Stupid mutants.

What you think about how you think.
Electro432
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Re: Stupid mutants.

Postby Electro432 » Thu Jul 13, 2017 10:25 pm

Oh dear the majority of what I said was not translated here. I'm clearly still a dinosaur haha.

EM your posts are highly educational. Wish I had more time to engage, so thanks for being thought provoking.
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Re: Stupid mutants.

Postby bobbo_the_Pragmatist » Thu Jul 13, 2017 11:05 pm

Lance Kennedy wrote: The human immune system constantly 'learns ' new stuff in order to perform its function .

I'm not a science guy. Just a casual reader of pop literature. Still.......seems to me this statement reveals much of Lance's incompetency. Lance: you are anthropomorphizing a completely "unknowing" system. Its a basic and common misconceptualizing of our Darwinian struggle. Darwin is NOT goal directed, it is wholly the consequence of the stimulus and responses that have already taken place. Nothing "hides." Nothing evolves "to do" anything.

Its a simple mind fart. To be corrected with a bit of oxygen.................take a deep breath.
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Re: Stupid mutants.

Postby Nikki Nyx » Sat Jul 15, 2017 9:59 pm

Lance,
I deliberately avoided this thread for several days, because you have conducted your half of the debate disingenuously. You've changed your original argument several times, failed to provide supporting evidence as requested, repeatedly misrepresented my argument, and indulged in ad hominem attack.

Your original argument:
Lance Kennedy wrote:When a new pathogen invades, it develops a new antibody which is specific to that pathogen and which provides future immunity to that pathogen.

Beta lymphocytes respond to the presence of novel pathogens by analysing the protein antigen, on the surface of the pathogen, and creating from new, an antibody which works on that antigen by a lock and key mechanism.

There are potentially E200 different potential proteins, and thus an enormous number of possible antigens for the immune system to deal with. It is physically impossible for the immune system to have antibodies for each and every possible antigen...Thus it is essential for the immune system to be able to analyse antigens and manufacture novel antibodies at need.
Your statements are wrong. A B cell does not "analyze" an antigen; in fact, a B cell cannot be activated by an antigen unless it has a receptor specific to that antigen. The B cell's antigen-receptor must be occupied by the antigen in order for the B cell to be activated.
As each lymphocyte develops in a central lymphoid organ, it becomes committed to react with a particular antigen before ever being exposed to the antigen. It expresses this commitment in the form of cell-surface receptor proteins that specifically fit the antigen. When a lymphocyte encounters its antigen in a peripheral lymphoid organ, the binding of the antigen to the receptors activates the lymphocyte, causing it both to proliferate and to differentiate into an effector cell. An antigen therefore selectively stimulates those cells that express complementary antigen-specific receptors and are thus already committed to respond to it. This arrangement is what makes adaptive immune responses antigen-specific.

The term “clonal” in clonal selection theory derives from the postulate that the adaptive immune system is composed of millions of different families, or clones, of lymphocytes, each consisting of T or B cells descended from a common ancestor. Each ancestral cell was already committed to make one particular antigen-specific receptor protein, and so all cells in a clone have the same antigen specificity. According to the clonal selection theory, then, the immune system functions on the “ready-made” principle rather than the “made-to-order” one. LINK


I never stated, as you claim, that the immune system is static. From my first post in this debate, I spoke of affinity maturation, somatic hypermutation, and antibody class switching. My sole argument with your viewpoint, as you initially stated it, was that your "made to order" interpretation was dead wrong. You didn't want to admit you were wrong, so you made multiple attempts to rephrase your position into a different one, you deliberately misstated my argument, and you attempted to portray me as ignorant and lacking understanding. That's pretty low, and you should be ashamed of yourself for such tactics, especially here. It's behavior unbecoming a skeptic.

Thank you, EM, for providing the link to the textbook, Molecular Biology of the Cell. I got to review lots of information I'd forgotten, and learn some new things too, which is always awesome. ;)
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
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Re: Stupid mutants.

Postby Lance Kennedy » Sat Jul 15, 2017 11:38 pm

Bobbo

When I put the word 'learn ' in inverted commas, that should tell you that I am not talking of genuine learning.

