It is a fundamental misunderstanding of modern intensive agriculture and thermodynamics to think of biofuels as an energy source.  They are in fact massive parasites of fossil fuel energy with only a small fraction of their energy content from photosynthesis.   If biofuels were an energy source, we would see ethanol used to make more ethanol and biodiesel used to make more biodiesel.  Instead we use huge amounts of fossil fuel natural gas and petroleum to make the ammonia fertilizer, herbicides, pesticides, farm equipment fuel, bio-refinery process energy, and hydrogen gas to hydrotreat the final product into the drop-in fuels the airlines and military require.  Petroleum is even the feedstock for the organic chemicals used to synthesize the designer enzymes for the most advanced biofuel processes.  In the end, biofuels are a hugely wasteful transformation of fossil fuel energy to generate a false fig leaf of being clean and green.  After more than $6B a year in subsidies since 2005, corn ethanol, the most productive US biofuel per acre of cropland, is still 40 cents more a gallon than premium gasoline when corrected for MPG energy content. (see E85 price in "AAA’s Daily Fuel Gauge Report." http://fuelgaugereport.opisnet.com/index.asp ).  The laws of physics won't change no matter how many billions of dollars are thrown at them.  Despite the hype and misinformation spread by advocates, even algae needs ammonia or urea as energy inputs and huge amounts of fresh water (evaporation make-up water for even saline algae must be fresh or salinity will rise), and the lifecycle studies are showing worse than a 1:7 EROI, which means the end product hydrotreated biodiesel has less than one-seventh of the energy input to create it.  Time to stop fleecing the taxpayer and driving up the food prices to boot.  This is epic failure.  Dr. Chu and Secretary Panetta and Sir Richard Branson need to take a high school physics and chemistry refresher, and then force any prospective biofuel producer to walk them through the hydrogen and carbon mass balance stoichiometry and enthalpies of their process and show where all the energy inputs and outputs are happening.  They would inevitably see that biofuels are attempts at perpetual motion in chemistry--turning hydrocarbons into carbohydrates and then back into hydrocarbons, and it is hidden or disguised inputs of petroleum energy that make this parlor trick work.

Cliff, can you provide any references for the argument you are making?  It is very intriguing and something I would be interested in researching further.

Some of the more thorough studies:
1. Hill, J., E. Nelson, D. Tilman, S. Polasky, and D. Tiffany. “Environmental, Economic, and Energetic Costs and Benefits of Biodiesel and Ethanol Biofuels.” Proceedings of the National Academy of Sciences 103, no. 30 (2006): 11206.
2. Murphy, David J, and Charles A. S. Hall. “Year in review—EROI or Energy Return on (energy) Invested.” Annals of the New York Academy of Sciences 1185, no. 1 (January 1, 2010): 102–118. http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.2009.05282.x/abstract.
3. Patzek, Tad W. “A First-Law Thermodynamic Analysis of the Corn-Ethanol Cycle.” Natural Resources Research 15, no. 4 (February 22, 2007): 255–270. http://www.springerlink.com/index/10.1007/s11053-007-9026-9.
4. Clarens, Andres F., Eleazer P. Resurreccion, Mark A. White, and Lisa M. Colosi. “Environmental Life Cycle Comparison of Algae to Other Bioenergy Feedstocks.” Environmental Science & Technology 44, no. 5 (March 2010): 1813–1819. http://pubs.acs.org/doi/abs/10.1021/es902838n.
5. Kloeck, Gerd. “It’s the Process, Stupid. Biofuels from Microalgae Are Not yet Sustainable.” Genetic Engineering and Biotechnology News, January 5, 2010. http://www.genengnews.com/blog-biotech/it-s-the-process-stupid-biofuels-from-microalgae-are-not-yet-sustainable/587/.
6. Murphy, Cynthia Folsom, and David T. Allen. “Energy-Water Nexus for Mass Cultivation of Algae.” Environmental Science & Technology 45, no. 13 (July 2011): 5861–5868. http://pubs.acs.org/doi/abs/10.1021/es200109z.
7. Patzek, Tadeusz W. “A Probabilistic Analysis of the Switchgrass Ethanol Cycle.” Sustainability 2, no. 10 (September 30, 2010): 3158–3194. http://www.mdpi.com/2071-1050/2/10/3158/.
And read up on the non-performance of Cello, Range Fuels, Amyris, Gevo, Choren, Cellana (and stand by for similar news from KiOR, Solazyme, Syntroleum, Iogen, etc.).

So, "Cliff," I understand you to say that because we don't make enough ethanol or renewable diesel or biodiesel fuel to power our farm equipment and refineries and because we haven't yet converted our chemical industries to using bio-inputs instead of fossil fuel inputs, that we are still using fossil fuels and hydrocarbons as the basis of our power/chemical economy.  And because of that current state of affairs, you would halt all effort to get to the point where we do not rely on fossil-based inputs?

Take a look at www.AdvancedBiofuelsUSA.org for information on efforts to make this transition.

"Biofuels" is not limited to ethanol fermentation, or soybean oil esterification. These are indeed using "food" agriculture, and can be shown as having small, or negative energy balance. By the way, the starchy corn we are feeding the cows (and our kids, in the form of high fructose corn syrup, in any sweet beverage) should be really called a chemical, not food. There is a vastly better solution in using energy crops like miscanthus and switchgrass, which can grow today 10 Tonnes/acre/year, for thermo-chemical processing. Namely, gasification into synthesis gas (carbon monoxide and hydrogen, mostly) and then synthesis gas into gasoline via Mobil's 1972 "Methanol to Gasoline" (MTG) patent. This was already demonstrated in NZ in the 1980s, in a 14,000  BPD gasoline plant built by Bechtel. The feedstock there was natural gas, but the process, from Methanol and on, is exactly the same. I should know, as I have built a 40 kg/h pilot for biomass-gasification and gasoline synthesis at Primus Green Energy, in Hillsborough NJ. Careful mass & energy balances show that you CAN make a cost effective conversion, with a yield of 90 gallons gasoline per 1 Tonnes of dry biomass. Yes, this can save our grand children from suffocation, and no, it does not need to have huge government subsidies. This mechanism can be quite profitable, even without levies or the Ethanol blending bonus ($0.51/gallon), or the EPA RIN (Renewable Index Number).