Humans, the immune system and vaccination - The science behind it.

[sapdiggity]

After finding out about the AVN this morning, I was filled with rage. But it is starting to occur to me that alot of your arguments are about emotional concern, which in fact even makes many posts quite aggressive. I understand that many of you have children that have been adversely affected by vaccinations and are therefore concerned, but attacking vaccinations is not the answer. Education is. What I am to write is simply what I understand of science from my years studying as a Medical Microbiology and Immunology student - I also have another major in Pharmacology. So, my information will not be backed up with references but I would like to assume I know what I am talking about.

It seems that few are taking the time to actually understand how vaccinations work, and why we are seeing the array of effects that we are.

In short, we are supposed to.

6.5 billion people on the planet, with fascinating levels of genetic variation between us.. how can anyone expect that ANYTHING in the world could have a standardised effect on all of us?

Let us begin with the concept of vaccination:

Our immune system acts a mini-scale system of evolution. We are constantly producing antibodies and immune cells of different constituents and properties in an attempt to battle ANY given foreign object that enters our body. Of course, like evolution - the cells or antibodies that were found to have a positive effect on our immune state are stored and memorised for future use. For example, let's say that we get infected by a bacteria..

- Our first soldiers of the ADAPTIVE immune response (not referring to innate, as it has nothing to do with vaccinations) are IgM antibodies. Imagine these as a set of keys poking out of a giant keyring in all different directions - these keys are randomly made, but who knows? Maybe one will happen to fit into the keyhole (in this case, the offending bacterial antigens). The antibody interacts with the bacteria and is found to be able to bind it.

- This step is important in the development of IgG antibodies - in this case, it is a single key made for a single keyhole. This key also has thousands of copies made of it, each of them slightly different than the last. Perhaps one of these new keys will have a BETTER fit for our keyhole than the existing one?

- Finally, we find the ideal key and begin to mass produce it to deal with the increasing level of locked doors popping up around our body (the metaphor is starting to stretch a little...). We clear the infection, and so long as the keyhole remains the same, we know exactly what key we need to use.

Viruses and parasites illicit different responses, but the concept is the same. Our body randomly develops tools to try and combat the illness, the more effective ones remaining with us.

Now, where does vaccination come in?

Well, in order for our immune system to generate this response, it had to first meet the offending pathogen. That is the purpose of vaccination - it directly introduces this pathogen to our systems to allow us to generate an immune response to the 'keyholes' (antigens or surface proteins) but usually without the nasty effect of the pathogen harming us while we are learning this response. No matter how hard we try, fact of the matter is, we are still introducing the pathogen directly into our systems via vaccination. So, essentially, vaccination is a 'quick step' - but it can also save your life.

You are probably thinking now, if vaccinations just help our bodies do what it does naturally, we don't technically need them! True... but there are a number of cases where there is no way our feeble bodies would be able to handle this intruder. 

Let us take Clostridium tetani, for example (otherwise known as Tetanus) - this bacteria likes to talk hold in deep wounds due to the creation of a suitable environment from the injury. This bacteria then, through its metabolic activity, produces toxins that act to lock down our muscles (starting with the most active ones, hence 'lockjaw'). Our immune system cannot possibly fight this bacteria - because it needs time. However, the toxins produced by C. tetani will most certainly kill you before your body has any idea what is going on. That is why tetanus shots are particularly important but something like the flu shot, for example, may not be.

Now, how do we make vaccinations? Good question. How to properly introduce a pathogen into our systems without it trying to harm us is still a hell of a question - especially since that is exactly what it was made to do. This is something that we have been working on for a VERY long time with many advancements in the field still to come. This is why it concerns me that people discredit vaccinations due to their lack of effectiveness in the first or second world war... dude... it was a long time ago. Before razors were invented, people like Julius Ceasar had to have hairs individually plucked from their face. Will you give medicine some time, please?

Without further a do, here are our current vaccination methods (from what I can recall off the top of my head, there are likely many more)

- Inactive pathogen - The pathogen has been inactivated somehow. This can occur through a variety of methods - genetic manipulation, for example, may remove some of the pathogen's essential virulence factors that allow it to infect us, therefore introducing its antigens into our body without it causing serious harm. But this may not work... why? The pathogen too, likes to evolve. It is possible that it could, through its own mechanisms, REVERSE our deletion of a crucial gene or virulence factor. Does this happen all the time? Of course not - but pathogens, like us, evolve. It would be arrogant of us to assume that in 1000 pathogens we deactivate, not 1 would possess the capability of fighting back.

- Pathogen belonging to another species - certain pathogens can share antigenic properties between strains that infect different types of hosts; humans and horses, for example. A pathogen that could infect a human may not be able to infect, say, a horse and vice versa - but key immunological antigens between the two are shared. This means that if we cross infected each other somehow, the infection would not take hold but we are still exposed to the antigen, allowing our body to react. Why might this not work? Pathogens adapt!! The HIV virus was originally only found in monkeys, what allowed it to infect humans was a random genetic mutation. This can also occur in a cross-species vaccination attempt. 

- Straight up antibodies - in cases like Tetanus shots, for example, we cannot rely on our immune system to generate the appropriate antibodies in time. To counteract the dangerous toxin of C. tetani, vaccinations contain large amounts of antibodies - introducing them to our system is the same as having large amounts of white blood cells already adapted and doing the same time. This is why Tetanus vaccinations must be repeated as levels of these antibodies in the blood gradually reduce over time. 