Nikki

Still pushing the 19th century barrow.
Sad.

I have already given you suitable references which you ignored. The immune system works via adaptation. I do not care that the adaptation occurs before beta lymphocytes are made. The point is that an antibody MUST be sensitive to the antigen. It must "mature" its affinity so that there is a ' lock and key' fit to the antigen. Without some adaptation that is impossible. The immune system is dynamic and adaptive, regardless of how often you insist it is static and incapable of adapting to need. If the immune system did not adapt, humanity' ancestors would have gone extinct many millions of years ago.

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Re: Stupid mutants.

Postby Lance Kennedy » Sat Jul 15, 2017 11:42 pm

This reference gives a better idea of what sensitization is in relation to antibodies. Anyone reading it with their mind open to new ideas will see that it requires the antibody to become specific to an antibody.

https://en.m.wikipedia.org/wiki/Sensiti ... immunology)

Interestingly, there is an effect which is similar in its result to the lack of adaptability you promote. It is called the Hoskins Effect. It happens when a previous infection causes antibodies to be produced and remain in the body, but when the second infection is close to the first in antigenic nature. That results in an immune error, in which antibodies are released suitable for the first infection, but not the second. A measured reduction in lysis performance is the result, showing how important proper adaptation is.

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Re: Stupid mutants.

Postby ElectricMonk » Sun Jul 16, 2017 2:11 am

Nothing in the link you posted.
Also, the textbook is up to date.

I would say do better, but that is redundant since you can't do worse, Lance.
I've come up with a set of rules that describe our reactions to technologies:
Spoiler:
1. Anything that is in the world when you’re born is normal and ordinary and is just a natural part of the way the world works.
2. Anything that's invented between when you’re fifteen and thirty-five is new and exciting and revolutionary and you can probably get a career in it.
3. Anything invented after you're thirty-five is against the natural order of things.
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Re: Stupid mutants.

Postby Lance Kennedy » Sun Jul 16, 2017 2:20 am

The silly thing, EM is that your textbook does not say what you claim it says.

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Re: Stupid mutants.

Postby ElectricMonk » Sun Jul 16, 2017 2:36 am

Lance Kennedy wrote:The silly thing, EM is that your textbook does not say what you claim it says.


Why don't you show us which claim the textbook disproves?
I've come up with a set of rules that describe our reactions to technologies:
Spoiler:
1. Anything that is in the world when you’re born is normal and ordinary and is just a natural part of the way the world works.
2. Anything that's invented between when you’re fifteen and thirty-five is new and exciting and revolutionary and you can probably get a career in it.
3. Anything invented after you're thirty-five is against the natural order of things.
- Douglas Adams

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Re: Stupid mutants.

Postby Lance Kennedy » Sun Jul 16, 2017 3:57 am

Your original claim, EM, was that the immune system "does not learn" . But it adapts. If it did not, we would not acquire immunity to illnesses we have experienced. Therefore you were wrong. Your reference does not deny that the immune system adapts. As I have said all along, the immune system is dynamic and adaptive.

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Re: Stupid mutants.

Postby bobbo_the_Pragmatist » Sun Jul 16, 2017 4:04 am

Lance Kennedy wrote:Bobbo

When I put the word 'learn ' in inverted commas, that should tell you that I am not talking of genuine learning.


When are you going to "learn" not to do that? Contra, if quotes mean your are not talking genuinely, why aren't your entire posts in quotes?

"Know" "what" "I" "mean"?
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Re: Stupid mutants.

Postby Lance Kennedy » Sun Jul 16, 2017 4:28 am

There is an article in Wikipedia under the title "adaptive immune system", which says, and I quote.

" Somatic hypermutation (a process of a accelerated somatic mutations) and V(D)J recombination (an irreversible genetic recombination of antigen receptor gene segments) leads to a small number of genes generating a vast number of different antigen receptors."

It goes on to explain how this creates antigen specificity which is inherited by daughter cells.

All this happens after a pathogen invades, and presents its antigen epitope for antibody adaptation. Basically, we get adaptation of a dynamic immune system. Gee, fellas. This is what I have been saying all along !

