How do you think people get bigger exactly? A bigger muscle is a stronger muscle - what do you think your body is adapting to when it adds muscle as a result of exercise? Why is resistance at a fairly high percentage of your maximal effort necessary for hypertrophy? I mean, you don't get too big walking around and bodyweight exercises seem to cap out after a while.
Things that make you go hmmm. I'm not saying a bigger person will outlift or be stronger than a smaller person (physics/leverage/neural components weigh in on this), but I'm saying that when you get bigger you will have gotten stronger. No one added significant muscle that didn't add weight to the bar or just do a ton more work. You are stressing the muscular system here and the adaptation of hypertrophy is a method the body uses to cope and improve to be able to better tolerate the stress.
I would hope it's hitting you like a bolt of lightning now and that you aren't lost. If you are lost reread the above.
Now what's necessary for hypertrophy vs. just pure strength. Well, obviously there is some type of intensity (% of 1 rep max or weight on the bar) involved in both. People say that 8-12 reps is for hypertrophy but 1-3 reps is for strength, why? I mean, intensity (%1RM) is linearly related to potential for microtrauma right? Why do you need to do more reps and why isn't a heavy weight better. Well, a heavy weight is better. The problem is, is that you can't do a whole lot of work with it and get a reasonable amount of microtrauma for hypertrophy - hence, it mainly stresses the neural components more than the muscular.
So in fact, a rep is a rep, it's finding that happy medium between intensity (%1RM) and the number of reps performed. Hey wait - why do we do sets if we can just do 25 reps with some weight and be done. Well, because the weight you can do for 25 reps has to be low intensity to get 25 back to back (hence, less microtrauma). So we cluster reps into sets to keep the intensity high and still get a given number of reps done. This is why you can break the rule with 3 rep sets being for strength only if you lower the intensity (%1rm) to where you can do 8-10 sets and get 24-30 reps. You'd probably get more total workload too (reps X sets X weight used) as the time density is lower with additional clustering/rest. There are few absolutes. Microtrauma is also why static holds with very heavy weight tend to not work so well, you need to move a weight over a range of motion and leverages to get the microtrauma.
Also, let's not forget the neural components that have nothing to do with hypertrophy . Hypertrophy over a period is strategically induced microtrauma through progressive loads (i.e. increased workload by raising weight/more work with same weight/combination). Enhanced neural capability leverages your ability to do this and the resulting hypertrophy gains. Better neural = better potential hypertrophy. Don't believe me, think about the much loved "newbie gains" where everything works. What is this phenomenon - muscle is muscle? Well the main driver is rapidly developing neural adaptation and that drives weight on the bar which drives hypertrophy. Doh.
So now we know hypertrophy and that neural adaptation is a good thing not some unrelated oddball of nature to be shunned. I'm not saying you need to do a pure powerlifting or peak strength routine and focus on the extreme end of max singles and doubles either - merely that some neural focus is quite helpful. Well what's the best way to get a lot of hypertrophy for those looking to add muscle mass? Well, the body is a system and adapts best as a system. This is what makes squats, deads, rows, cleans, presses, and snatches very effective. You are using a large portion of your body's musculature to move a heavy weight (think intensity) through a fundamental range of motion. This is full body microtrauma stressing a large portion of the body's musculature all at once. So adding weight to these exercises should net hypertrophy over the entire body. And we all know how hard it is to grow a muscle in isolation and that the body tends to stay within reasonable parameters of balance (otherwise the curl boys would all have huge arms - the training is there, the body just doesn't work like that).
