Paul Jaminet, Ph.D. and Shou-Ching Shih Jaminet, Ph.D.
Part 1 - Summary Ketogenic Diets, I: Ways to Make a Diet Ketogenic | Perfect Health Diet
So we have three ways to make the diet ketogenic:
1) Make Wilder’s “ketogenic ratio” high by eating a lot of fat, very few carbs, and not too much protein.
2) Supplement with the ketogenic amino acids lysine and leucine.
3) Supplement with coconut oil or another source of short-chain fats.
If we do (2) or (3), then the diet can be ketogenic even if it has a fair number of carbs.
So now we have an arsenal of ways to generate ketones. We have to look at diseases and diet risks to figure out which way of making the diet ketogenic is optimal.
References Owen OE et al. Brain metabolism during fasting. J Clin Invest. 1967 Oct;46(10):1589-95. http://pmid.us/6061736.
Part 2 - Summary Ketogenic Diets 2: Preventing Muscle and Bone Loss on Ketogenic Diets | Perfect Health Diet
I believe the extreme limits on carb and protein intake in conventional clinical ketogenic diets are responsible for their growth stunting, muscle destroying, fattening effects.
In order to supply sufficient protein and carbs while maintaining ketosis, it is necessary to provide ketogenic short-chain fats and amino acids.
Clinical testing of such supplemented diets has so far produced encouraging results. Providing supplemental amino acids to epileptic children on ketogenic diets improved their health and allowed them to maintain ketosis with higher protein intake. Seizure frequency was reduced even as side effects diminished.
Personally, I wouldn’t attempt a long-term ketogenic diet without the aid of coconut oil (or MCTs), lysine, and the branched chain amino acids.
For the NBIA/PKAN kids, it seems that the amino acid supplements should be some mix of lysine, leucine, isoleucine, and valine, with the isoleucine and valine included solely to reduce leucine toxicity. The optimal amount of isoleucine and valine should be smaller than is found in branched-chain amino acid supplements, since leucine by itself may help prevent iron accumulation and increase ketosis. Also, one rat study  indicates that isoleucine alone, excluding valine, might be enough to relieve leucine toxicity. Excluding valine would increase the ketogenicity of the supplement mix.
I think the NBIA/PKAN kids will need to experiment with primarily lysine and leucine, and secondarily isoleucine and BCAA supplements, to see what mix works best for them.
References Groesbeck DK et al. Long-term use of the ketogenic diet in the treatment of epilepsy. Dev Med Child Neurol. 2006 Dec;48(12):978-81. http://pmid.us/17109786. Hat tip CarbSane.
 Ribeiro LC et al. Ketogenic diet-fed rats have increased fat mass and phosphoenolpyruvate carboxykinase activity. Mol Nutr Food Res. 2008 Nov;52(11):1365-71. http://pmid.us/18655006. Hat tip CarbSane.
 Evangeliou A et al. Branched chain amino acids as adjunctive therapy to ketogenic diet in epilepsy: pilot study and hypothesis. J Child Neurol. 2009 Oct;24(10):1268-72. http://pmid.us/19687389. Hat tip Nigel Kinbrum.
 Tsubuku S et al. Thirteen-week oral toxicity study of branched-chain amino acids in rats. Int J Toxicol. 2004 Mar-Apr;23(2):119-26. http://pmid.us/15204732.
 Yudkoff M et al. Brain amino acid requirements and toxicity: the example of leucine. J Nutr. 2005 Jun;135(6 Suppl):1531S-8S. http://pmid.us/15930465.
 Mawatari K et al. Prolonged oral treatment with an essential amino acid L-leucine does not affect female reproductive function and embryo-fetal development in rats. Food Chem Toxicol. 2004 Sep;42(9):1505-11. http://pmid.us/15234081.
 Tsubuku S et al. Thirteen-week oral toxicity study of L-lysine hydrochloride in rats. Int J Toxicol. 2004 Mar-Apr;23(2):113-8. http://pmid.us/15204731.
Ketogenic Diets | Perfect Health Diet
by husband-and-wife team from the Perfect Health Diet blog:
Paul Jaminet, Ph.D. Paul was an astrophysicist at the Harvard-Smithsonian Center for Astrophysics, became a software entrepreneur during the Internet boom, and now provides strategic advice to entrepreneurial companies while pursuing research in economics (see pauljaminet.com for more information). Paul’s experience overcoming a chronic illness has been key to our views of aging and disease. Paul can be reached by email to firstname.lastname@example.org.
Shou-Ching Shih Jaminet, Ph.D. Shou-Ching is a molecular biologist and cancer researcher at Beth Israel Deaconess Medical Center and Harvard Medical School, and Director of BIDMC’s Multi-Gene Transcriptional Profiling Core. Shou-Ching was born in Korea to Chinese parents, grew up in Korea, attended college at National Taiwan University in Taipei, and graduate school at University of Newcastle in Australia, before coming to the US to work at Sloan-Kettering Cancer Center, Children’s Hospital Boston, and Beth Israel Deaconess and Harvard Medical School. Her publications may be found by searching Pubmed for “Shih SC.”