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Re: Stupid mutants.

Postby Lance Kennedy » Sun Jul 16, 2017 4:30 am

Bobbo

Quotes, used that way, are a very, very widespread technique by writers of all kinds. About time you learned to interpret.

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Re: Stupid mutants.

Postby bobbo_the_Pragmatist » Sun Jul 16, 2017 4:47 am

Lance: you are such a "straight man."

........................... Pro's and Con's to all we do.

Humor.

We shouldn't let it pass us by, even when its munching on our butts. Thats mostly why butts were created.
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Re: Stupid mutants.

Postby ElectricMonk » Sun Jul 16, 2017 11:40 am

Lance Kennedy wrote:There is an article in Wikipedia under the title "adaptive immune system", which says, and I quote.

" Somatic hypermutation (a process of a accelerated somatic mutations) and V(D)J recombination (an irreversible genetic recombination of antigen receptor gene segments) leads to a small number of genes generating a vast number of different antigen receptors."

It goes on to explain how this creates antigen specificity which is inherited by daughter cells.

All this happens after a pathogen invades, and presents its antigen epitope for antibody adaptation. Basically, we get adaptation of a dynamic immune system. Gee, fellas. This is what I have been saying all along !




Lance, all of this was in the Textbook that you don't want to read because it came from my link. Conveniently for you,you are leaving out the critical bit that comes before the somatic hypermutation, which requires genetically-generated antigen recognition mechanisms.

Admit it, before this thread you had never heard of the preimmune antibody repertoire.
I've come up with a set of rules that describe our reactions to technologies:
Spoiler:
1. Anything that is in the world when you’re born is normal and ordinary and is just a natural part of the way the world works.
2. Anything that's invented between when you’re fifteen and thirty-five is new and exciting and revolutionary and you can probably get a career in it.
3. Anything invented after you're thirty-five is against the natural order of things.
- Douglas Adams

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Re: Stupid mutants.

Postby Lance Kennedy » Sun Jul 16, 2017 7:36 pm

Before all this, EM, you believed that the immune system "could not learn."

My thesis is, and always has been, that the immune system is dynamic and adaptive. I have proven my case.

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Re: Stupid mutants.

Postby Nikki Nyx » Sun Jul 16, 2017 7:55 pm

Lance Kennedy wrote:Nikki

Still pushing the 19th century barrow.
Sad.
Lance, learn to read, because you're just digging your hole deeper and deeper. The textbook from which I have repeatedly quoted is from this century which, you might recall, is the 21st.

Lance Kennedy wrote:The immune system works via adaptation.
No {!#%@}, Sherlock. I said so, in my first post.
Nikki Nyx wrote:Antibodies are designed to be incredibly specialized:
After the B cells leave the bone marrow, but before they interact with antigen, they switch and make both IgM and IgD molecules as membrane-bound antigen receptors, both with the same antigen-binding sites. On stimulation by antigen and helper T cells, some of these cells are activated to secrete IgM antibodies, which dominate the primary antibody response. Later in the immune response, the combination of antigen and the cytokines that helper T cells secrete induce many B cells to switch to making IgG, IgE, or IgA antibodies. These cells generate both memory cells that express the corresponding classes of antibody molecules on their surface and effector cells that secrete the antibodies. The IgG, IgE, and IgA molecules are collectively referred to as secondary classes of antibodies, both because they are produced only after antigen stimulation and because they dominate secondary antibody responses. As we saw earlier, each different class of antibody is specialized to attack microbes in different ways and in different sites.


Lance Kennedy wrote:I do not care that the adaptation occurs before beta lymphocytes are made.
It doesn't. You're wrong again. Now you're confusing the innate with the adaptive. Affinity maturation occurs after an antigen is encountered.

Lance Kennedy wrote:The point is that an antibody MUST be sensitive to the antigen.
Do you preview your comments before posting them? Both of these words are wrong. A B cell must have an antigen-receptor for a specific antigen in order for that B cell to be activated. Not "sensitive." The B cell's antigen-receptor must be occupied by the matching antigen. Then the primary immune response begins.