- Isolated antigens - in applicable cases, a vaccination can be completely harmless by simply adding the isolated antigens for our body to respond to - whole cells are not even introduced, and hence cannot cause infection. 

Again, I'm sure there are many more examples but the point remains - every method of vaccination is under development, new methods are even being developed as well. But the fact of the matter is - vaccinations are incredibly helpful, but not magic! They rely on an interaction between the vaccinations themselves and our immune system - and with 6.5 billion people in the world, each with genetic variation, how can anybody say the exact same thing will happen in all of us? There is not a single thing in the world, drug related or otherwise, that would have exactly the same effect on everybody.

Let us extrappolate this information and use it to address some current issues. One that particularly disturbs me is vaccination somehow causing Autism..

Let us look at the nature of Autism. It appears to affect developing children and its mechanism is largely unknown. However, given the nature of vaccinations, we could easily assume that if vaccinations could cause Autism, so could simply becoming ill. This is almost like an example of how religion came to be - without a logical explanation, people are likely to believe whatever fits the puzzle best (in their opinion). However, as much as you'd like to, blaming Autism on vaccination simply because the nature of Autism is not fully known is a foolish assumption to make. Until we can find a plausible link between the onset of Autism and ANYTHING (plausible link - something that could be recreated in a lab or at least have the concept proven), saying it is due to vaccinations is about as foolish as assuming it is due to breathing too much oxygen or not playing enough Xbox.

Now I am going to suggest something that NEEDS TO BE FURTHER DISCUSSED - many issues regarding vaccinations are whether or not they are necessary. I would like to firstly state - they ABSOLUTELY are. But that statement can't be taken literally by itself:

For example, let us look at flu shots. The general panic of the populace is what made flu shots so desirable and is why so many vaccinations started development - money! You can argue that desire for money is evil in such a case, but it is not. Without the reward of money, MANY medical advancements would not even be bothered with - it is a sad truth that money makes the world go round. Unfortunately this leads to a nasty side effect - where developers have lied about the extent of a drug's effectiveness or adverse effects because it would otherwise not be approved. This would be difficult to accomplish but the motive is there - it costs hundreds of millions, if not billions of dollars to develop a new drug or vaccination. It it turns out, after $10000000000 investment, the drug wouldn't work and you wouldn't make a penny... admit it, you might be tempted to tell a fib. But this is simply a statement of human nature and the nature of business, it does not strictly apply to the medical community and therefore should not be used as an example to demonise the medical community. 

But who actually NEEDS a flu shot? Only those who are in danger from being infected by the flu, of course! A healthy adult would never truly suffer from a flu infection - he/she would simply fight it off and never deal with that strain of virus again. Flu shots should be reserved for the elderly and immuno-compromised; what us healthy adults need to do is ASSIST this process! I was offered $1000 to participate in a flu shot trial - had I been in the country, of course I would have accepted. I would have been able to provide valuable information towards the development of an effective vaccination with the worst possible side effect being I get infected by the flu.

Now let us discuss what goes into the flu shot - I have no frikkin' clue. What I CAN tell you, however, is that no respectable member of medical development would put a dangerous chemical into a treatment unless it was vital; do you really think they would be able to pass that through all the peer reviews, critics, drug/vaccination approval boards... etc?? Anything that is added to a vaccination, other than the pathogen itself, would likely be to achieve one of the following:

- Reducing the likelihood of virulence activation
- Increase effectiveness of body's recognition of introduced pathogen
- Assisting host tolerance to the introduced substance

- Other beneficial examples that I cannot think of

Of course, addition of such chemicals may have an adverse effect, but it should not be stated that they were added simply to harm us because vaccinations are evil.

This is all I can think of as a starting point, from here I will happily answer any question anyone might have to the best of my ability.

I discovered this group with a large amount of anger, but now I feel like having a calm educated discussion instead. I hope you will all indulge me.

[punter]

“I understand that many of you have children that have been adversely

affected by vaccinations and are therefore concerned, but attacking vaccinations

is not the answer. Education is.”

 

Because if we all just submit to and believe everything said by our glorious medical overlords then looking after autistic children becomes a walk in the park.

 

It says a lot about the psyche of those in the medical community that when they hear about a child killed or maimed by a vaccine their first thought isn’t the welfare of the parents/child but about their precious reputations.

 

“I would like to assume I know what I am talking about.”

 

I would like it if we could assume that too, but alas, it is clear the Emperor has no clothes.

 

“It seems that few are taking the time to actually understand how vaccinations work, and why we are seeing the array of effects that we are.”

 

I have asked many times how they work and nobody has the slightest clue. I once a highly respected immunologist that question and he admitted he didn’t know.

 

“Our immune system acts a mini-scale system of evolution. We are constantly

producing antibodies and immune cells of different constituents and properties

in an attempt to battle ANY given foreign object that enters our body. Of

course, like evolution - the cells or antibodies that were found to have a

positive effect on our immune state are stored and memorised for future use.”

 

No. Not like evolution. In evolution those that are best suited to survive will procreate (more than others). In our immune system those who are most suited to attacking the virus/bacteria will be the ones to be sacrificed (bind to antigens). But you didn’t think of this did you?

 

No matter. You can always get filled with rage again.

