There is a great deal of controversy about the health effects of high fructose corn syrup (HFCS) on health, specifically obesity. Many media articles are quick to blame HFCS for the rise in obesity among American youths. More recently, the Corn Refiners Assoc. has launched an ad campaign explaining that HFCS is nutritionally the same as table sugar, and is "natural." Predictably, neither side is being entirely honest in this debate.
First, it's important to define some things. Table sugar, the sweetener to which HFCS is most often compared, is sucrose, which is a molecule of glucose bound to a molecule of fructose. In the body, sucrose is metabolized by sucrase enzymes to its constituent monosaccharides, which yields a G:F ratio of 1:1. In HFCS, cornstarch is broken down to more or less pure glucose syrup. The glucose is then inverted to yield approximately 1:9 G:F. Then pure glucose is added to give HFCS, which is usually 45:55 G:F. The upshot of all of this is that after the first stage of metabolism, the two compounds aren't really that different.
Now, none of that is really scientific. There are a host of studies that both sides like to point to. In general all of them agree that HFCS is linked to obesity, diabetes, and other related diseases and conditions.
The big question is whether or not HFCS is significantly different from sucrose. In terms of direct effects, it appears that the two are similar. More indirectly, fructose and weight gain from fat consumption have been linked in some studies. It is important to recall, though, that fructose and HFCS are far from the same thing.
The upshot of all of this is that high sugar diets are bad for you, regardless of which sweetener you use. HFCS should probably be avoided when possible, but as far as I'm concerned, that's mostly because sucrose just tastes better.
Disclaimer - The study I'm citing here is a literature review plus some original work funded by HFCS manufacturers. Their acknowledgment section mentions this and claims that their work was in no way influenced by their funding. Whether that is believable or not is up for debate.
http://www.hfcsfacts.com/images/pdf/CriticalReviewsinFSandN47-6-561-582.pdf
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