The author gets tripped up by not outlining what "modeling" is, and what the purpose of a model is, and in doing so, he throws the baby out with the bathwater.
A model doesn't have to be a perfect 1:1 representation to be useful, or even correct, if the right questions are asked. For example, none of us could perfectly predict exactly how much more in debt our nation will be tomorrow than today, but we can all predict it will be a positive amount. And we might be able to come up with an estimate, even if we can't tell the exact number. Similarly, just because I can't tell you what the temperature will be in Central Park next July 19 at 10 am Eastern, but I can tell you that it's warmer than right now. That's why climate models can be useful, even if weather models aren't able to predict weather 100% next week.
In a sense, it seems that Dougherty is recognizing this, but it's also what scientists are already doing. One approach doesn't preclude the other.
I might try giving Dougherty's book a read this weekend, if I get the chance.
"Essentially, all models are wrong, but some are useful." --- George E. Box