Lance Kennedy wrote:It must "mature" its affinity so that there is a ' lock and key' fit to the antigen. Without some adaptation that is impossible.
The term is "somatic hypermutation," and I've mentioned and described it repeatedly. Your analogy is inaccurate, however. Affinity maturation does not mean that the antibodies produced change from being ineffective to effective; it means they change from being somewhat effective to incredibly super-effective...over time.
...with the passage of time after immunization, there is usually a progressive increase in the affinity of the antibodies produced against the immunizing antigen. This phenomenon, known as affinity maturation, is due to the accumulation of point mutations specifically in both heavy-chain and light-chain V-region coding sequences. The mutations occur long after the coding regions have been assembled, when B cells are stimulated by antigen and helper T cells to generate memory cells in a lymphoid follicle in a peripheral lymphoid organ. ...the process is called somatic hypermutation.

Only a small minority of the altered antigen receptors generated by hypermutation have an increased affinity for the antigen. The few B cells expressing these higher-affinity receptors, however, are preferentially stimulated by the antigen to survive and proliferate, whereas most other B cells die by apoptosis. Thus, as a result of repeated cycles of somatic hypermutation, followed by antigen-driven proliferation of selected clones of memory B cells, antibodies of increasingly higher affinity become abundant during an immune response, providing progressively better protection against the pathogen.


Lance Kennedy wrote:The immune system is dynamic and adaptive, regardless of how often you insist it is static and incapable of adapting to need.
I have not insisted that. Not multiple times. Not even one {!#%@} time. You're not even reading what I'm posting, Lance. But do keep changing your argument, by all means. At the rate you're going, in a couple days, you'll be agreeing with me.
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
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Re: Stupid mutants.

Postby Nikki Nyx » Sun Jul 16, 2017 7:57 pm

Lance Kennedy wrote:This reference gives a better idea of what sensitization is in relation to antibodies. Anyone reading it with their mind open to new ideas will see that it requires the antibody to become specific to an antibody.

https://en.m.wikipedia.org/wiki/Sensiti ... immunology)
Your link is dead. And this is nonsense.
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
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Re: Stupid mutants.

Postby Lance Kennedy » Sun Jul 16, 2017 8:58 pm

Nikki

Your biggest mistake was supporting EM in the first place. Yes, I will concede that you did not say the immune system was static. But EM did, and you dived into the debate to support him. So my mistake was understandable.

I actually did make another big mistake, but neither you nor EM picked up on it.

Anyway, my original assertion was correct. The immune system is dynamic and adaptive.

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Re: Stupid mutants.

Postby ElectricMonk » Mon Jul 17, 2017 2:53 am

The winner in a scientific discussion is always the person who learned the most from it.

This makes you, Lance, a sad, bad loser.
I've come up with a set of rules that describe our reactions to technologies:
Spoiler:
1. Anything that is in the world when you’re born is normal and ordinary and is just a natural part of the way the world works.
2. Anything that's invented between when you’re fifteen and thirty-five is new and exciting and revolutionary and you can probably get a career in it.
3. Anything invented after you're thirty-five is against the natural order of things.
- Douglas Adams

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Re: Stupid mutants.

Postby Lance Kennedy » Mon Jul 17, 2017 3:32 am

Actually, EM, I found the discussion quite useful. Unlike you, I did not stick to one reference, but did quite a Google search, and read at least a dozen internet articles on the subject. It was useful revision and update. But I did not start the debate obsessed with a fallacy.

I am sad that Nikki chose to support you, and I wonder if she actually realised what you were arguing. In hindsight, I suspect she had not realised you believed the immune system 'could not learn ', meaning you believed it was a static and non adaptive system.

Do you still believe that ?

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Re: Stupid mutants.

