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RomeoStevens comments on Ketogenic Soylent - Less Wrong Discussion
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Gut bacteria is the best hypothesis.
s/the best/currently fashionable/
Yes, I know about the fecal transplant papers.
are there others that are actually plausible?
What do you mean, plausible?
Gut flora is not much of a hypothesis to start with -- it just says "we think the composition of gut flora affects obesity but we have no clue about the mechanism". It's a black box with gut flora involved.
For a trivial example, we can substitute "leptin regulation" for "gut flora" and get a similar hypothesis -- also black-box and also quite plausible.
Fecal transplants provide a way of testing the gut flora hypothesis.
Exactly what is the hypothesis that you're testing? That gut flora affect metabolism and, as a consequence, a variety of things including weight? Sure, I agree. I suspect most everyone will agree.
But that's a far cry from being the "best hypothesis" as to why some people easily gain weight and some do not.
There are known pathologies of gut bacteria that affect lipid metabolism. That less extreme and thus hard to detect variants exist seems a reasonable claim.
Yes, see my post above. Basically the idea is that everyone has an internal feedback system which sends a signal telling you whether or not to eat more food. Just like eyesight, for the most part this system worked reasonably well in the ancestral environment. However the system isn't perfect, particularly when exposed to a modern diet. (By analogy, a lot of people have trouble reading without glasses.) John Walker refers to this system as a "food clock."
If your internal food clock does not work correctly, and you don't exercise conscious control over what you eat, then your weight will tend to drift upwards over time.
I find this hypothesis to be very plausible and consistent with the available evidence.
As far as the gut bacteria hypothesis goes, I am skeptical because if it were correct then obesity could be easily combatted with so-called "nutrtionism," i.e. by adding or subtracting a few key components from the diet but otherwise eating ad libitum. As of yet, nobody has found a nutritionistic solution to obesity.
This is my (relatively uneducated) guess as well. I think that foods which didn't exist in our ancestral environment plus antibiotics have done nasty things to many people's gut microbiome and this plays a big part in the obesity epidemic.