Let us look to the new system first
Whether we might like it or not, there is a qualitative difference between the kinds of the abilities required of pupils attempting Intermediate III, compared with those demanded by Higher. In the former the tasks and assessments are designed to be under the complete control of the instructor and, because the demands made on the student are relatively simple, there can be a direct cause and effect relationship between the task and the learning outcome. Since it allows formal assessment over short intervals, this clearly has advantages for students not yet in a position to make a long-term investment in learning.
Higher, by contrast, demands the capacity for abstract and independent thinking. This requires a different orientation to the subject on the part of the student an only come with maturity.
It also has to come from the student's own inner resources and cannot be imported directly and mechanically from outside, though there is a great deal the teacher can do to nurture it. Study at Higher level also requires a longer-term commitment.
To pretend that there is a clear linear relationship between the one level of activity and the other and to seek to impose this through an artificially-contrived assessment system is asking for trouble. In English, for example, a wish-list of skills desirable at Higher has been quite arbitrarily extrapolated downwards to Intermediate II and I (with minor adjustments in the language of the descriptors, supposedly to compensate), regardless of whether these are appropriate to the age or likely experience and maturity of the student.
When, as is the case, the resulting scientifically neat model does not fit reality, then the examiners are quite understandably put to considerable effort interpreting it. This would certainly explain the anomalous results which have been widely reported from Higher Still. I would be less confident than Professor Raffe that the current problems do not reflect any intrinsic weaknesses in the new system.
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