Postby Nikki Nyx » Mon Jul 17, 2017 6:19 pm

Lance Kennedy wrote:Your biggest mistake was supporting EM in the first place.
"Biggest mistake" implies that I have made several mistakes, and I have made none.
Lance Kennedy wrote:Yes, I will concede that you did not say the immune system was static.
You now owe me an apology, since your ad hominem attacks were based on your misunderstanding of my argument.
Lance Kennedy wrote:But EM did, and you dived into the debate to support him.
My initial post was made in regards to only one point: that the immune system has a preimmune antibody repertoire, which EM stated and you denied.
Lance Kennedy wrote:So my mistake was understandable.
No, it wasn't. Had you actually read my posts, you would not have made your mistake.
Lance Kennedy wrote:I actually did make another big mistake, but neither you nor EM picked up on it.
Since you haven't read my posts, how would you know?
Lance Kennedy wrote:Anyway, my original assertion was correct. The immune system is dynamic and adaptive.
That was not your original assertion. Again, your initial argument was, and I quote:
Lance Kennedy wrote:It is physically impossible for the immune system to have antibodies for each and every possible antigen, since the possible number of different antigens is greater than the number of atoms in our universe. Thus it is essential for the immune system to be able to analyse antigens and manufacture novel antibodies at need.

...the human genome CANNOT contain enough antibodies to cope with them all.

The human body DOES NOT contain all the antibodies it needs to deal with all diseases.

Beta lymphocytes respond to the presence of novel pathogens by analysing the protein antigen, on the surface of the pathogen, and creating from new, an antibody which works on that antigen by a lock and key mechanism.
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
—Lazarus Long, from Time Enough for Love, by Robert A. Heinlein

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Re: Stupid mutants.

Postby Lance Kennedy » Mon Jul 17, 2017 7:57 pm

Nikki

The thing about our debate that puzzled me the most was your support of EM and his untenable position. When I first saw your posts, when you joined this forum, they impressed me as being rational and intelligent. Yet here you were supporting a guy who claimed the immune system "could not learn ", Meaning that EM was claiming the immune system was static and non adaptive. That was a big puzzle to me, and the only explanation seemed to be that you were ignorant on immunology, even if you were knowledgeable in other areas. I think that was my error, and I apologise for that error.

In fact, EM and I arguing about the adaptability of the immune system. He posted his reference, from the immunology textbook, to back up his claim that the immune system was non adaptive. When I argued against that, I was not suggesting that the textbook was wrong. I was telling EM that his interpretation was wrong. When you weighed in to support the idiotic argument, I had to assume you were also going with a wrong interpretation.

The pre immune antibody repertoire was used by EM to suggest that no adjustment to antibody structure and number was needed. That was utterly wrong. Yet you appeared to be supporting his argument. That, in my mind, made you wrong as well.

If you are happy to support my original contention that the immune system is dynamic and adaptive, then we probably have no argument. Just misunderstandings.

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Re: Stupid mutants.

Postby bobbo_the_Pragmatist » Tue Jul 18, 2017 5:10 am

All anyone actually interested in this subject needs to do is: DEFINE "adaption" as it applies to the immune system.

Otherwise..........all you are going to do is talk past each other as amply demonstrated.

THE DICTIONARY (sic).................... what a concept. 99% of arguments already "solved" just sitting there waiting to be read. Can't force anyone to read a dictionary...... they tend only to eat the covers.

Hoomans. What ya gonna do?
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Re: Stupid mutants.

Postby Matthew Ellard » Tue Jul 18, 2017 5:16 am

bobbo_the_Pragmatist wrote:All anyone actually interested in this subject needs to do is: DEFINE "adaption" as it applies to the immune system.
I was going to join this thread and show off my pure genius.......I then started to look at immunology papers for the first time.......I then ran away like buggery. :D

This is a really really really hard topic and I'm going to show off my genius by not touching this topic with a ten foot pole. It's simply beyond my brain power.

(I think you would need to be an expert across many other fields before you even thought about dabbling in immunology)
:D

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Re: Stupid mutants.

Postby bobbo_the_Pragmatist » Tue Jul 18, 2017 5:35 am

Matthew Ellard wrote:...This is a really really really hard topic and I'm going to show off my genius by not touching this topic with a ten foot pole. It's simply beyond my brain power.

I came to this conclusion a while back kibitzing with you and "forget who it was" regarding the genome and all its variations and subtleties. Matt, whether true or not "I believe" we are smart enough to be able to read up on a subject and "gets something out of it." Ha, ha==>but for me, NOT SO with the genome and not so with immunization issues.

