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having belief without evidence is regarded as a virtue

I don't find that the author has more than the shallowest understandings of faith. "Doubting Thomas" stands in the context of the whole gospel narrative and Thomas' part in it, not merely the oversimplification to which the author finds useful response. In writing that, however, I don't mean to discourage the author's thrust of argumentation.

To have faith is not merely "punting" from a plane of scientific pursuit. Faith is a gift from God, not a human endeavor. Faith should not be considered a virtue, as God gives such a gift to whom He pleases, not as a reward for scientific cleverness, or blithe, carefree willingness to "take a leap." It's not virtuous for Jews to exercise an arrogance that they are God's chosen people. As Old and New Testaments suggest, God is able to supplant the chosen vine, and make even rocks children of Abraham (Mt 3:9, Lk 3:8, etc.).

For those with a scientific, ungifted-by-God point of view, such may understand that faith is not at all without evidence, as such is readily seen in nature, viz. Romans 1. The point is that faith will never have the proof "from within the system" (viz. Goedel) as this author desires. If proof is required, we'll be inherently disappointed, as in such case, the rocks could believe and inanimate objects not in the image of God would be part of the set of faithful believers, pleasing to God. That's not God's creation.

However, I do find the author's reflections on science-as-taught do suggest a healthy direction for that endeavor.

When I was in high school some 30 years ago, our science and math teachers brought in some speaker who posed some interesting problems. One of those struck me deeply. The speaker posited we were to imagine we were viewing a car race from a crowded seat just beside the raceway. Each car had a race-assigned unique, sequential number. The cars, however, whizzed around the track quickly, and our view would allow us only to make out the numbers on some percentage of the cars. The speaker wanted to know how many cars were in the race, and expected us to answer with the highest number we'd recognized. I was aghast! In most cases, I thought that would be silly, as it would presume we'd seen the highest number car go by.

I thought we should better construct a model that assessed an approximation for the percentage of the cars that whizzed past verus whose numbers we were able to discern. Assuming randomness, we should consider the set of car numbers we actually saw. The average of those numbers, assuming we got a representative sample, would trend toward an average of the overall, mitigated by the percentage discerned. The highest numbered car we saw would probably not be as "trustworthy" as double the averaged car numbers seen. Again, assuming we'd seen a sufficiently representative sample, the higher of 2x the average or the highest car number plus some number to offset the likelihood that we had not actually seen the highest car number should be our guess of how many cars were in the race.

The speaker was surprised that such an explanation would come from a freshman.

Analogously, I do agree with the article's author that there is indeed faith involved in the science we have handed down. (Start with a faith as underlined above, if one must.) It needn't stay that way, if a critical mass of believers in science can learn to live in a system that incorporates extrapolation beyond what they know, given a healthier appreciate of how little they actually "know" combined with circumspection about the likelihood (that is, unlikelihood) that the rickety system yet constructed doesn't and can't account for a very large percentage of the "multiverse". It would be wonderful if we could see yet in our lifetimes a convergence that ameliorates the divisiveness many with political motives seem to plant and foster, based on science adopting approrpriate respect for how little falls within their system of explanation. It is reasonable that they all be wonderfully and energetically motivated to continue to make recede the span between God's knowledge and our own, all with a healthy and correct dose of humility (Psalms 139).