Summary: commercial flour has numerous health/nutritional issues
Action needed: do our own milling, or at least use unbleached whole flour.
The book Nourishing Traditions emphasizes the importance of soaked and fermented whole grains. Today I did some reading in order to corroborate or reject this claim. Indeed we can find four problems with flour as available today:
Contamination of grains by mold is a major problem, as evidenced by a multitude of papers on the topic. “Aflatoxin is a naturally occurring toxin produced by the fungus Aspergillus flavus. This toxin is the most potent carcinogen found in nature.”  “The aflatoxins, particularly aflatoxin B1 should be regarded as a quadruple threat, i.e., as a potent toxin, carcinogen, teratogen and mutagen. AFB1 induces liver cancer in several animal species, and has also been linked to liver cancer in human beings.”  Metabolites of aflatoxin make their way into the milk of animals fed with contaminated feed, and survive pasteurization intact .
Unfortunately, small and medium farms might lack the equipment and knowledge for proper storage, leading to 3.2 and 1.75 times higher mold concentrations as compared to large enterprises . Lest this study be dismissed as specific to Lithuania, US corn production also has a massive problem: “All of the commercial hybrids had high levels of aflatoxin accumulation […]. Aflatoxin levels for all hybrids greatly exceeded the FDA threshold level [by factors of 5 to 400].” 
What can we do?
- Storage conditions have a large influence; specialized granaries may offer better conditions than small family farms .
- Alternative types of grains may be less prone to contamination. The same study found that wheat was 3 to 8 times higher in toxin levels than barley .
- Toxin production also depends on agricultural practice. Stress such as insect damage predisposes plants to infection. Competition with other (beneficial) soil microbes also inhibits toxin biosynthesis .
The third point seems at odds with the first – industrial agriculture would tend towards unhealthy monocultures, but may offer better storage conditions. One thing is for certain: my previous assumption – that flour of a given type does not differ between brands – is incorrect. Unfortunately, it is unclear how we can differentiate between contaminated and safe flour.
Apparently driven by an irrational desire for ‘purity’ (at least in terms of color), most commercial flour is bleached white. Enter the law of unintended consequences: “increased levels of neurodegenerative disorders in humans may have arisen due to inclusion in the diet of methionine sulfoximine (MSO), a byproduct of the bleaching of flour by nitrogen trichloride. MSO acts directly to inhibit the production of two crucial molecules, glutathione (GSH) and glutamine. Decreases in GSH, a key antioxidant and free radical scavenger, diminish the body’s antioxidant defenses and may lead to increased oxidative stress.” 
The introduced chlorine is almost completely (99.3%) incorporated into the flour . Although no concrete evidence of damage from chlorination was found, “the toxicological significance of chlorine-modified carbohydrates is not known. The potential formation of halocarbons from carbohydrates raises some concern about their production in treated flour.”  Indeed, “exposure to [higher levels of] chlorinated flour lipids in the diet for 2 weeks reduced the growth rate and increased relative liver weights in rats”. 
Sounds like we are better off avoiding bleached flour.
Flour rancidity (oxidation of unsaturated fatty acids) occurs within 10 days ; storage of flour for 30 days markedly reduces the protein quality . Finally, rancidity results in mutagen and carcinogen aldehydes . There is a simple solution: storage in whole-grain form slows rancidity development ; milling the grain immediately before use ensures freshness. Refrigeration would also slow enzyme activity .
The term “empty calories” is well-known. How does this come about?
- Discarding the bran and germ to obtain “white” flour loses nutrients and antioxidants (even in the resulting bread) .
- Storing flour over a period of weeks reduces levels of beneficial vitamins .
- Heating grains inactivates enzymes .
The third point is industry’s “solution” to rancidity. A recent patent application by Kraft sheds more light on the motivation . To the credit of its inventors, the text is remarkably clear and helpful (compared to my experience with software patents). However, its focus is entirely on industrial convenience and anything that might “deleteriously affect dough machinability”. There is not a single mention of nutritional value, the harm posed by rancid lipids, or that the enzymes destroyed in this process would be helpful if ingested.
How we can do better
We can solve all of these problems by sourcing high-quality grains and milling them to flour immediately before using them. As usual, more effort leads to higher quality. But is the proposed undertaking feasible?
Apparently, home flour mills are small, self-contained and quite convenient: grains in, flour out . Let’s estimate the heat transfer: an 85 mm diameter ceramic millstone of roughly 3 cm thickness weighs around 340 g. A 360 W motor grinds 100 g flour in 1 minute. Assuming moderate load factor and varying torque, we have about 100 W of energy being converted to heat. With a specific heat of 1.09 kJ / (kg*degC), the millstone will end up 16 degC warmer. However, most of that heat remains inside the mill; an impromptu measurement found the flour is about 6 degC warmer than ambient temperature . This is well within the safety margin; enzymes will remain intact. Note that continuously operated commercial mills run hotter, and depending on the millstone material, may cause temperature differentials of 36 degC (granite) or even 87 degC (marble) , thus destroying any nutrients.
The above research has convinced me that a flour mill is a useful investment.
We return briefly to the initial question: does soaking and fermenting flour help? Grains contain phytic acid, an “antinutrient” that reduces bioavailability of minerals such as calcium and potassium . Fermentation reduces phytic acid by 12%, sprouting by 18%, and a traditional process combining both removes 68% . “The synergistic effect of cooking and fermentation improved the nutrient quality. The antinutrients were reduced to safe levels to a greater extent than did any of the other processing techniques or their combinations employed.”  Finally, “protein digestibility was significantly improved when the processed grains were fermented for 12 h”; this “could be attributed to the partial degradation of complex storage proteins to more simple and soluble products” or “to the degradation of tannins, polyphenols and phytic acid by microbial enzymes .
We can consider the Nourishing Traditions book to be corroborated on this point. In summary: it pays to grind grains ourselves, and soak/ferment them overnight.
 US patent 6,616,957