolution (BMC, Department of Cell and Molecular Biology) TNBIOL13. (No new admissions, see instead Molecular Life Sciences TNNOBI00). Molecular evolution concerns studies of evolutionary processes at the molecular level. Included are comparative analyses of complete genomes from bacteria, archaea and eukaryotes. The aim is to understand evolutionary processes and quantify the frequencies of nucleotide substitutions, deletions, duplications, translocations, inversions, horizontal gene transfer events and genome fusions. This subject also includes studies of the mechanisms of cell division, protein interactions and mapping of metabolic networks. The studies can be performed in vivo, in vitro or in silico.

Structural Biology, Strukturbiologi (BMC, Department of Cell and Molecular Biology) TNBIOL18. (No new admissions, see instead Molecular Life Sciences TNNOBI00). Structural biology studies the relationship between structure and function in biological macromolecules. The conformation of the molecules and their complexes are experimentally determined primarily by X-ray crystallography. The results, combined with different computational methods, are then used to explain the mechanisms of different biological processes or for the purpose of designing medicinal drugs. In addition, novel methodologies for both the experimental and theoretical parts of structural biology are being developed.

Animal Ecology, Zooekologi (EBC, Department of Ecology and Genetics) TNBIOL21. Animal ecology is the part of ecology that studies how animals interact with their environment. Animal Ecology studies how traits of animals (growth, behavior, gene expression, etc.) are affected by interaction within the species and with other organisms, as well as with the environment (eg climate change).The animal ecology specialisation focuses on the study of ecological and evolutionary processes, and adaptations at the level of communities, populations, individuals and genes. Animal ecology includes, for instance, life history evolution and trade-offs, phenotypic plasticity, behavioural ecology, natural and sexual selection, sexual conflicts, evolution of mating systems, speciation and hybridisation, biodiversity, conservation biology and theoretical ecology. Methods include observational and experimental studies of animals in the field and laboratory, experimental evolution, comparative phylogenies, molecular genomics, bioinformatics and theoretical modelling.

Animal Developmental Biology, Zoologisk utvecklingsbiologi (EBC, Department of Organismal Biology) TNBIOL22. Animal developmental biology deals with the physiological, morphological, and molecular processes and their underlying mechanisms that govern the development of the fertilized egg. The field covers also genetic, evolutionary and teratological aspects of embryonic development and reproduction.

Evolutionary Organismal Biology, Evolutionär organismbiologi (EBC, Department of Organismal Biology) TNBIOL23. Evolutionary Organismal Biology is a discipline that analyses large-scale morphological evolution from a phylogenetic perspective. Particular emphasis is placed on linking morphological and developmental data within a common phylogenetic framework, in order to illuminate the correlation between the evolution of molecular patterning and the resulting morphological evolution. The subject area also covers palaeontological research with focus on morphological evolution and phylogeny.

Evolutionary Functional Genomics, Evolutionär funktionsgenomik (EBC, Department of Ecology and Genetics) TNBIOL24. The goal is to understand the functional role of genetic variation present in animal and plant genomes in their natural environment. The attainment of this goal requires a combination of approaches including ecology, evolution, population genetics, genomics and functional genomics. The research program includes both experimental studies of variation at different levels (DNA, gene expression, phenotype), and theoretical work. The relevance of specific genetic variation to adaptation is tested in functional and ecological studies.

Systematics, Systematik (EBC, Department of Organismal Biology) TNBIOL25. The subject concerns systematics with an emphasis on phylogeny and evolutionary processes at different taxonomic levels. This also includes the description and analysis of biodiversity, molecular studies using single and multiple genes, dating and statistical analysis of evolutionary trees.

Animal Conservation, Zoologisk bevarandebiologi (EBC, Department of Ecology and Genetics) TNBIOL26. (No new admissions in TNBIOL17 Population biology). Animal Conservation is a subject that involves studies on dispersal, migration, demographics, effective population size, inbreeding depression, and minimum population viability of rare or endangered species. The subject includes phenomena that affect the maintenance, loss, and restoration of biodiversity and the science of sustaining evolutionary processes that engender genetic, population, species, and ecosystem diversity.

Environmental Toxicology, Miljötoxikologi (EBC, Department of Organismal Biology) TNBIOL27. (No new admissions in TNBIOL03 Environmental Toxicology). Research in Environmental Toxicology aims at determining how chemicals in the environment can disturb molecular and cellular functions and give rise to adverse health effects in exposed organisms, including humans. Of particular interest are long-lasting adverse effects originating from exposure during sensitive life-stages such as early development.

