I have seen primary heads almost in tears when their bright, confident, self-sufficient Year 6 children become under-stimulated secondary pupils sitting in rows.

There is no doubt that these first years of secondary education need reform. Yet I fear politics is to doom the attempt to disappointment.

Over the next few weeks teachers from some 200 schools in 17 English education authorities will attend a two-day course to launch the latest phase in the bid to transform key stage 3.

Pilots for English and maths teaching will be rolled out to all schools in September. But the last phase - Teaching and Learning in the Foundation subjects (TLF) - is the one which offered the most exciting prospects. Sadly, I believe it is also the one which is going to create the greatest disappointment. TLF could have offered the most radical improvement in the education of 12 to 14-year-olds since the abolition of the 11-plus. Instead, the materials and methods represent no more than a thin summary of the sort of advice given in initial teacher-training.

There is no doubt that reform of KS3 teaching is needed. Enormous changes have taken place in primaries, and the pressure of league tables has made secondaries think hard.

So I was delighted when David Blunkett, at the North of England conference last year, announced the new KS3 effort. I was delighted because of the emphasis the Education Secretary said would be put on thinking skills. A year is a very long time in politics, and I fear it is politics which robbed this vision of substantial realisation.

What went wrong? The history is murky and all that matters now is that the materials and methods of TLF were produced under extreme time pressure.

What was to have been a transformation of teaching and learning has become little more than a bland recipe for “good teaching” devoid of any rationale, justification, or reference to the considerable research data.

Let me take an example from an area in which I claim some expertise, the teaching of thinking. This isa politically sensitive area because former chief inspector Chris Woodhead, journalist Melanie Phillips, and Tory leader William Hague do not believe in thinking. For some reason the present Government, rather than facing them down with substantial research evidence, seems to be frightened of the adverse publicity that this unholy trio might generate.

What the research shows consistently is that if you face children with intellectual challenges and then help them talk through the problems towards a solution, then you almost literally stretch their minds. They become cleverer, not only in the particular topic, but across the curriculum. Twenty years of our own cognitive acceleration work has shown that intellectually challenging 12-year-olds increases their intelligence and leads to higher GCSE grades.

So why do the TLF materials ignore such evidence? Why do their activities on thinking consist of asking teachers to classify some activities as “reasoning” or “creative” or “evaluative”, and wholly misses a wonderful opportunity for, yes, transforming teaching and learning at KS3?

More generally, the draft materials offer a model of “training by numbers”. The whole philosophy is as bad as the old multi-attainment target national curriculum, or the dreadful Teacher Training Agency’s “competencies”.

Unfortunately, children are not machines to be tended by technicians. They need to be educated by professionals who are trusted to understand something of the theory of what they do and apply it flexibly and intelligently.

My experience in schools convinces me that most teachers are perfectly capable of this, that they welcome discussing theoretical bases for teaching practice, and that they loathe being told what counts as “good teaching” on take-it-or-leave-it terms.

There is, however, hope. This TLF is a pilot which could be changed. I believe radical re-thinking is required - and a fundamentally different philosophy.

Professor Philip Adey is director of the Centre for the Advancement of Thinking at King’s College London. He was a consultant in the early phases of the TLF materials Research Focus, 22