The world took notice when the UN Food and Agriculture Organization reported that livestock accoutned for 18% of global greenhouse gas emissions.  Their report, entitled, Livestock's Long Shadow, affected myself and many other individuals.  It made us realize the impact our food choices have on the environment and our health.
I have to admit that my world was a little bit shaken up after reading news articles about the so-called CowGate following a paper presentation by Dr. Mitloehner.  Dr. Mitloehner criticized Livestock's Long Shadow because it performed a Life Cycle Assessment of the environmental impact of livestock production.  However, in it's comparison to other industries, the UN didn't consider the other aspects of other industries.  That's a good point.  Perhaps, the UN miscalculated the overall 
percentage of global GHG attributable to livestock (although others as prominant as former World Bank scientists have found that the UN way UNDERESTIMATED the impact of livestock--and that livestock is responsible for around half of all GHG emissions.)
As Livestock's Long Shadow is central to my work, I dropped everything to look into the validity of Dr. Mitloehner's claims.
However, Dr. Mitloehner then concluded that reducing consumption of meat and dairy wouldn't reduce GHG emissions.  Obviously, Dr. Mitloehner's "findings" are more suspect than the report his is criticizing.
 While Dr. Mitloehner was correct in pointing out the UN FOA unfairly performed a LCA of livestock and not other industries, the press release concerning the ACS presentation and the media coverage has drawn conclusions that are erroneous and very dangerous.
After looking into the matter, I found that Dr. Mitlohner's article arose out of a 2007 beef industry survey.  The survery  found that consumers were actually switching away from meat because of GHG emissions. Well, you can imagine how this scared the crap out of the livestock industry.
In response, the National Beef Cattlemen's Association started a PR campaign in which down home farmers told the story of how farmer's are the true conservationists.  Oh yeah and they bought themselves some "experts" too. 
- Dr. Mitloehner’s ACS press release about “Clearing      the Air” was misleading and flawed
 
- It failed to consider
 
-  the land use implications of livestock        production
 
- that the US is the biggest importer of grass fed        beef, and is the leading cause of deforestation in Brazil and Argentina,        as well as GHG emissions problem in Australia        and New Zealand.
 
- It was inconsistent with       previous presentation on same paper which concluded
 
- Livestock is a “dominant        contributor” in developing countries
 
- The significant change that affects carbon levels        in the United States        is the conversion of agricultural lands to development, which reduces        land available for carbon sequestration
 
- History of       Cowgate, “Clearing the Air”
 
- Prior to 2005, no beef       industry surveys showed consumer concern
 
- In 2007, following the       release of Livestock’s Long Shadow (LLS), the beef industry group National       Cattlemen’s Beef Association (NCBA) was shook up by reports that       consumers were willing to consume less beef due to concerns about GHG       emissions
 
- In 2008, the NBCA made a       concerted effort to counter bad publicity with internet campaigns, and       decided to commission research that would counter the negative publicity
 
- In Jan 2009, the NCBA       released a fact sheet to counter the findings of LLS
 
- In May 2009, NBCA VP of       Issues Management, Rick McCarty told the beef industry that newly       commissioned research out of UC Davis would counteract the bad publicity       they had received following LLS
 
- October 2009, UC Davis       researcher Dr. Mitloehner releases his study, “Clearing the Air” which       criticizes LLS. The study was funded by the NBCA (Check-off funds).
 
- Nov 2009- Dr. Mitloehner  writes an article for California       Cattlemen Magazine that closely tracks the fact sheet produced by       the NBCA
 
- Nov. 2009 - As a result of       the attacks on the relevance of LLS to the USA, beef industry lobbyists       were able to successfully exempt themselves from key aspects of mandatory       GHG emissions disclosure.  The beef       lobby also ensured that they would not be subject to carbons tax for       their part in GHG emissions.
 
- March 2010- Dr.       Mitloehner  presents “Clearing the       Air” with misleading sound bites that criticize LLS.  He asserts without support that       reducing meat consumption will not reduce GHG emissions.
 
- Hundreds of media outlets       and blogs cover the report, dubbing the paper Cowgate, and stating that       Dr. Mitloehner work entirely discredits LLS, even though “Clearing the       Air” made no such conclusions.
 
- FUNDING, BIAS ISSUES
 
- Dr. Mitloehner and UC Davis have received millions       in funding from industry groups.
 
- Dr. Mitloehner received        direct funding in the amount of $730,000 in recent years from livestock        industry groups.  
 
- UC Davis’ agriculture        emissions program is reliant upon industry funding as well, as his        coauthor of many of his studies has also received $420,000 from industry        groups to fund air emissions research.
 
- He failed to disclose many        of the grants on his UC Davis grant disclosure page, including grants        from California Dairy Farmers, California Cattlemen Assoc. &        California Feeder Council and Eli Lilly-Elanco.
 
- Dr. Mitloehner also        receives millions of dollars in funding from the USDA, which represents        the interests of the beef and dairy industry.
 
- Dr. Mitloehner’s industry        funded research has also been beneficial in the past.  He         received a $500,000 from Ag Air Research Council, which is funded        by the National Pork Producers Council, National Milk Producers        Federation, National Chicken Council, the National Turkey Federation,        United Egg Producers, and Tyson Foods.
 
- The study resulted in a        finding that dairy cows released half the emissions as was previously        thought.
 
- Dr. Mitloehner’s Press Release is Self-Serving
 
- Dr. Mitloehner asserted        that reducing meat and dairy consumption won’t reduce GHG        emissions.  However, his research        is funded by the beef and dairy industries.
 
- Dr. Mitloehner’s only        solution for reducing GHG emissions is increased funding of the type of        research that he is performing.