I do blame "the literature" on this for not having clear demarcations on what is actually being discussed, and failure to define terms and issues before launching into terminology and issues best understood by practitioners in the field and barely at all if not in error by the rest of us.

Science is like that. A GULF..... between qualified scientist and the literature they produce and deal with, and the Rest of Us.

Happens in Climate Science too.

............................................ hmmmmm. I'm thinking right now "but not true" in Economics or Politics? Now...... how can I/we analyze THAT specialized field??? ............................................................ One way: unlike the harder sciences, we actually have on display the RESULTS of the applications of various harebrained academics theories in Economics and Politics........all failures. We don't get such experiences in the harder sciences.

Its still "ALL DEFINITIONAL." The fact that we can't understand the definitions....... doesn't change a thing.
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Re: Stupid mutants.

Postby ElectricMonk » Tue Jul 18, 2017 6:09 am

The immune system is like a museum of ancient warfare: evolution doesn't throw anything away, since the opponents can always resort to very old tricks. So we still carry bacteria-vs-bacteria weaponry with us.
Because of that, it's a terrible pick&mix of different strategies, some specific, some broad, and all working at the same time to various degrees.
The adaptive immune response is the latest "technology" in this arms-race, and it is only found in vertebrates. It brings the danger of auto-immune reactions, since an adapted antibody might mistakenly bind to host tissue and trigger an antigen response.
This is why the preimmune antibody repertoire is so critical, because the body could test it in an environment that was guaranteed to be pathogen-free ( the uterus): none of the pre-generated antibodies affect the body (unless there is a genetic defect).
If the body could generate antibodies from just any source, most of the time it would create auto-immune antibodies because no clear way to tell foreign from own biomolecules.
I've come up with a set of rules that describe our reactions to technologies:
Spoiler:
1. Anything that is in the world when you’re born is normal and ordinary and is just a natural part of the way the world works.
2. Anything that's invented between when you’re fifteen and thirty-five is new and exciting and revolutionary and you can probably get a career in it.
3. Anything invented after you're thirty-five is against the natural order of things.
- Douglas Adams

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Re: Stupid mutants.

Postby Lance Kennedy » Tue Jul 18, 2017 7:47 pm

EM

Now that you have accepted that the immune system is adaptive, we no longer have an argument.

I am still very disappointed in Nikki, though. If she had actually carefully read what I was saying, she would not have dived in to support unscientific nonsense.

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Re: Stupid mutants.

Postby Matthew Ellard » Wed Jul 19, 2017 12:53 am

bobbo_the_Pragmatist wrote: I do blame "the literature" on this for not having clear demarcations on what is actually being discussed, and failure to define terms and issues before launching into terminology and issues best understood by practitioners in the field and barely at all if not in error by the rest of us.


My gut feeling is that immunology is such a rapidly evolving body of knowledge, that expressions that meant "X" ten years ago, have evolved into a slightly different meaning that current expert users understand, but we mere mortals can't quite follow, through quickly looking things up. :D

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Re: Stupid mutants.

Postby Lance Kennedy » Wed Jul 19, 2017 2:01 am

Matthew

I could write a brief essay giving a very simplified version if you wish.

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Re: Stupid mutants.

Postby ElectricMonk » Wed Jul 19, 2017 5:01 am

An essay about immunology without the key component of the preimmune antibody repertoire?
No thanks.
I've come up with a set of rules that describe our reactions to technologies:
Spoiler:
1. Anything that is in the world when you’re born is normal and ordinary and is just a natural part of the way the world works.
2. Anything that's invented between when you’re fifteen and thirty-five is new and exciting and revolutionary and you can probably get a career in it.
3. Anything invented after you're thirty-five is against the natural order of things.
- Douglas Adams

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Re: Stupid mutants.

Postby Lance Kennedy » Wed Jul 19, 2017 5:53 am

Believe it or not, EM, but the pre immune antibody repertoire is not an essential for a basic account. You misunderstood what it meant anyway. You thought it was the final form of antibody presentation, and it is not. There is a process that follows, in which beta lymphocytes respond to antigens and begin to produce an antigen specific antibody at the rate of 2000 molecules per second. The preimmune antibody repertoire is not actually very useful once the attack on a specific pathogen is under way. Only the specific antibody to that pathogen is going to be effective.