 

“- This step is important in the development of IgG antibodies - in this

case, it is a single key made for a single keyhole. This key also has thousands

of copies made of it, each of them slightly different than the last. Perhaps one

of these new keys will have a BETTER fit for our keyhole than the existing

one?”

 

Even ignoring my above – completely devastating – point there are an infinite number of possible mutations of bacteria/viruses (we are told for example that the flu virus mutates all the time). The probability that anything in or produced by our body is a suitable match is some finite number divided by infinity. This equals zero by the way.

 

 

“You are probably thinking now, if vaccinations just help our bodies do what

it does naturally, we don't technically need them!”

 

I wasn’t thinking the former but I agree with the latter (even disregarding the “technically” bit).

 

“True... but there are a number of cases where there is no way our feeble bodies would be able to handle this intruder.”

 

Feeble bodies ey? Tell me something sapdiggity. If our bodies are so incredibly feeble – could you please explain how it is that all throughout history people who have spent their entire lives around sick people (physicians, nurses etc) have managed to have their lives measured in years rather than minutes? How could anybody survive such an onslaught of trillions of pathogenic bacteria, viruses, prions etc that all their patients have coughed, sneezed, breathed, touched all over them.

 

“That is why tetanus shots are particularly important but something

like the flu shot, for example, may not be.”

 

Again. I wasn’t thinking the former but I agree with the latter.

 

“This is why it concerns me that people discredit vaccinations due to their lack of effectiveness in the first or second world war... dude... it was a long time ago.”

 

Well concern yourself no more dude! I think they are as lacking in effectiveness today as they were in the world wars.

 

“Before razors were invented, people like Julius Ceasar had to have hairs individually plucked from their face. Will you give medicine some time, please?”

 

You can have a million years. But in the meantime don’t experiment on my children.

 

“The pathogen too, likes to evolve. It is possible that it could, through its own mechanisms, REVERSE our deletion of a crucial gene or virulence factor. Does this happen all the time? Of course not - but pathogens, like us, evolve. It would be arrogant of us to assume that in 1000 pathogens we deactivate, not 1 would possess the capability of fighting back.”

 

We discussed this in another thread here: https://groups.google.com/forum/#!topic/vaccination-respectful-debate/4VbMKx1iSYM

 

“This is why Tetanus vaccinations must be repeated as levels of these antibodies in the blood gradually reduce over time.”

 

That’s one explanation. The other is that the vaccine paradigm is like when we used to sacrifice virgins to make it rain. If it rained it proved it was the right thing to do, if not that just proved we needed to sacrifice more virgins. The whole notion of boosters is because vaccinations are a religion. They aren’t falsifiable and they aren’t science. No matter what happens the conclusion is always the same: more vaccines given to more people more often.

 

“- Isolated antigens - in applicable cases, a vaccination can be completely harmless by simply adding the isolated antigens for our body to respond to - whole cells are not even introduced, and hence cannot cause infection.”

 

None of them can cause infection. But practically all of the ingredients can contribute to its toxicity.

 

“However, as much as you'd like to,”

 

None of us would like to. There isn’t a single parent of an autistic child out there who wouldn’t feel massively relieved that their decision to vaccinate their child had nothing to do with their child’s illness and instead it was something they had no control of like their genes etc. But some people are too intellectually honest to take the easy route. As a corrolary, I have no doubt there are many, many parents of autistic children who can’t bring themselves to admit this.

 

“blaming Autism on vaccination simply because the nature of Autism is not fully known is a foolish assumption to make.”

 

I suppose it would be. But blaming it on vaccination due to witnessing challenge, dechallenge, rechallenge is perfectly reasonable. Indeed, in the field of medicine it is considered the closest possible thing to proof of causation for every other type of drug except vaccines. Can you explain why CDR is irrelevant in these cases sapdiggity?

 

“Until we can find a plausible link between the onset of Autism and ANYTHING (plausible link - something that could be recreated in a lab or at least have the concept proven), saying it is due to vaccinations is about as foolish as assuming it is due to breathing too much oxygen or not playing enough Xbox.”

 

See above comment.

 

“For example, let us look at flu shots. The general panic of the populace is what made flu shots so desirable and is why so many vaccinations started development - money! You can argue that desire for money is evil in such a case, but it is not. Without the reward of money, MANY medical advancements would not even be bothered with - it is a sad truth that money makes the world go round.”

 

Well self-interest actually. Personally I don’t think it is “sad” anymore than it is “sad” that we all need to breathe oxygen. Good, bad, whatever doesn’t come into it. How economic systems accommodate our desires can definitely be bad or good though. In the case of the free market system prices and profits are determined by the amount of a good people choose for their own benefit vs how easy it is to supply that good. This is all to the good. But in our socialised medical system, prices and profits are determined by artificial constraints on supply (patents) and governments telling us we must get drugged or else. This is definitely very bad.

 

“Unfortunately this leads to a nasty side effect - where developers have lied about the extent of a drug's effectiveness or adverse effects because it would otherwise not be approved.”

 

Yes. But none of this would matter if approval was irrelevant in the first place. If there were no government approval then nobody would trust it and everybody would do their own due diligence. Under such a scenario I doubt anybody would ever vaccinate ever again (although this decision would not be up to me of course). But in our current scenario we are told by bureaucrats who are in a revolving door relationship with pharma companies that the vaccine is perfectly safe. The government tells us all “how could you second guess our “experts” like this? Are you a conspiracy theorist? Do you think you are smarter than all the world’s scientists?”

