I may be overlooking something in the outline, but it looks like this is "just" a computer programming book. I don't say "just" to insult you by any means, but more the result of observing the word "Scientist" in the title and an having expectation to see something more than programming.
I think IT folks, and likely folks outside of IT, lack the scientific skills needed to be successful. First and foremost, there is a lack of problem solving skills. Many IT people I have worked with have great technical skills as long as you tell them what to do and solve the problems for them. Beyond that, I see a lacking of analytical skills and what I'll call a lack of "Scientific Investigation" skills. If you consider that to create solid solutions a programmer should be very methodical when reviewing requirements, create test plans, and writing tests, etc then it seems to parallel following a rigid procedures of a scientific investigation.
Again, if I am overlooking coverage on this topic in the book, my apologies & please point it out. Assuming that I have not too quickly scanned the book, please consider the possibilities of writing/coaching for a "Scientist" and share any thoughts you have on it here.
As a scientist, I totally agree with the importance of teaching scientific inquiry. One challenge of writing this book has been striking a balance between theory and application, at a level that beginners can work with. As the preface says, "Think Java is an introduction to computer science and programming intended for readers with little or no experience." We don't get readers to the point that you describe, but it's a step in the right direction. The chapters are designed to pose a problem, walk through the process of solving it, and introduce vocabulary along the way.
Let me give some more context about the subtitle. Allen originally started writing Think Java in 1999 in response to the status quo of 800-page textbooks that are often full of dense, technical material. He chose the subtitle to emphasize that this book is not primarily about the Java language, but rather a way of thinking. In a previous version he wrote, "Computer scientists have an approach to problem-solving, and a way of crafting solutions, that is unique, versatile and powerful. I hope that this book gives you a sense of what that approach is, and that at some point you will find yourself thinking like a computer scientist."
Looking at the table of contents, it may not be apparent what Think Java offers beyond just programming. But the "thinking" aspect comes out in the text itself. We use a relatively informal tone to guide the reader to explore and apply concepts. As we continue to work on the book, we'll look for more opportunities to bring "the scientist" to the forefront.