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Re: Stupid mutants.

Postby Matthew Ellard » Wed Jul 19, 2017 6:00 am

Lance Kennedy wrote:Matthew. I could write a brief essay giving a very simplified version if you wish.

Thank you the offer. I have a rough idea how immunology works but it is better if I read what other people are saying.

Matthew's Rule No 282 : "Learn from the mistakes of other people. It reduces personal embarrassment"


I used to be the main debater in the Anti-holocaust-denial sub forum for five years and then all those bastard highly qualified historians joined. .........so I now sit, read and learn from them, without making posts anymore. It's like getting free lectures from the best universities without paying a cent. :D
Last edited by Matthew Ellard on Wed Jul 19, 2017 6:01 am, edited 1 time in total.

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Re: Stupid mutants.

Postby Nikki Nyx » Wed Jul 19, 2017 6:00 am

Lance Kennedy wrote:Yet here you were supporting a guy who claimed the immune system "could not learn ",
Meaning that EM was claiming the immune system was static and non adaptive.
The two statements are not equivalent, Lance.
The immune system cannot learn. The immune system is static and non-adaptive.
If you have a degree in biology, you certainly should know this.

The definition of "adaptation" in biology is "any alteration in the structure or function of an organism or any of its parts that results from natural selection and by which the organism becomes better fitted to survive and multiply in its environment." The definition of "learning" in biology is "an ability in organisms to use past experiences to make informed decisions for a particular situation." The immune system is adaptive, but it does not learn.

Lance Kennedy wrote:That was a big puzzle to me, and the only explanation seemed to be that you were ignorant on immunology, even if you were knowledgeable in other areas.
I'm certainly not ignorant about the human immune system after reading EM's textbook. I commend it to your attention.

Lance Kennedy wrote:In fact, EM and I arguing about the adaptability of the immune system.
No, you were not. Again, you've made an attempt to rephrase your argument so you can believe you won. But EM never once argued against adaptability in the sense of either affinity maturation or somatic hypermutation. Quite the contrary, in fact.
ElectricMonk wrote:See, the key-lock analogy is a poor one for antigen binding: it's perfectly sufficient to fit partially to get a recognition response. Then the lymphocyte can mutate it's genetic template to better fit the antigen and ramp up production of the improved antibodies.

This way, an initial E12, evolved to vaguely fit viruses/bacteria in the environment, can generate even more and up-to-date antibodies. But the basic template needs to be triggered at least partially or there will be no immune response.

And it should go without saying that even though E30 configurations are in theory possible, the overwhelmingly majority will never be generated by a foreign agent because they wouldn't fold. Others will have symetries or similar sidechains that hardly affect their three-dimensional shape and chemical properties at all.

Is this adaptive enough for you?


Lance Kennedy wrote:He posted his reference, from the immunology textbook, to back up his claim that the immune system was non adaptive.
No, Lance. This is you, again, trying to reframe EM's argument to make your reframed argument appear correct. Remember, you changed your argument from this:
Lance Kennedy wrote:Beta lymphocytes respond to the presence of novel pathogens by analysing the protein antigen, on the surface of the pathogen, and creating from new, an antibody which works on that antigen by a lock and key mechanism.

...the human genome CANNOT contain enough antibodies to cope with them all.

...the human immune system creates antibodies 'on order ' to deal with novel pathogens.
...to this:
Lance Kennedy wrote:Antibodies are adaptive to need, and modified to suit the antigen. That is what I have been saying.
...and pretended it had been your argument all along. Unfortunately, you then went back to this:
Lance Kennedy wrote:The antigen comes first before the antibody that is specific to that antigen.
...your original argument. However, even your rephrased argument is wrong. Antibodies are not "modified to suit the antigen." Various mutations occur in both heavy-chain and light-chain V-region coding sequences, but only a small number of these mutated antigen-receptors actually have increased affinity for the antigen. Repeated stimulation by the antigen means they survive and proliferate. It's natural selection...adaptation. NOT "learning."