 

Who knows more about cars: me or the Toyota CEO? Presumably the latter but nobody would think he/she should be able to dictate my choice of transport because they would all understand his knowledge pales in comparison to his vested interest. Doctors, pharma companies, immunologists, health bureaucrats would probably all have their reputations as healers and a large slab of their income on the line. They will never admit they are wrong.

 

Hence the rage.

 

“This would be difficult to accomplish but the motive is there - it costs hundreds of millions, if not billions of dollars to develop a new drug or vaccination.”

 

I’m pretty sure pharma companies spend more on marketing than they do on research but I could be mistaken. But I agree they have plenty of reasons to lie.

 

“Flu shots should be reserved for the elderly and immuno-compromised”

 

But you can’t draw the logical conclusion. If we shouldn’t get the flu vaccine but so many doctors/health bureaucrats/politicians tell us we should why on earth should we trust such people? The CDC’s own data shows that ever since flu shots rates of flu have risen (the data is rubbish I should note but it is the same type of data they use to “prove” other vaccines worked) but they still tell us to get it. If they are prepared to lie through their teeth on this issue – why should we ever trust them on any other?

 

Why are the AVN the ones who need to be sanctioned? Why aren’t you filled with rage for those who are using their position of authority to lie to the unsuspecting public rather than those who are merely asking questions?

 

“What I CAN tell you, however, is that no respectable member of medical development would put a dangerous chemical into a treatment unless it was vital;”

You know, sometimes it is better not to say anything at all. They “prove” their concoctions are safe by taking a group of people and giving them the vaccine and another group of people and giving them an older vaccine, or a vaccine for an unrelated disease or aluminium. They never test against an inert placebo – for any vaccine flu or otherwise. The fact that all of these tests go past the bureaucrats, peer-review etc just goes to prove how utterly worthless all these processes are. It is gross scientific fraud. Not to mention deliberately causing grievous bodily harm against the subjects.

 

“Of course, addition of such chemicals may have an adverse effect, but it should not be stated that they were added simply to harm us because vaccinations are evil.”

 

Vaccines are just inanimate objects. Those who seek to force them upon people, cover up their damage, take plush jobs from pharma companies in exchange for years of sycophancy in drug regulatory bodies and/or put their reputations ahead of their obligations to help their patients on the other hand...

[John Davidson]

Oh dear. You really have gone off the rails "punter". You try to use CDC data (out of context and no reference to the source, of course) that influenza rates have increased since vaccination (which is just wrong), and then say that CDC data is wrong. Come on, you can't have it both ways.

[Peter McCarthy]

[Quote: Tristan]

"No. Not like evolution. In evolution those that are best suited to survive will procreate (more than others). In our immune system those who are most suited to attacking the virus/bacteria will be the ones to be sacrificed (bind to antigens). But you didn’t think of this did you?"

Yes like evolution. Those immune cells that recognise antigens particular to the illness multiply and diversify to augment and adapt the immune response.

But you couldn't think of this could you?

[punter]

There is nothing wrong with accepting your opponent's premise in order to undermine their entire argument - regardless of whether you agree with that premise or not.

 

It is called making a logical argument.

 

"that influenza rates have increased since vaccination (which is just wrong)". See http://www.cdc.gov/flu/about/qa/hospital.htm

 

You are really really good at this John. And don't let anybody tell you otherwise.

[punter]

"Those immune cells that recognise antigens particular to the illness multiply and diversify to augment and adapt the immune response"

 

Oh well why didn't anybody say so? Thanks Peter. Now it is all clear. I didn't get it before but now that you give me your word that, contrary to all sense and reason, these things can multiply more than the other immune cells despite being the ones who are sacrificed I believe it wholeheartedly.

[Peter McCarthy]

They aren't sacrificed. What makes you keep saying that?

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[punter]

Survival of the fittest is about the organism most adapted to that environment being the most to produce offspring.

 

Why do the immune cells that are most likely to bind to antigens have an advantage in terms of producing the most offspring (assuming they produce any)?

 

There are other problems with this explanation by the way (its arbitrariness for starters - if we already have the immune cells in our bodies (just not a sufficient quantity) why would our bodies wait until we are infected with a disease before it allows them to reproduce? Unless of course there is some inherent danger in having too many of those cells (which would seem a good reason to refuse vaccination)).

 

But you need to clear this hurdle first.

 

 

On Thursday, 4 July 2013 13:50:25 UTC+10, mtp_69_i wrote:

They aren't sacrificed. What makes you keep saying that?

On 4 Jul 2013 08:55, "punter" <trista...@hotmail.com> wrote:

"Those immune cells that recognise antigens particular to the illness multiply and diversify to augment and adapt the immune response"

 

Oh well why didn't anybody say so? Thanks Peter. Now it is all clear. I didn't get it before but now that you give me your word that, contrary to all sense and reason, these things can multiply more than the other immune cells despite being the ones who are sacrificed I believe it wholeheartedly.

 

 

On Monday, 1 July 2013 08:48:00 UTC+10, mtp_69_i wrote:

[Quote: Tristan]
"No. Not like evolution. In evolution those that are best suited to survive will procreate (more than others). In our immune system those who are most suited to attacking the virus/bacteria will be the ones to be sacrificed (bind to antigens). But you didn’t think of this did you?"

