The provision of advice on animal welfare is an important part of the work of scientists in applied ethology, neurophysiology, veterinary epidemiology and other disciplines. Those who request guidance often expect advice that will help them to make progress in difficult discussions. Scientists want to live up to these expectations, but it is also important for them to clarify any scientific limitations. They are normally aware of limits to their advice, but these limits are sometimes not explicitly stated. Using the phrase broadly, we call this kind of limitation ‘scientific uncertainty’. We distinguish between the following four types of uncertainty: I) Ontological uncertainty, relating to the existence of animal feelings and other states relevant for animal welfare. 2) Conceptual uncertainty, stemming from the fact that some of the concepts used in animal welfare science are value-laden if used outside a narrow scientific context. 3) Lack of scientific evidence, stemming from a lack of scientific data on the problem in question. 4) Uncertainty about priorities, relating to the practical conclusions to be drawn in a situation with an open-ended set of ethical and other practical considerations. Scientific uncertainty is unavoidable. It is therefore essential, when giving scientific advice, to state the assumptions on which the advice is based. This makes scientific advice more objective, but also of more limited value to those who do not share the underlying assumptions.

Ethical principles guide decisions about what we consider to be right or wrong proposals and actions, so that when value judgements are made these engage us in ethics. Ethical thinking is clearly relevant to decisions about the way we treat animals, and such thinking has led to the commonly held view that animal use by people is acceptable provided that such use is humane. The ethical requirement that we treat animals humanely means that we must minimise the harms we do to all animals in our care or under our control. Accordingly, we must assess what harms are done to the animals, how bad each harm is in terms of its intensity and duration, what methods are available or can be developed to minimise each harm, and the relative effectiveness of those methods of harm minimisation. We must also seek to use the most humane methods currently available that can be practically applied. Ethically driven scientific evaluations of this sort have improved the humaneness of livestock slaughter and vertebrate pest control. For instance, detailed studies of different pre-slaughter stunning methods have validated their use to pre-empt the pain and distress that otherwise conscious animals would experience during the fatal neck cut and the short period of consciousness (sensibility) that follows it Likewise, reducing injuries caused by restraint traps has improved the humaneness of this vertebrate pest control method, and comparing the effects of different poisons has allowed the least humane ones to be identified. Difficult questions nevertheless remain at the problematic interface between quantitative scientific observations and their interpretation regarding the suffering that animals may experience, as well as questions about the relativities of different types of suffering.

In choosing among alternative wildlife management techniques, trade-offs between animal welfare and conservation, utility or economics are often apparent. This paper reviews the roles of science, scientists, regulators and educators in attempts to overcome this inter-dependence and to make simultaneous progress on all fronts. Illustrations are drawn in particular from trapping and pest population control. Against the real progress that can undoubtedly be made through scientific study, there is a regrettable lack of structure because of poor philosophical and logical coherence within the welfare movement.

Scientists recently attracted considerable public attention when they presented a featherless chicken tailored for production in hot climates. Although this chicken was actually the result of traditional breeding, it is an example of what might be achieved if targeted gene manipulation techniques become widely applied in agriculture. Through interfering directly with an animal's genome, scientists hope to be able to create animals with exactly the desired characteristics, such as lean meat or temperature tolerance. Industry and geneticists may be enthusiastic about the possibility of producing pork with polyunsaturated fatty acids or high-yielding dairy cows to be kept in tropical climates, but the European public often reacts with alarm at these prospects. A consistent pattern of the surveys conducted among members of the European public is that, of all of the potential biotechnology applications, those involving animals are the ones that people find the least acceptable. People fear a development of techniques that may get out of control, and they also have ethical concerns about humans’ right to ‘play God’ and about the welfare of the animals involved. All of these aspects seem to be relevant for an ethical discussion about animal biotechnology. Animal welfare scientists can play an important role by providing information for an animal welfare risk assessment at an early stage of research projects that involve the genetic modification of animals, and also by helping to develop guidelines for the housing and husbandry of animals with special needs. On the other hand, ethical problems remain that lie outside the area of science. In this paper we discuss the role of animal welfare science in aiding ethics decisions about animal biotechnology. We give a summary of the different ethical concerns expressed by ethicists and by the general public. Focusing on one of them, animal welfare, we give an introduction to the animal welfare implications of recent developments in reproductive and gene technologies. The importance of animal welfare aspects is discussed in relation to other ethical concerns about animal biotechnology.