The emissions impacts of ethanol have been thoroughly tested by the EPA, DOE, and public and private researchers. The results of these tests have clearly indicated ethanol has superior emissions qualities, and fewer heath concerns, compared to gasoline. The entire basis of the OP is from a COMPUTER MODEL... not real life, not real science folks. Junk. That article was dis-credited by nearly the entire science community within hours of being made public. I shall do my best as a "MythBuster" below.

EPA and DOE tests, numbering in the hundreds, that used real vehicles quantify the actual physical emissions of these fuels, and provide proof, something far beyond a computer "model".

According to the DOE Argonne National Labs, E85 reduced greenhouse gases by 29% when compared to conventional gasoline.

Out of the most recent 17 studies, 14 found that ethanol SIGNIFICANTLY reduced greenhouse gas emissions when compared to gasoline. 3 showed modest reductions.

Who do you trust more? One guy's computer model, or the American Lung Association? The American Lung Association is a major proponent of cleaner burning fuels such as ethanol and biodiesel. The American Lung Association credits gasoline blended with ethanol for reducing smog formation by at least 25%, and ozone ( bad on the ground ) by 20%.

Ethanol is non-toxic. You can drink it. It is in wine, whisky, and beer.
Gasoline contains toxins like benzene, toluene, and xylene.

The computer model conclusion that E85 forms formaldehyde in any meaningful quantity is FALSE, as proven by studies done by a California Environmental Policy Council. CEPC concluded that ethanol reduced formaldehyde formation compared to gasoline.

A 1997 study done in Denver, CO compared formaldehyde formation from winter blend gasoline with E10 in the winter of 95/96, to the MTBE winter blended gas of 88/89 and found NO STATISTICAL DIFFERENCE in the two.

The Stanford computer model predicted "E85 generally increased benzene". This seems totally illogical, since benzene is a component of gasoline, but is not found at all in ethanol. None. Zip. Nada. As Spock would say: "Illogical". I'll go one step further and say, "impossible". Ethanol blended gasolines, E10, E20, E30, or E85 must always, by nature, contain less benzene. Did someone program the computer wrong? Or was this an elaborate April Fool's joke? ( What date was the original made public??? )

The study's author is a long time advocate of wind energy charging batteries to be used in EV's. It appears he may be trashing ethanol to make wind power look more promising.

One of the "contributors" to the author's study was professor Tad Patzek.
Patzek's research on ethanol has been universally rejected and disproved by numerous government and private scientists. As has Mark Jacobson's.

Sounds like these guys just wanted 15 minutes of fame. To heck with real data.

On the food vs. fuel issue, let me just add, that for every 100 pounds of corn that goes into an ethanol plant, 70 pounds comes back out, and IS used, primarily, AS FOOD! Ethanol plants only take the sugar out of the corn. All the proteins, fats, oils, and fiber remains, and is used.

So when you see numbers like "20 billion bushels of corn went to ethanol plants last year" ( I made up that number ) you now know that 14 billion bushels of that made it into the food supply.
And that little fact, is NEVER reported by the anti-ethanol media.

Also corn is a commodity just like gas, and the price changes all the time, just like gas... and will be down, maybe to record LOW prices very soon. It just turned out in THIS year, contractors can build ethanol plants faster than farmers can plant corn ( plus contractors can build in winter, and farmers can't harvest in winter ). Once the number of corn ethanol plants levels out, the supply of corn will level out, along with the price.

Plus, ethanol can be made from any starch or sugar. Not just corn. Corn is just in the lime-light right now... which in time, will also pass.

I really hope, and suspect, ethanol will be here to stay.