Yes like evolution. Those immune cells that recognise antigens particular to the illness multiply and diversify to augment and adapt the immune response.

But you couldn't think of this could you?

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[Peter McCarthy]

Tristan, we've been here. You aren't interested in the answers. You don't understand them. You don't understand the data that supports them and you don't believe in the conclusions they allow us to draw.

This is just a little game for you where you feign interest in the science and then when it gets too hard to keep up you tell us you don't believe any of it anyway and thus it must be wrong...

Not that I'm worried. I know that you've heard everything I'm going to say before. I know you refused to believe it or research it further yourself then, just as you won't now. I'm just going to enjoy reading your replies as you further cement your place as the AVNs premier science denialist.

To answer your first question;

[Quote: Tristan]

" Why do the immune cells that are most likely to bind to antigens have an advantage in terms of producing the most offspring (assuming they produce any)?"

Their advantage comes from the way certain immune cells (specifically B cells in the example I'll use but T cells also work in a similar way) control their replication.

All naive B cells (unchallenged ie. never previously exposed to an antigen) are held in a senescent state, living and primed for antigen recognition, but non-dividing.

Their cell surface is decorated with membrane bound antibodies. These antibodies when membrane bound have two important functional domains. On the extracellular side is the antigen binding domain which essentially binds an antigen with an incredibly high degree of specificity. On the intracellular side is a trans-activation domain which is able to initiate an intracellular signalling cascade upon antigen recognition. As such, these membrane bound antibodies are called B cell receptors (BCR) because of their ability to signal following antigen binding.

When a B cell encounters an antigen it recognises (through exquisitely precise molecular interactions occurring within Angstroms between the BCR and the antigen), structural and physical properties of the B cell receptor change. These changes cause the activation of an intracellular signalling cascade (transduced by molecules within the cell changing their structural, physical and spatial properties in response the the BCR changes), which results in the (now activated) B cell undergoing a burst of cell division and cell differentiation (differentiation means changes in the physical properties of the B cell which, in this case enable it to now produce, improve and secrete the antibody that recognised the antigen). These "offspring" provide part of the army that fights the foreign entity that was initially recognised by the first B cell.

As such, throughout your life, B cells that have recognised a specific antigen and thus given rise to more copies of themselves will be present in higher numbers than B cells that have never encountered an antigen and therefore never given rise to more "offspring".

The important point here is that it has nothing to do with probability. Whether they are "likely" to recognise an antigen (as you say in your question) doesn't come into it. The immune system isn't sentient. It can't know what may come. It just puts out many different B cells, each with its own specific and unique antigen recognising BCR, and allows "natural selection" to take its course.

Likewise, these cells don't have an innate "advantage". They were simply selected for through the process I've described. It may be advantageous to the organism within which these B cells exist. And that may then play into a more Darwinian model of natural selection that I imagine you are relating this to. But in the context of the body and how it functions, these cells are just playing their role in the body's survival against pathogens.

With respect to your second question.
[Quote: Tristan]

" why would our bodies wait until we are infected with a disease before it allows them to reproduce? "

Again, the immune system is not sentient. Nor does it have a crystal ball it can use to peer into the future with and know precisely what antigens it will need to be able to recognise in the 80-odd years it has to protect you. Having an immune system that is adaptive and dynamic rather than static and predetermined is clearly more advantageous. (We can flesh this out if you need to but why not write out a list of pro's and con's before trying to argue against it?) And I'm sure Darwin himself would agree this adaptive quality of our immune system has been one of the most important determinants of survival throughout the evolution of high organisms such as ourselves.

Hopefully this clears things up for you.

[punter]

“Their advantage comes from the way certain immune cells (specifically B cells in the example I'll use but T cells also work in a similar way) control their replication.”

[...]

“These changes cause the activation of an intracellular signalling cascade (transduced by molecules within the cell changing their structural, physical and spatial properties in response the the BCR changes), which results in the (now activated) B cell undergoing a burst of cell division and cell differentiation (differentiation means changes in the physical properties of the B cell which, in this case enable it to now produce, improve and secrete the antibody that recognised the antigen).”

The explanation you provide is not “natural selection”. It is: “we hypothesise that for some inexplicable reason B-cells can only ever multiply when they are bound to a (highly specific) antigen, ergo encountering an antigen leads to immune system memory.”

 Your answer is nothing more than “it just does”. Not to mention the fact that it is completely ridiculous. How could the correct “intracellular signalling cascades” happen for each and every B-cell/antigen combination?  If we are vaccinating for a particular disease, how could we know that the “cascade” doesn’t cause the B-cell to go out attacking other immune cells – or organs? Even if a vaccine worked for one person it would be an absolute miracle if the same cascade were to happen in most (any?) other people.

“Again, the immune system is not sentient. Nor does it have a crystal ball it can use to peer into the future with and know precisely what antigens it will need to be able to recognise in the 80-odd years it has to protect you.”

 You missed the point. It supposedly already has these B-cells it just hasn’t made them reproduce. According to your theory the immune system has a small number of B-cells for every specific antigen but, for no apparent reason, waits until the body endures a near death experience before it thinks to itself “we had better make those B-cells reproduce now in case we get the same thing in the future!” But why not just make them in significant quantities from birth? How on earth could evolution have given our bodies the capacity to “adapt” in this way rather than just produce large amounts of B-cells in the first place? The only possible explanation is that a) there is inherent danger in doing such a thing; or b) your theory is nonsense.

