These health posts never turn out good. It always ends up with hackers/geeks arguing how to eat, lose weight, be healthy, etc and so forth. No one agrees. There is too much arguing about what is right, wrong, can't be done, you have to eat this... as if nothing is safe to eat now.

Anyway, I don't want to argue or comment that certain foods are evil, carbs are bad and should be avoided, or about anything what Gary Taubes said or published. Everyone is different and different things work for different people. That said, I would like to link a very good post on Reddit with a list of studies that I think people should peruse and possibly reference for the future.

http://www.reddit.com/r/Fitness/comments/nv8ip/do_you_have_a...

Some highlights that might be of interest and relevance to the OP and comments:

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Calories

Detailed explanation of how calorie counts are derived, analysis of whether low-carb/high-protein diets can provide a metabolic advantage.

http://www.ncbi.nlm.nih.gov/pubmed/8561057

"We conclude that a calorie is a calorie."

Similar weight loss with low- or high- carbohydrate diets.

http://www.ncbi.nlm.nih.gov/pubmed/1734671

"The results of this study showed that it was energy intake, not nutrient composition, that determined weight loss in response to low-energy diets over a short time period."

Energy intake required to maintain body weight is not affected by wide variation in diet composition.

http://www.ncbi.nlm.nih.gov/pubmed/1734671

"Even with extreme changes in the fat-carbohydrate ratio (fat energy varied from 0% to 70% of total intake), there was no detectable evidence of significant variation in energy need as a function of percentage fat intake."

Fat loss depends on energy deficit only, independently of the method for weight loss.

http://www.ncbi.nlm.nih.gov/pubmed/18025815

"This study showed that independently of the method for weight loss, the negative energy balance alone is responsible for weight reduction."

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Carb Timing:

Greater Weight Loss and Hormonal Changes After 6 Months Diet With Carbohydrates Eaten Mostly at Dinner

http://www.nature.com/oby/journal/vaop/ncurrent/full/oby2011...

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Fructose

The bitter truth about fructose alarmism

http://www.alanaragonblog.com/2010/01/29/the-bitter-truth-ab...

Debunking Lustig and the fear of fructose. Health implications of fructose consumption: A review of recent data. No relevant data accounting for a direct link of moderate fructose and health risk markers.

http://www.ncbi.nlm.nih.gov/pubmed/21050460

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Glycemic Index

There are large problems with isolating foods cased on the glycemic index/load. First, food is rarely eaten in an isolated way. Fat, protein, fiber count, etc. will all slow down digestion. Second, there is evidence to support that it doesn't even make a difference in weight or blood markers.

http://www.ncbi.nlm.nih.gov/pubmed/17413101

http://www.ncbi.nlm.nih.gov/pubmed/20504977

http://www.ncbi.nlm.nih.gov/pubmed/16629877

http://www.ncbi.nlm.nih.gov/pubmed/17923862

http://www.ncbi.nlm.nih.gov/pubmed/17823436

http://www.ncbi.nlm.nih.gov/pubmed/16177201

http://www.ncbi.nlm.nih.gov/pubmed/12458971

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Vegetarians

Vegetarians have a reduced skeletal muscle carnitine transport capacity. Vegetarians have reduced muscle carnitine transport capacity . Carnitine helps fat burning and build bone.

http://www.ncbi.nlm.nih.gov/pubmed/21753065

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(I hope I did this right so it's formatted in a legible way.)

Edit: formatting and added a couple more links.