As Promised, here is my length reply. It's reference light while I explain the immune system, and reference heavy when I discuss vaccination.
I'm going to go in a specific order in my response. First, I'm
going to briefly outline my credentials, because I think you
should know who is saying what. Next, I'll briefly outline a
simplified version of the immune system. Then I will
specifically address your concern that the immune system is
weakened by vaccines. Last, I will outline why I care enough to
spend time writing this out.
This is going to be long. It may take multiple posts.
For the sake of readability, I will mostly cite review articles.
These are more designed for people outside the immediate field
(usually), and also tend to synthesize evidence from across the
field/discipline.
My credentials: I studied microbiology for four years to earn my bachelors of
science. During this time I took multiple courses on immunology,
pathology, and infectious disease.
During the final two years of my study, I researched and tested a
vaccine that is currently in clinial trials (I did not design the
vaccine, that was done for ~20 years before I go there).
I am currently in graduate school, and I am approaching the end
of my second year. In short, I know my shit, and I am very
familliar with vaccination and the science surrounding it.
A brief summary of the immune system as it relates to
vaccinations: (please note, I am citing a textbook for this:
Cellular and Molecular Immunology. I am not going to address
anything controversial here, but rather what's established.)
There are two branches of the immune system which work together
to tackle pathogens (pathogens are organisms which make us sick:
bacteria, viruses, and fungi) and cancers.
The first branch is the innate immunity. The innate immunity is
the workhorse of the bodies immune system, and does most of the
dirty work of slaughtering pathogens.
The innate immunity is less directly important to vaccines
because it has no "memory." It works by attacking a specific set
of patterns found on pathogens.
You can think of the innate immunity like a mindless soldier who
only recognizes tank treads, guns, and the wings of a plane. If
they see tank treads, the cells of the innate immunity say
"that's a fucking tank. I am going to kill this motherfuckering
tank," if they see a gun, they go "that's a soldier, I am going
to kill this motherfucking soldier," or if they see a wing, they
go "that's a plane wing, im going to kill this motherfucking
airplane."
This approach has a flaw: if the enemy has no tank treads, guns,
or wings, then the innate immunity ignores it. The innate
immunity never changes the way it does things, and it never
remembers anything (without the help of the adaptive immunity,
which we'll address next).
In order to compensate for this, "higher" organisms (sharks
onward if I remember correctly) have a second defense.
This second defense is called the adaptive immunity. The
adaptive immunity is what we work with when we use a vaccine.
The adaptive immunity is more complex. In the innate immunity,
cells mostly recognize the exact same things (the previously
mentioned "tank treads", etc). Each cell will respond the same
way to the same signal.
Each adaptive immune cell looks for a single protein, using its
own unique receptor. The single protein it looks for is called
an antigen. The receptor name varies based on what kind of cell
we're talking about. Since we're taking a VERY high level
overview, we will completely ignore the different types of cells
NOTE: Those interested in further reading should look up B cells,
memory cells, CD8 and CD 4 + t cells, tregs, th1, th2, th 17 and
NK cells. For further reading on the innate immunity, look up
mast cells, macrophages, neutrophils (PMNs), eosinophils and
neutrophils.
This protein is unique, and is made by a very complicated genetic
processing mechanism. The adaptive immunity generates around ten
million different protein receptors (this is controversial: some
project that this number is actually in the billions).
I'm going to explain what I said above again, because it is
complicated. Every adaptive immune cell has a unique receptor.
This unique receptor responds to a unique pattern on a molecule,
which we call an antigen. There are around 10 million different
patterns your body's adaptive immune cells recognize.
As opposed to the dumb soldier from the innate system, think of
adaptive immune cells as romantics looking for a soul mate. They
aren't interested in anyone but "the one." They spend their
whole lives wandering, searching, endlessly drifting with arms
wide open. They are looking for their antigen, their soul mate.
This is a simplification, but it works for our purposes.
So what happens when an adaptive immune cell finds its soul mate?
It gets turned on of course. It activates, it replicates, it
goes fucking wild. It screams to the heavens and to the earth,
and it secretes every fucking cytokine (cellular messages) it
can. It says "HEY LOOK YOU MOTHERFUCKERS, I FOUND MY SOUL MATE!!
YOU ALL SAID IT WOULD NEVER HAPPEN, BUT WHO'S LAUGHING NOW YOU
BITCHES!"
Some adaptive immune cells make antibodies, and others just
signal other cels, and still others make our own cells kill
themselves (to prevent viral spread, think of it like a scorched
earth policy).
When an antibody attaches, it's like a tag. The adaptive cell is
telling everyone "HEY LOOK IT'S MY SOUL MATE! HOW DO YOU LIKE ME
NOW AUNT MILDRED?! YOU NEVER FOUND ANYONE, YOU BARREN OLD HAG!"
When the other cells recognize the soul mate, they go...."dude,
that's not a fucking human, that's a fucking parasite/bacteria/
fungi/whatever." Then they kill it.
This is how the innate immunity can help out the adaptive: the
adaptive immune cell's antibody essentially acts like a tag that
says "I'm a tank, please kill me."
Now that we understand how the adaptive immune system works in
general, let's talk about "memory."
When the adaptive cell sees its soulmate, it rapidly divides and
makes clones. These clones all have the same soul mate. They
make the same signals and antibodies.
When the body is finally done killing the soul mate (the
pathogen), these cells are in anguish. The soul mate is gone.
There's nothing left to live for. Time to die! They all kill
themselves.
But not all of them.
Some of them remain hopeful. They won't give in. They will wait
for years and years for the soul mate to come back. And if they
do, they'll expand again! We call those remaining cells "memory
cells" and they give the immune system its "memory." They'll
hang out for 20-30 years, just waiting.
Now here's the important part: the first time an adaptive immune
cell sees its soul mate, it takes around 3 weeks to fully
respond. It's cautious: it doesn't want to get married then look
like a fool.
However, when the soul mate comes back, the adaptive cell throws
caution to the wind. It remembers. It knows that THAT's its
soulmate. And so it takes only a few days to fully respond.
That's how a vaccine works. We figure out what proteins are the
best "soulmates" or antigens on a pathogen. We isolate that
protein. If it's a toxin, we inactivate it. Then we inject it
into you.
Remember how many unique adaptive cell receptors there were?
It's around 10 million-a few billion depending on who you ask.
The point is, it's a fucking lot. Most of them are circulating
around, looking for a soul mate at any given moment.
At least a few of them will be activated by any given protein.
So when we inject a vaccine, we just determine which ones get
activated, because we gave them their soul mate.
Nothing happens to the cells that don't get activated. They just
keep looking for a soul mate.
The cells that do activate will proliferate and make memory
cells. Those cells will respond when there is a real threat,
because they'll remember their soul mates.
The claim that this weakens the immune system makes no
theoretical sense. I will turn to actual experiments testing
this later, but know that it doesn't make sense to begin with
theoretically.
We haven't removed anything, we've simply given one specific cell
an activation code. That cell can only help.
For confirmation see Abbas' Cellular and Molecular Immunology, or
the following reviews
Pathogen Recognition and Innate Immunity http://www.sciencedirect.com/science/article/pii/S009286740600190
5 http://www.sciencedirect.com/science/article/pii/S014067360004904