 “Having an immune system that is adaptive and dynamic rather than static and predetermined is clearly more advantageous.”

 Ummm, you just said that the B-cells bind with a high degree of specificity. So they can’t be very adaptive (in this sense) can they? The probability of having a B-cell that just so happens to bind to a particular antigen (with the high degree of specificity you claim) is a finite number (number of types of B-cells in our body) divided by an infinite number (number of possible mutations of different viruses/bacteria). Did you not see this when I already pointed it out?

 “And I'm sure Darwin himself would agree this adaptive quality of our immune system has been one of the most important determinants of survival throughout the evolution of high organisms such as ourselves.”

 If you want to start talking about authority I should point out that Alfred Russell Wallace was just as important in the theory of evolution as Darwin and he understood that allopathic medicine was nothing more than a bunch of lies. No idea what Darwin thought.

[jl]

 You missed the point. It supposedly already has these B-cells it just hasn’t made them reproduce. According to your theory the immune system has a small number of B-cells for every specific antigen but, for no apparent reason, waits until the body endures a near death experience before it thinks to itself “we had better make those B-cells reproduce now in case we get the same thing in the future!” But why not just make them in significant quantities from birth? How on earth could evolution have given our bodies the capacity to “adapt” in this way rather than just produce large amounts of B-cells in the first place? The only possible explanation is that a) there is inherent danger in doing such a thing; or b) your theory is nonsense.

These small numbers of B cells require time to multiply and produce enough antibodies to combat the infection, it doesn't "wait until the body endures a near death experience", they start multiplying and fighting the infection after binding the antigen. Having significant quantities of B cells of many specificities (most which would not be activated) would be really inefficient wouldn't you say? Besides it has been proven in animal models and humans in fact that the immune response is faster (hence recovery) the more times the organism has been exposed to the same pathogen (in all respects i.e. not mutated)

 Ummm, you just said that the B-cells bind with a high degree of specificity. So they can’t be very adaptive (in this sense) can they? The probability of having a B-cell that just so happens to bind to a particular antigen (with the high degree of specificity you claim) is a finite number (number of types of B-cells in our body) divided by an infinite number (number of possible mutations of different viruses/bacteria). Did you not see this when I already pointed it out?

There may be an infinite number of possible mutations but some sequences in bacteria are conserved- i.e. some genetic sequences code for an essential protein that the bacteria may not live without (the same principle that a car needs wheels to work). So a good B cell/immune response will be directed to those conserved and hence difficult to mutate structures = we don't need an infinite number of B cell specificities (although it's quite large 10^9 to deal with most things that life throws at us (;  )

[punter]

“These small numbers of B cells require time to multiply and produce enough antibodies to combat the infection, it doesn't "wait until the body endures a near death experience", they start multiplying and fighting the infection after binding the antigen.”

You missed the point – I suspect deliberately. We are told that infection is dangerous – possibly fatal. So that being the case why would our bodies take such a risk when it has the means to prevent the infection from occurring in the first place?

“Having significant quantities of B cells of many specificities (most which would not be activated) would be really inefficient wouldn't you say? “

I would say. But you may or may not note that I am not the one who believes our bodies should be vaccinated for every illness under the sun. Some have even suggested that babies can easily cope with 100,000 vaccines in a single day. You might want to tell such people they are horribly misguided.

“Besides it has been proven in animal models and humans in fact that the immune response is faster (hence recovery) the more times the organism has been exposed to the same pathogen (in all respects i.e. not mutated)”

It has been ‘proven’ has it? Well that is different.

If I believed that immunologists/virologists could actually do one hundredth of what most people imagine they can do I wouldn’t be having such discussions. But I don’t believe it. I believe that immunology and virology are a complete joke.

“There may be an infinite number of possible mutations but some sequences in bacteria are conserved- i.e. some genetic sequences code for an essential protein that the bacteria may not live without (the same principle that a car needs wheels to work).”

In that case why do we need a new flu vaccine every year? (I realise that is for a virus but the principle remains). Why is it that whenever a new disease crops up after a vaccine the doctors blame a mutation in the bacteria/virus for the fact that the vaccine didn’t actually reduce the number of people who got sick?

[Peter McCarthy]

[Quote: Tristan]

“we hypothesise that for some inexplicable reason B-cells can only ever multiply when they are bound to a (highly specific) antigen, ergo encountering an antigen leads to immune system memory.”

It's not inexplicable. The changes in gene expression, the changes in temporal, physical and spatial aspects of the molecules involved in this process, the acquisition of antibody secreting activity, antibody diversification, clonal expansion of antibody producing B cells responding to an antigen etc etc that explain this phenomenon have been studied. Your unwillingness or inability to understand these things doesn't change that.

[Quote: Tristan]

How could the correct “intracellular signalling cascades” happen for each and every B-cell/antigen combination?

How could it not?? Are you suggesting every cell has a unique complement of molecules that some how all allow it to maintain the identity of a B cell and ye all work in completely different ways?? These signaling pathways are highly stereotyped and highly HIGHLY conserved through evolution. BCR activation in one B cell follows the same molecular pathway in all B cells. The difference lies in the DNA that encodes the specific antibody each B cell produces. B cells have a fascinating difference from most other cell types in this respect in that they can specifically rearrange this DNA to facilitate massive diversification of the antigen recognising portion of the antibodies they produce.

