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When I look for a PhD position, they always write that they need a master’s degree. However, most of the times I see that I have all the experience they are looking for. PhD is a lab-based work, so what they will do with the degree? Shouldn’t they take someone who is more good at lab work?

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A PhD degree should indicate that you are ready to do research in your field. That requires a combination of skills, including understanding of your research area and related areas, not just lab work.

Typically, in the USA the PhD program includes coursework to build and demonstrate that understanding. An alternative, which makes the PhD program itself shorter, is to require a related master's degree.

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    For example, most US PhD programs which start after a bachelor's degree are planned for 5 years, while in most cases, a German PhD is planned for 3 years but requires a 2 year master's degree, so in the end the times are comparable. – Sumyrda Jun 12 '16 at 14:49
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A PhD is degree you receive for research. There are formal prerequisites that you have to meet, depending on the law of the country and the university regulations. Usually, the PhD advisor cannot alter these requirements. In some cases though, there might be room for lowering formal prerequisites if a committee approves this.

In some countries (including Germany), a masters degree is the usual "proof" that you reached the scientific level to work on a PhD.

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