Human Evolution and Genetics, Människans evolution och genetik (EBC, Department of Organismal Biology) TNBIOL28. Human evolution and genetics is a subject that focuses on the evolutionary processes that have shaped, and shaped, our own species. The focus is on understanding the evolution and demographic history of man and hominids from a genetic perspective and with the help of theoretical and empirical studies. These studies examine the human genome, genetic variation, traits and evolutionary processes. Also human interactions and co-evolution with other organisms and phenomenon is studied. The subject embraces human genetics, population genetics / genomics, computational biology, molecular genetics, archeogenetics, and gene-culture co-evolution. The subject also has touch points towards medical genetics, paleontology, archeology, anthropology, osteology and evolutionary linguistics.

Aim and objectives for the education

Overall aim and objectives of the education

Doctoral education shall develop the knowledge and skills needed to be able to conduct research independently (Higher Education Act, 1992:1434). The Higher Education Ordinance’s System of Qualifications (Appendix 2, 1993:100) sets out the requirements to be met for a doctoral and licentiate degree, respectively (see individual study plan template).

Subject-specific objectives *

Based on the basic education in the subject area, studies at the research level should provide competence that lies at the forefront of research in the biological field studied.

During the program, the doctoral student will, through active participation in courses and the execution of dissertation work under supervision, achieve a significant theoretical subject expertise as well as extensive practical competence in the methodology relevant to the subject.

Those who have obtained a doctoral degree should be able to independently plan and carry out research projects in the field of biology. In addition to the academic environment, the doctorate must be able to be responsible for research and development work in, for example management and business. In addition, the training will lead to the doctoral student actively participating in the scientific discussion. The doctoral student should also be able to present their goals and results in oral and written form to various target groups in English and, in the case of Swedish-speaking doctoral students, in Swedish.

Those who have obtained a licentiate degree must have experience in independent research work and have attained the subject and methodological skills required for active participation in research projects in the chosen field, and be able to critically relate to the scientific development in the subject.

Entry requirement

General entry requirements

General entry requirements for doctoral education are regulated in the Higher Education Ordinance as follows:

An applicant shall be considered as meeting the general entry requirements if they have

completed a degree at the advanced level (Master’s level), or
completed course requirements of at least 240 credits, of which at least 60 credits are at the advanced level (Master’s level), or
acquired substantially equivalent knowledge in some other way in Sweden or abroad.

The University may permit an exemption from the general entry requirements for an individual applicant, if there are special grounds (Chapter 7, § 39 of the Higher Education Ordinance).

In order for a person who has completed course requirements of at least 240 credits (under the second item above) to be considered eligible at Uppsala University, the 60 credits at advanced level must include a degree project of at least 15 credits (AFUU § 2, UFV 2022/729).

Special entry requirements *

For doctoral studies in Biology it is required that the accepted candidate has passed courses in relevant topics of at least 60 credits at the advanced level. It is required that the student is well acquainted with the theories in the current research field through advanced level courses and have completed a master degree project in a relevant discipline. Provided that the above course requirements are met, the special eligibility can be obtained through studies in the natural science programmes, biomedicine programmes or engineering programmes. Equivalent knowledge can also be acquired in other ways in Sweden or abroad. For specific projects, additional skills and training can be required.

Advertisement, selection and admission

Information and advertisement

Admission shall be made on a competitive basis following open advertisement of a doctoral place, with the exception of that which is specified in Chapter 7, § 37 of the Higher Education Ordinance. The advertisement shall be made available locally and on the University’s website (www.uu.se) at least three weeks before the application deadline and should be given appropriate national and international dissemination.

Selection

Selection among the applicants shall be carried out with consideration given to their ability to successfully conduct their studies. The assessment criteria for selection are:

knowledge and skills relevant to the thesis work and the subject/specialisation
assessed ability to work independently, for example
- ability to formulate and address scientific problems
- written and oral communication skills
- ability to carry out independent critical analysis
other experience relevant to doctoral studies, e.g. professional experience.

The assessment criteria may be demonstrated, for example, by supporting documents, an interview or a skills test.

In addition, an assessment is made of the applicant’s general competence and personal qualities, as well as their ability to collaborate. If a number of applicants are judged as being equal, preference shall be given to applicants from the underrepresented legal gender among the doctoral students in the subject/specialisation.

The mere fact that an applicant is deemed to be able to be awarded credits for prior studies or professional experience for the purpose of doctoral studies shall not give an applicant preference over other applicants during selection (Chapter 7, § 41 of the Higher Education Ordinance).

Admission

A doctoral student is admitted to a doctoral programme in a doctoral subject/specialisation. Admission of a doctoral student with full-time employment in their doctoral studentship at Uppsala University is decided by the head of the relevant department, except in cases specified in the Faculty’s guidelines for doctoral education (TEKNAT 2021/301). Admissions with other forms of funding are decided by the Faculty Board’s Working Committee after preparation in the Doctoral Education Board.

Structure and content of doctoral education

Doctoral education consists of courses and research work, and can take various forms, as specified in the individual study plan.