Now, it may sound like I'm just saying, "trust me on this". And I am. Largely because I've spent nearly 15 years in molecular biology and so I like to think I have a reasonable idea about this. You on the other hand have had no training in molecular biology. Have a fundamental lack of understanding of how cells work (as evidenced by your questions) and belligerently refuse to do your own research. So, yeah, take it or leave it.

[Quote: Tristan]
 You missed the point

No. You missed the point. Why doesn't the body make enough B cells to fight every single pathogen it may or may not ever encounter??  Where does the body draw the line? How much is enough? Should we evolve to just be an organism made out if B cells just in case? The body doesn't know how many or which ones it will need. How could anyone? Do you??

By the same token, why do organs only grow to a roughly defined size? Or why can't we regenerate our organs (mostly)? One idea is that as we've evolved to live longer, we have had to develop ways to curtain the freedom of our body to just grow and grow. I'm sure you are familiar with cancer. Cancer is essentially unregulated growth of cells. Cancer is bad. Cancer makes it harder to live longer and becomes more of a problem as you get older because of the increasing possibility of deleterious changes to your DNA over time. By having mechanisms in place that control cell growth and require strict and highly controlled signals to promote growth, the body is able to reduce the likelihood that cells will begin growing out of control. However, this doesn't mean that B cell activation is cancer because this expansion of cells after antigen challenge is still controlled and the amount of expansion is finite. But, if B cell proliferation were less tightly controlled, it might be possible for cell growth to get out of control more easily and thus lead to cancer. Again, just one idea from my years of studying molecular biology.

[Quote: Tristan]

The probability of having a B-cell that just so happens to bind to a particular antigen (with the high degree of specificity you claim) is a finite number (number of types of B-cells in our body) divided by an infinite number (number of possible mutations of different viruses/bacteria).

You're just making stuff up here. I don't have actual numbers in front of me either though so let's just logic this one out a bit. Your cells use much the same amino acids, lipids, carbohydrates and small chemical modifications to build themselves as most pathogens use. As such through the bodies huge molecular diversity much of the infinite possibilities you talk about already exist in us. Luckily, during our development, our immune system looks very unkindly on immune cells that attack our own body and promptly eliminates them (autoimmune disease are examples of where this process breaks down). As such, only molecular arrangements that are not present in our body are left over in the B cell repertoire. Now, this still may seem to leave too big a number of possibilities. Importantly, B cells don't have to recognise every single antigen a pathogen presents. They only need to recognise one. So, of all the different combinations of chemical and molecular arrangements a pathogen might present to the immune system. If ANY of them trigger a response then the pathogen is in trouble. So you see, the odds are actually stacked heavily in favour of an immune system that only recognises foreign molecular entities (antigens) because any one pathogen is likely to have at least one antigen that the immune system will react to.

Importantly, if a B cell recognises an antigen from one single pathogen, it is highly likely that antigen will also be present in the pathogens daughter/mother/neighbour etc because of conservation and evolution. Great stuff! Sure, if that antigen mutates then it may not be recognised. But, that mutation may also be disadvantageous to the pathogen. Anyway, and again, years of work in mol biol vs University of GNM.

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[Peter McCarthy]

[Quote: Tristan]

In that case why do we need a new flu vaccine every year? (I realise that is for a virus but the principle remains). Why is it that whenever a new disease crops up after a vaccine the doctors blame a mutation in the bacteria/virus for the fact that the vaccine didn’t actually reduce the number of people who got sick?

And yet again we see how little effort you've put into understanding the things you try and argue against the most...

Immunity to the flu (whether acquired naturally or through vaccination) declines over time. (Find me anyone that has life long immunity through natural exposure to flu.)

Throw into that the fact that seasonally the assortment of circulating flu viruses can change and include flu viruses that are not often encountered by humans (swine or avian flu for instance) and you have a pathogen that can cause significant health problems (particularly in infants, the elderly, immuno-compromised) and is easily and rapid transmitted by close contact. If you could reduce your risk of contracting such an illness, I reckon you'd be hard pressed to justify not doing so.

As far as doctors always blaming mutations for ineffective vaccines goes. I don't know of too many examples of that.

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[punter]

“Your unwillingness or inability to understand these things doesn't change that.”

OK. The explanations are all there somewhere. Somewhere between the constitution, Mabo and the vibe.

[Quote: Tristan]

How could the correct “intracellular signalling cascades” happen for each and every B-cell/antigen combination?

“How could it not?? Are you suggesting every cell has a unique complement of molecules that some how all allow it to maintain the identity of a B cell and ye all work in completely different ways??”

Let me help you out: you claim that the body produces lots of different types of B-cells. Some of which are suited to a particular antigen. When I asked you how it could be that attacking an antigen would lead to that particular B-cell having an evolutionary advantage over other B-cells you said it was because of some “intracellular signalling cascade”. By cascade I assume you meant that there was a complex chain of events. Of course you just made it all up but I ran with it all the same.

Now, because the probability of my B-cells (in terms of antigen receptor type) ever being exactly the same as everybody else’s is zero it goes without saying then that even if most of us have B-cells that will bind successfully with the antigen the complex chain of events that it triggers will almost certainly have a significantly different outcome. It might even be a harmful one. For example it may trigger the B-cell to multiply without ending.

