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I don't have the book, I don't find any references to scales in lungs beyond this source. They sound fairly antifunctional, and I'd expect them to cause quite a hub-bub if they could be substantiated.
You could try contacting the people at http://www.dinofish.com/ the email address is [email]dinofish@cloud9.net.[/email] While you are at it, ask how many other differences there are ...

Enjoy.
Got a response to my email. Looks like I'm not the only one hesitant to accept a claim of scales in lungs.
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Yes, this is very odd. There are a lot of errors in the Thompson book, or so
I was told by Prof Eugene Balon. I would suggest going to the bibliography I
offer on dinofish.com and looking up the early papers. I have to wonder if
the lung referred to is different from the swim bladder, which in Latimeria
is fat filled. - Jerome Hamlin
It looks like I'll be discontinuing my investigation now. Not really worth a lot more effort just to debunk one more Glen Morton assertion.

Scales in the lungs would be a very counter-intuitive design feature. That's sounding something more like a funky DNA experimental project than what I expect to find in nature. Reminds me of the chicken story.

Dark Matter + Dark Energy = Dark Truth

"We find that such evidence demonstrates that the ID argument is dependent upon setting a scientifically unreasonable burden of proof for the theory of evolution." - Judge Jones Kitzmiller case
http://www.talkreason.org/articles/Falsify.cfm

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