The research project must be well-defined and the level of ambition must be set taking into account both the degree objectives of the programme and the net study time (maximum 48 months for a doctoral degree or maximum 24 months for a licentiate degree).

Requirements for doctoral degree *

The requirements for the doctoral degree consist of passed examinations in the courses included in the approved individual study plan of each doctoral student, as well as a passed public defense of the degree project. The studies awarded a doctoral degree comprise 240 higher education credits (four years of full-time studies), of which the doctoral thesis comprises a minimum of 120 higher education credits and the course part a minimum of 40 higher education credits.

Requirements for licentiate degree *

A doctoral student who has acquired at least 120 higher education credits (two years of full-time studies) is eligible for a licentiate degree. The requirements consist of passing the examinations included in the program stage and receiving a passing grade on an academic paper of at least 60 higher education credits. The part of the course amounts to a minimum of 20 higher education credits.

Supervision

The head of department is responsible for ensuring that sufficient time is allotted for the department’s doctoral students to receive the necessary supervision. A doctoral student has the right to request a change of supervisor (Chapter 6, § 28 of the Higher Education Ordinance).

Individual study plan

The principal supervisor, in consultation with the professor responsible for doctoral studies (FUAP), is responsible for drawing up an initial individual study plan prior to admission. The head of department approves the study plan in connection with admission. The individual study plan shall contain a timetable for the doctoral studies, specification of how supervision is organised, and a description of the undertakings of the doctoral student and the department during the period of studies. The individual study plan also specifies the courses included in the doctoral student’s education.

The individual study plan must be revised at least annually in collaboration between the doctoral student and their supervisor. The revision involves following up on the doctoral student’s progress in relation to the degree objectives and previous plan, as well as planning for further studies. The FUAP approves the revised study plan.

Courses

Faculty-common courses

A course in research ethics, with a minimum of 2 credits and content equivalent to the courses provided by the Faculty, shall be included for the licentiate and doctoral degrees. An introductory course to doctoral studies and a course in scientific writing are also recommended.

Doctoral students who teach should undergo teacher training for higher education. This is specified in the individual study plan, and can either be a credit-bearing course element or take place within the framework of the doctoral student’s departmental service.

Teacher training for higher education, lasting 5 weeks, is equivalent to 7.5 credits at the Faculty, and may be included in the doctoral programme.

Basic Swedish language training for doctoral students who do not have Swedish as their first language may be a credit-bearing course element or take place within the framework of the doctoral student’s departmental service.

Subject-specific courses *

The doctoral studies should include courses that are intended to provide a wider insight into the subject complementary to the competence acquired during research. The courses can consist for example of natural science courses, methodology courses, literature studies, seminars, educational courses and participation in international workshops and symposia. The combination of the courses can vary and the courses planned for each doctoral student should be clearly stated in the individual study plan.

In addition to courses at Uppsala University, the doctoral are encouraged to undertake courses at other universities within and outside the country.

Course examiner

For doctoral courses, the teacher responsible for the course normally serves as the examiner. The head of department appoints an examiner for a doctoral course. The task of the examiner is only to determine grades on examinations. The principal supervisor, in consultation with the FUAP and other supervisors, decides which courses and to what extent (number of credits) the doctoral student is allowed to be credited for in their doctoral studies, and this is documented in the individual study plan.

Credit transfer

It is up to the principal supervisor, in consultation with the FUAP and other supervisors, to decide which examinations (courses or other elements carried out during the study period of the doctoral education) the doctoral student will be allowed to count towards their doctoral studies and to what extent (number of credits). This shall be documented in the individual study plan. The task of the examiner is only to determine grades on examinations.

An assessment must be made as to whether credits can be awarded for prior studies or professional or vocational experience (that have been completed prior to admission to doctoral education) (Chapter 6, § 8 of the Higher Education Ordinance). At the Faculty, the FUAP is responsible for the assessment.

Thesis, doctoral defence and licentiate seminar

Thesis

The research work shall result in a scientific thesis that must be defended at a public doctoral defence. The research task may be carried out individually or in collaboration with others within or outside the department. However, the doctoral student must be trained to conduct independent research.

The doctoral thesis can be designed either as a monograph, i.e. a unified, coherent scientific work, or as a compilation thesis, i.e. a compilation of scientific papers with a summary of these. The thesis work must be equivalent to at least 120 credits (Chapter 6, §§ 4–5 of the Higher Education Ordinance, and Appendix 2, System of Qualifications). Theses within the Faculty shall include a popular science summary that is in Swedish and at least two pages long.