On the other hand, if you think that no matter what the outcome will be exactly the same regardless of the differences in B-cell receptor types then clearly the whole “intracellular signalling cascade” is just a fabrication (which is what I initially assumed).

“So, yeah, take it or leave it.”

OK I’ll leave it. Not that I don’t think you are an incredibly honest individual or anything. I’m sure you are the sort of person who would look down a microscope, observe something that would see the end of your career and say “oh well, science is science. I suppose I had better quit and work in alternative medicine instead”.

“No. You missed the point. Why doesn't the body make enough B cells to fight every single pathogen it may or may not ever encounter??  Where does the body draw the line? How much is enough? Should we evolve to just be an organism made out if B cells just in case? The body doesn't know how many or which ones it will need. How could anyone? Do you??”

I will repeat my exchange with lj for your benefit.

lj:“Having significant quantities of B cells of many specificities (most which would not be activated) would be really inefficient wouldn't you say? “

me: I would say. But you may or may not note that I am not the one who believes our bodies should be vaccinated for every illness under the sun. Some have even suggested that babies can easily cope with 100,000 vaccines in a single day. You might want to tell such people they are horribly misguided.

“Cancer is essentially unregulated growth of cells. Cancer is bad. Cancer makes it harder to live longer and becomes more of a problem as you get older because of the increasing possibility of deleterious changes to your DNA over time.”

Why are you telling me things that you know I don’t believe as though I will just accept it at face value?

“But, if B cell proliferation were less tightly controlled, it might be possible for cell growth to get out of control more easily and thus lead to cancer. Again, just one idea from my years of studying molecular biology.”

Thanks.

“Your cells use much the same amino acids, lipids, carbohydrates and small chemical modifications to build themselves as most pathogens use. As such through the bodies huge molecular diversity much of the infinite possibilities you talk about already exist in us.”

How does that help your cause? It doesn’t matter if our body has the potential to produce an infinite number of different B-cells what matters is that it couldn’t possibly do so at any one time. Or even over the course of a lifetime. Like I said, there are (or will be) a finite number of different types of B-cells. There is an infinite array of possibly mutations of bacteria/viruses. Ergo, the probability you would ever have the correct B-cell type is exactly zero. Now, the only way you could escape this problem is if you arbitrarily decided that B-cells covered a “range” of different types of pathogens (similar to what you have done below). But this leaves you with the problem of having to explain why we need a different flu shot every year or why the pertussis bacteria has mutated etc. Like I have pointed out previously, you can’t answer one question without creating a bunch more.

“So, of all the different combinations of chemical and molecular arrangements a pathogen might present to the immune system. If ANY of them trigger a response then the pathogen is in trouble.”

See above. If what you are saying is true then it just opens up the problem as to why scientists blame mutations in the bacteria/virus whenever a vaccine fails to reduce a disease (well they always fail but specifically when even their own data is telling them that it is failing).

Indeed, your “explanation” presents another problem. If what you are saying was right then whenever a vaccine is introduced even if the majority of people were able to develop some sort of immune response they would be responding to different parts of the antigen. How would scientists measure the correct antibody response then? Does that mean specific titres are irrelevant? You can’t answer one question without creating a bunch more.

“Sure, if that antigen mutates then it may not be recognised. But, that mutation may also be disadvantageous to the pathogen.”

So why do we need a different flu vaccine every year Peter? Why?

“Anyway, and again, years of work in mol biol vs University of GNM.”

I know. It must be extremely embarrassing to be picked apart so comprehensively given our respective qualifications. No idea why you would want to highlight it but kudos on your humility.

Maybe we can have a debate on economic matters to see if you can match me on my turf? Might make you feel better (although it probably won't).

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[punter]

“Immunity to the flu (whether acquired naturally or through vaccination) declines over time. (Find me anyone that has life long immunity through natural exposure to flu.) “

Que? I can’t find anybody who has immunity of any duration for anything from anything. Do you not realise that I don’t even believe in the germ theory of disease? How could I possibly believe in natural immunity? I realise many people opposed to vaccines do – and they are entitled to their opinion – but I am not one of them.

“Throw into that the fact that seasonally the assortment of circulating flu viruses can change and include flu viruses that are not often encountered by humans (swine or avian flu for instance) and you have a pathogen that can cause significant health problems (particularly in infants, the elderly, immuno-compromised) and is easily and rapid transmitted by close contact. If you could reduce your risk of contracting such an illness, I reckon you'd be hard pressed to justify not doing so.”

That isn’t an answer. How severe flu may or may not be is inconsequential to whether the vaccine for it works or whether the concept of it mutating all the time poses a problem for the accepted explanation of immune system memory.

“As far as doctors always blaming mutations for ineffective vaccines goes. I don't know of too many examples of that.”

Really? Well it is a good thing I am here to help you out. http://www.hopkinsmedicine.org/healthlibrary/conditions/infectious_diseases/influenza_flu_85,P00625/ Note the phrase: “These mutations sometimes reduce the ability of the vaccine-induced antibody to inhibit the newly mutated virus, thereby reducing vaccine effectiveness.”

I assume you have also never heard of the term “antibiotic-resistant” bacteria either? Well that’s OK because my helpfulness knows no bounds. http://www.nature.com/scitable/topicpage/antibiotic-resistance-mutation-rates-and-mrsa-28360

And this covers a bacteria that is evading both antibiotics and vaccines

I honestly can’t believe you said that.

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