True, it's not Hafen himself who wrote this article, but it is on his site Faith is Not Blind with his blessing and enthusiastic agreement.
So what's wrong here? Nothing really, except...... there is always an except......
The article is fine for showing scientific models are incomplete, we already knew that. And it is obviously true that when new knowledge comes about, we truly need to change our interpretation of what we thought we knew, i.e., update our knowledge. It is to the last paragraph which I have an issue or two.
Scientific modeling teaches us that when we discover gaps between what our idealization of the world predicts and what we observe, it is not something to cause us to deny or despair, but instead it is an invitation to deepen our understanding and construct new models that more accurately describe what we observe. Principles that we have already proven are not likely to be discarded, but rather subsumed into a larger theory with wider application to our lives. Brigham Young said, “Our religion is simply the truth” and it “embraces all truth that is revealed and that is unrevealed, whether religious, political, scientific, or philosophical.” When we encounter gaps between the ideal and reality, we don’t need to fear, but instead we can press forward to deepen our understanding and knowledge of the truth.
So, my issue is, I have used this scientific model as a basis of updating my knowledge concerning the Joseph Smith Papyri and the Book of Abraham. There most certainly are gaps between what Joseph Smith said and what Egyptologists say. I didn't despair, I then went to the apologists, and actually became one myself, emphasizing the Book of Abraham facsimiles. Then I learned as I studied that more and more the apologists appeared to me to be the ones with all the gaps, and appeared to me to be guessing more and more haphazardly, as they fished first for a theory that worked, then try another, and now another which contradicts the former ones, and when that was refuted come up with another, and when that was refuted....... so, Brigham Young simply doesn't come across as valid, since there are gaps in Mormonism, proof of which is when the current prophets discard what earlier ones had revelation, which later ones say were not revelation. And current Egyptologists still have not found much to agree with either in the Book of Abraham not any argument apologists have presented yet, in any of their theories. After so many tries and strikes, (in baseball you are only allowed three, apparently in apologetics you are allowed a dozen, but what to do when you still strike out after a dozen efforts?!) one realizes the model is faulty. But they are not adjusting to the current best model, namely, that Joseph Smith was simply wrong, and the apologists are too, thus negating more of Brigham Young.
By deepening my understanding and knowledge, and without fearing, I discovered the model of Mormonism and the Book of Abraham simply don't work at all. The model that does actually work? Joseph Smith made a mistake when claiming to translate the papyri and find the Book of Abraham, the Book of Joseph in the papyri. Joseph Smith was just wrong as flat earthers were earlier in history wrong, and still wrong today. The evidence is overwhelming on this and other issues. Models are fine, re-tuning them is even better with new knowledge. But discarding them also works when they just do not work in any fundamental way.
That is what the article leaves out. It generalizes a single scientific discovery for discussion, then it assumes this applies all throughout Mormonism as a religion in all generalities, otherwise, why the Brigham Young quote? It also works for and/or against religious claims and/or scholarly claims. In this instance, the model fails on issues dealing with the Egyptian papyri.
The article makes a fundamental assumption, which is a flaw. Take one example and then from that generalize in an entirely unrelated and different subject assuming that it is right for it as well. Sorry guys, no cigar there, but kudos for at least giving science on a basic level a good look, and more or less getting that single instance right and accurate.