The doctoral thesis must either meet the requirements for publication in an international scientific journal with independent quality review, or be a summary of scientific papers with equivalent quality requirements. If the doctoral student has co-authored a paper with another person, this may be taken into account only to the extent that the individual effort can be distinguished. This should be done through a description of the doctoral student’s contribution in the papers on which a compilation thesis is based. If parts of the work have previously been published by the doctoral student in a licentiate thesis, this shall be made clear.

The licentiate thesis is smaller in scope, but is subject to the same quality requirements for constituent papers as apply for the doctoral thesis.

In consultation with the FUAP and other supervisors, the principal supervisor shall assess when the thesis work has progressed to the point that a date for doctoral defence or licentiate seminar can be set.

Doctoral defence

The forms of defence and the grading of doctoral theses are regulated in the Higher Education Ordinance, the Faculty’s Guidelines for doctoral education (TEKNAT 2021/301) and Admission and grading regulations for doctoral studies at Uppsala University (UFV 2022/729).

The doctoral thesis shall be defended orally in a public doctoral defence. An examining committee appointed by the Faculty decides on the grade for the doctoral thesis.

Licentiate seminar

The Faculty’s guidelines for doctoral education (TEKNAT 2021/301) summarise the rules for the licentiate seminar.

The grade for a licentiate thesis shall be determined by the FUAP, or another professor delegated this duty, in consultation with the principal supervisor and the external reviewer. The principal or assistant supervisor for the doctoral student may not serve as examiner.

Degree*

The following degree titles have been established for Biology with specialisations:

Biology Filosofie licentiat- och doktorsexamen
Ecological Botany Filosofie licentiat- och doktorsexamen
Evolutionary Genetics Filosofie licentiat- och doktorsexamen
Physiological Botany Filosofie licentiat- och doktorsexamen
Comparative Physiology Filosofie licentiat- och doktorsexamen
Limnology Filosofie licentiat- och doktorsexamen
Microbiology Filosofie licentiat- och doktorsexamen, Teknologie licentiat- och doktorsexamen
Molecular Biotechnology Teknologie licentiat- och doktorsexamen
Molecular Cell Biology Filosofie licentiat- och doktorsexamen, Teknologie licentiat- och doktorsexamen
Molecular Evolution Filosofie licentiat- och doktorsexamen, Teknologie licentiat- och doktorsexamen
Molecular Immunology Filosofie licentiat- och doktorsexamen
Molecular Biology Filosofie licentiat- och doktorsexamen
Structural Biology Filosofie licentiat- och doktorsexamen, Teknologie licentiat- och doktorsexamen
Population Biology Filosofie licentiat- och doktorsexamen
Animal Ecology Filosofie licentiat- och doktorsexamen
Animal Developmental Biology Filosofie licentiat- och doktorsexamen
Evolutionary Organismal Biology Filosofie licentiat- och doktorsexamen
Evolutionary Functional Genomics Filosofie licentiat- och doktorsexamen
Systematics Filosofie licentiat- och doktorsexamen
Animal Conservation Filosofie licentiat- och doktorsexamen
Environmental Toxicology Filosofie licentiat- och doktorsexamen
Human Evolution and Genetics Filosofie licentiat- och doktorsexamen

The English translation for both degrees is Degree of Doctor/Licentiate of Philosophy.

Both the subject and the specialisation are listed on the degree certificate. The degree title (Teknologie/Filosofie licentiat- och doktorsexamen [Degree of Doctor/Licentiate of Philosophy]) shall be determined by the content of the doctoral education, and not by the doctoral student’s degree from a qualifying programme. If a doctoral student wishes to change their degree title to one that differs from that established for the doctoral subject dispensation is required from the Faculty Board (Working Committee). The request for a change of degree title must be made no later than the time of opponent and examining committee appointment or submission of the thesis for printing, whichever occurs first.

Doctoral and licentiate degree certificates are issued upon application in Ladok.

Regulatory framework and responsibilities for doctoral education

Doctoral education is regulated in the Higher Education Act (1992:1434) and the Higher Education Ordinance (1993:100). These are supplemented by the following local regulations: Guidelines for doctoral studies at Uppsala University (UFV 2022/728), Admission and grading regulations for doctoral studies and study programmes at Uppsala University (UFV 2022/729) and Guidelines for doctoral (third cycle) education at the Faculty of Science and Technology (TEKNAT 2021/301).

Responsibility for doctoral education ultimately rests with the University Board and the Vice-Chancellor (Chapter 2, §§ 2–3 of the Higher Education Ordinance). Through delegation, the Disciplinary Domain Board or Faculty Board has overarching responsibility and supervisory responsibility, but the day-to-day responsibility is exercised by the department in which the doctoral student is registered. Key functions in doctoral education are the head of department, professor responsible for doctoral studies (FUAP), director of doctoral studies, and the supervisor. See the Faculty’s Rules of Procedure (TEKNAT 2019/177) for a description of roles and responsibilities.