So what's the deal with the 5x5 stuff? Well, first tends to focus on the most effective lifts or the ones with the highest potential for hypertrophy. We are not concerned with balancing the outer head of the triceps here, this is for pure muscle, triceps are included but nothing in isolation is being heavily focused on. So what's with doing the big lifts that often and not splitting it up day by day? Two things:
1) How do you train for any sport or motion? Do it a lot, as much as possible until it's 2nd nature. Why? The nervous system and your body adapt to performing the motion and become much more efficient and better at it (doesn't that sound like weight on the bar - if you didn't get it reread it). Well why not do it every day then? The intensity that you are dealing with is too high and beats on your body's systems too much. Just the nature of the beast in weight training and why powerlifters don't just do max squats, deads, and benches every workout - it's the most direct way to train but it can't be done for long. And in the weight room, just like in life, it is very hard to get very good at a lot of things all at once or when changing those things all the time. You need to focus on a few things and hammer them to really get good at them.
2) Recovery is fairly fast, once your body gets used to training your muscles repair themselves fairly quickly generally within 2-3 days. Also, you need not be 100% recovered to train again. When you tan do you tan real hard one day and then wait inside until you are pasty white again? No, you have tolerable periodic exposure and this is how your body adapts. So more frequency is desirable up to a point but 1x per week tends to suck as a default. In addition, remember when we proxied microtrauma with workload (reps X sets X intensity or weight used)? Well do you think you could handle doing 15 sets of squats in 1 day? Think back to the pasty white skin tanning - is it better to get fried for hours and then sit inside whitening up or is it better to get some tolerable amount more frequently. But still understand that the total amount of microtrauma from the squat can be much higher if spread out over 3 days during the week - i.e. you can tan in three 30 minute sessions without burning but a single 90 minute session might toast you (so in 1 session a week maybe they can only get 60 minutes - hence 90 minutes is more). Also, think about volume and intensity (%1RM). What's a good balance to get enough microtrauma - well think back to workload. You could do one 25 rep set, weight too light probably (this is why there are intensity based cutoffs for workload calcs and walking doesn't make you big, intensity is too low), what about 3 sets of 8 - sure that would work that's fine, enough weight and work, well what about 5x5 - that works too, and with less density it's probably the way to get a good amount of workload with some pretty good weight (intensity).
So that's the jist and how strength and hypertrophy are related. That's also the jist on how why the 5x5 or any similar setup is structured that way and designed to work. Oh yeah, the other essential ingredient is food. Caloric excess will move the scale. If you aren't gaining weight, you aren't eating enough. You cannot add another wing to your house with only enough material to make small repairs on the existing structure.
And why the different templates and structures - just different ways of going about getting the body to acclimate. If you can acclimate fast enough to add weight to your best set of 5 three times a week - do it. If you can only add weight 1x per week that will work too and then you wind up with undulating loads during the week. When you can't add weight weekly, well then it's done periodically and your undulations move beyond purely weekly into larger blocks and you get periodization. All different ways to skin a cat, go with the fastest you can. And variables change and are altered. Different ways to get stronger - getting your squat from 200x5 to 220x5 can be handled in a lot of ways. Maybe it's 4 5lbs increases, one a week. Maybe it's taking your best 5 sets of 5 with 180lbs and pushing it up to 200. Maybe a combination or working on a weak link.
I hope this has helped someone. But that's the whole deal. Not too hard is it. And as to the original topic, programming is just about efficiently organizing work. To get as big as possible in the shortest period of time, a split with a ton of different exercises done 1x per week and lot of isolation is probably a very bad choice (and if you read above, you know why). But training the whole body or a big portion of the body in a session will let you get enough frequency and let you really focus on the lifts that can make that mass pile on as fast as possible. Then again, if you don't really want to add muscle and just want to work on your conditioning and aesthetics and balance - well, if you are pounding the compounds hard with that kind of frequency, it's hard to fit this work in. Figure out what you need to do and plan for it. It's that simple. You don't need to do everything at once and for most people they should focus on aesthetics on an as needed basis rather than trying to preempt all possible future problems that my arrise while hobbling their high priority mass gaining phase.
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MWAAHAHAHA....owie 
And just when I thought I knew everything. Dangit. 
hehehehe. I can't remember what I was looking for when I stumbled across this msg board, but I sure am glad I found it!
