First, please note that I am *not* one of the researchers that wrote this paper in 2007 (link a few paragraphs down), nor am I any of their references. I am just a geek who wants to lose weight, and will gather any and all information on the topic I'm currently interested in. I also want to help my friends and fellow weight-loss-fanatics realize what is truth, what is fantasy, and what is just plain BS. Feel free to skip to the bottom for the TL;DR section... I admit I can be long-winded

Second, it is very important to understand that there is a *ton* of misinformation out there. The majority of what you (and I) read, have been told, or even believe ourselves about weight loss, the so-called "starvation mode", and in general how our bodies take in and use energy is based on what some people call "bro science", essentially a regurgitation of things that *seem* correct, or have worked for someone else, or have otherwise been blessed as gospel by the masses. Even very credible-sounding and charismatic individuals will "train" the general public on how things should be done... and most of the time they're at least partially (and very plainly) incorrect. Often this misinformation started with a seed of truth and grew organically into the inaccurate, monstrous "belief" that people blindly accept, then wonder why they are having trouble meeting their fitness goals.
My fitness goals are probably very similar to yours. I want to lose fat, gain muscle, and stay that way for the rest of my life. My other goal, as a geek, is to sift through all the nonsense and over-hyped "truths" that we all accept. I want to find the science behind the myths. I want to know what shred of truth started them, if any, and focus on what has been discovered and proven through actual scientific method, not just spouted by the most popular trainer at the gym.
A tiny bit of background on me: I'm 33 years old, 6'6" tall, currently somewhere between 294 and 302 lbs (depending on which scale you ask) and by the most unreliable of methods currently at about 30.5" BF. That puts my BMI solidly in the obese range. Knowing that BMI is really not very accurate at taller (and shorter) than average heights, I don't calculate that number. Since the age of 20, I've varied from 285 to 215 to 290 to 270 to 350 and now to 300. ish. I've always been relatively active, as one of my main pastimes is outdoor and involves a decent amount of physical activity. I'm no marathon runner, nor have I ever been, but I don't get fat purely from sitting on my butt. It's safe to say that I have struggled with my weight my entire adult life, and I'm finally starting to understand why. For the same amount of time I have also worked as a systems architect. That means computers, and no I don't mean the ones that sit on your desks right now. Big ones, whole groups of them, and entire networks of hundreds (even thousands) of individual components that I need to make work together in a meaningful fashion. To the average person it's a mostly boring job, and it's certainly not related to the same fields of science as weight loss... but it has taught me how to do things scientifically and it has taught me how to recognize actual research, and (usually) decipher the resulting literature. Not tooting my own horn, just hoping to give you an idea of where I'm coming from.
So, I started reading everything I could find. I looked at all of the "bro science" (btw, broscience.com is worth a look, even if unscientific about many things) and I've looked at every bit of real science I can get my hands on. There have been many, many, many studies done for the past century or so on obesity. Recently, as in the past 30ish years, it has become a very hot topic. The past 10-15 years have yielded the most interesting studies. The one I picked to share with the boards is this one:
http://www.nature.com/ijo/journal/v31/n2/full/0803523a.html
The reason I picked it is because not only does it have some very good information of its own, but the works they refer to are some of the best I've been able to find. Not only that, but the link above contains links to most of those resources. PLEASE read this stuff for yourself. Hell, read whatever you can get your hands (or mouse pointer, as it were) on. Just don't believe everything you read, *especially* if there is a sales pitch attached to it.
Not all people selling weight loss mechanisms, fad diets, and supplements are crooks. I'm sure some of them realize what they're selling is snake oil, and some of them know that what they're selling is perfectly valid and useful. There's also the overwhelming majority in the middle that are innocently selling stuff they *think* is good but really just makes them money... at the same time costing us money, time, and our health.
TL;DR:
The most important things we all need to take away from the research in the linked article are these:
1) every human body is different. It is 100% impossible for an online calculator, or even an in-person doctor or trainer to give you the exact number of calories you should be taking in. Unless you submit to a long-term scientific trial, these numbers will be very inaccurate and may cause you much pain and anguish on your journey.
2) "starvation mode" is NOT A REAL THING, at least not the way people here refer to it. Adaptive thermogenesis *is* real, but it's not something that turns on or off from day to day, and it's not triggered in the same way or at the same point for everyone. Some people don't experience it much at all. For those that do, it doesn't just turn itself off when you start eating more. It's an adaptation that take a long time to happen and a long time to wear off.
3) Going below TDEE-20% is not bad. At least not on the surface. This is because the TDEE you get from any of the methods available is *almost definitely* wrong for you. The only group they really work for is the never-been-obese, never-been-overly-sedentary group. Even then they're not perfect. If you've ever been obese, or you have bad genes, or you've ever led a sedentary lifestyle, or you are just lucky... TDEE calculators are almost definitely not going to work well for you.
4) 1 Calorie is *not* the same for everyone. It does not take the same amount of energy intake for every person to do the same amount of work. Adaptive thermogenesis (or what most people think is "starvation mode") accounts for a much more or less efficient use of consumed Calories than what is calculated by standard methods for people that are obese or have been obese versus people who never have been obese. Genetics play a role. Hormone balance plays a role. a *ton* of things play a role... again, standardized calculators are never going to be able to account for the variance in each individual.
5) This is the most important. All of the research points to one overwhelming fact: The body adjusts to whatever you throw at it. If you are obese, your body adjust to being obese. If you lose weight, your body adjusts. These adjustments are in some respects very fast, and in some respects *very* slow. The studies referenced above show that even after 18 months of maintaining a significantly lower weight, your body actually uses less energy on a daily basis, for a given amount of activity. There are ways to combat these effects but for most people, the chance of ever having a "normal" metabolism is virtually nil.
The only scientifically proven way to have success and *keep* the results of that success is to be smart about it and stop relying on magical numbers systems. I don't mean to stop counting calories, that is important... but you have to adjust your intake for yourself. Do not be afraid to eat less than "TDEE-20%" one in a while because you think you're suddenly going to trigger this mythical starvation mode. It won't happen. It just doesn't work that way, no matter what the bros tell you. Two basic things contribute to long term reductions in Calorie burning efficiency via adaptive thermogenesis: reduction in intake and reduction in body weight. You can theoretically reduce the long-term effects by keeping your deficit small... but the conditioning benefits of losing the weight more quickly outweigh the detriments of a larger deficit... assuming you are active. The best way to combat adaptive thermogenesis is to exercise. Strength training, specifically, has the biggest impact. Increasing lean body mass is the best way to offset these effects. Adaptive thermogenesis *is* long-term. As such, you cannot escape it by suddenly eating more.
Last, but definitely not least, for people like me who have been (and possibly currently are) obese: when we finally do manage to lose the weight, we have to realize that our metabolism has been affected. We cannot resume our old eating habits, we can't even eat "normally". We have to *slowly* add calories back into our diets to find the point our personal metabolism allows us to reach maintenance. No online calculator will do this for you, you have to do it for yourself.
Hopefully I didn't make this post too long for people to read. I'll likely copy it to my blog so it sticks around longer. I want people to read it. I want you guys to succeed just like I want to succeed myself. Hopefully this helps someone. And no, I'm not selling anything