1. It's not so clear to me, even in the enlarged picture, that the T's and A's you specify are the only highlighted letters. (For instance the second A in 'Allah' looks like it has had some additional work. Some of the the O's, E's, and H's look funny too.) Maybe my eyesight is not so good. Maybe Ivins purposefully made it hard to detect. Maybe one has to compare all the anthrax letters to see it. It seems to me that you should clarify this in your book.
2. Why wouldn't a scientist like Ivins pick something more esoteric than Godel, Escher, Bach? He's probably working with DNA all the time. Why does he need GEB and a 1992 article on "DNA linguistics" to figure out a DNA-based code?
3. You make a point concerning the GEB idea of the framing of the code. But if Ivins wanted to step in later as the hero, he wouldn't have needed to point out that there was a code before this point. So he must have had a desire on some level for the code to be discovered earlier. Based upon your description of the code, it is not unlikely that a random person with a little familiarity with DNA could have eventually discovered the code. This would probably have narrowed the suspect list greatly, undermining the steps Ivins took to not be identified. Perhaps this makes some sort of weird sense if Ivins did not expect anyone to die. But surely he could have expected to be in a lot of trouble anyway.
4. If Ivins identified himself as the sender of the letters, he would also be identifying his obsession with his coworker and his obsessive hatred of New York. These probably wouldn't be compatible with Great American Hero status.
Yes. Some other letters look slightly highlighted, and one or two of the code letters doesn't seem highlighted enough (like the T in NEXT). I don't address this in my web page about the coded message in the letters, but I do address it in the notes I added at and near the end of my web page about the handwriting.
I will be trying to make all of this more clear in my new book.
"2. Why wouldn't a scientist like Ivins pick something more esoteric than Godel, Escher, Bach?"
Now you're asking me to get inside Ivins' mind. To him it was probably a brilliantly clever idea. It wasn't a code he had to invent. It wasn't a code that no one could break. It was a code that was explained in a Pulitzer Prize winning book. But, it was also a code that no one would likely realize was there. GEB explains the steps that you have to go through to realize the code is there. Step #1: You have to be looking for a coded message. Who would expect a coded message inside a threat letter?
What Ivins did makes sense if you accept that Ivins was a sociopath with a big ego who evidently enjoyed doing things right in front of other people without them realizing what he was doing. It evidently amused him to fool people that way. It would show how much smarter he was than they were, because they were so easily fooled.
"3. You make a point concerning the GEB idea of the framing of the code. But if Ivins wanted to step in later as the hero, he wouldn't have needed to point out that there was a code before this point. So he must have had a desire on some level for the code to be discovered earlier.
I don't follow your reasoning. The coded message was there in case he needed it. It was a message that he could decode and explain to others WHEN NECESSARY. It would have been a disaster if the code was deciphered before he was ready - as it turned out to be.
"Perhaps this makes some sort of weird sense if Ivins did not expect anyone to die. But surely he could have expected to be in a lot of trouble anyway."
I suspect he believed he would be saving millions of people, and although he didn't do it in a legal way, his methods might be forgiven if he was seen as a true hero. That's the way a sociopath with a big ego might think.
"4. If Ivins identified himself as the sender of the letters, he would also be identifying his obsession with his coworker and his obsessive hatred of New York. These probably wouldn't be compatible with Great American Hero status"
Maybe. The "PAT" part of the code wouldn't by itself say anything about any obsession. People with obsessions don't usually realize they have obsessions. Ivins would have viewed his obsession as just a caring admiration.
And the "FNY" code comes as part of the package. I don't know if he could have coded "PAT" without also coding "FNY." If it concerned him, he probably rationalized he could joke it away by explaining that it was about his co-worker's interest in the New York Yankees.
Very interesting questions. I hope I've answered them satisfactorily.