Lance Kennedy wrote:When I argued against that, I was not suggesting that the textbook was wrong. I was telling EM that his interpretation was wrong.
I don't believe you've read it. If you had, you'd see there's nothing to interpret. It's written in fairly straightforward language. I have read it, and EM's paraphrasing is spot on.

Lance Kennedy wrote:When you weighed in to support the idiotic argument, I had to assume you were also going with a wrong interpretation.
Why don't you just go read the entire chapter for yourself? It's not a character failing to be wrong, you know. I was wrong in another thread earlier today, and Gord corrected me, for which I thanked him. I bloody hate being wrong, but I'll absolutely admit it when I am. OTOH, when I'm not, wild horses couldn't drag me away.

Lance Kennedy wrote:The pre immune antibody repertoire was used by EM to suggest that no adjustment to antibody structure and number was needed.
It absolutely was not. See my quote from EM above.

Lance Kennedy wrote:If you are happy to support my original contention that the immune system is dynamic and adaptive, then we probably have no argument. Just misunderstandings.
That was not your original contention, and your definition of "adaptive" is still wrong.

This is my argument:
The immune system has a preimmune antibody repertoire of more than 1012 different antibody molecules. This repertoire is large enough to ensure that there will be an antigen-binding site to fit almost any potential antigenic determinant, with an affinity sufficient for successful binding of the antigen to its matching receptor on a B cell. Clonal Selection Theory mandates that B cells are monospecific. That is to say, all the antibodies produced by a particular B cell will have identical antigen-binding sites.

B cells begin their antibody-manufacturing lives by synthesizing IgM molecules and inserting them into the plasma membrane as antigen-receptors. After B cells leave the bone marrow, they make both IgM and IgD molecules as antigen-receptors, both with the same antigen specificity. At this point, prior to antigen stimulation, antibodies are membrane-bound. This is possible because each antibody molecule has a hydrophobic C-terminus on the heavy chain, which anchors it in the lipid bilayer of the B cell's plasma membrane.

When activated by an antigen and stimulated by helper T cells, the primary immune response begins. Some B cells are activated to secrete IgM antibodies. A secreted antibody molecule has a hydrophilic C-terminus on the heavy chain, thus allowing it to escape the B cell.

During the secondary immune response, many B cells to switch to making IgG, IgE, or IgA antibodies, generating both memory cells that express the corresponding classes of antibody molecules on their surface (still with the same antigen specificity) and effector cells that secrete the antibodies. It is when B cells are stimulated to generate memory cells that somatic hypermutation occurs: one mutation per V-region coding sequence per cell generation (about a million times greater than the spontaneous mutation rate in other genes). This accumulation of mutations is known as affinity maturation because, over time, it produces a progressively increasing affinity of the antibodies produced against the antigen. Only a minority of B cells will have increased affinity, and they are preferentially stimulated by the antigen to survive and proliferate. Most of the rest die by apoptosis, a form of programmed cellular suicide, so to speak.
EM, would you please check me and correct me if I've erred?

Lance, if you are "happy to support" this, which is a more in-depth explanation of EM's argument and my original contention as based on the textbook, then I'm happy to end this discussion. If not, you'd better start presenting some in-context evidence with links for the immune system's ability to "learn."
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
—Lazarus Long, from Time Enough for Love, by Robert A. Heinlein

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Re: Stupid mutants.

Postby Nikki Nyx » Wed Jul 19, 2017 6:03 am

bobbo_the_Pragmatist wrote:All anyone actually interested in this subject needs to do is: DEFINE "adaption" as it applies to the immune system.
I just did in my latest post. I defined both "adaptation" and "learning" as they are used in biology.
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
—Lazarus Long, from Time Enough for Love, by Robert A. Heinlein

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Re: Stupid mutants.

Postby Nikki Nyx » Wed Jul 19, 2017 6:06 am

Matthew Ellard wrote:
bobbo_the_Pragmatist wrote:All anyone actually interested in this subject needs to do is: DEFINE "adaption" as it applies to the immune system.
I was going to join this thread and show off my pure genius.......I then started to look at immunology papers for the first time.......I then ran away like buggery. :D

This is a really really really hard topic and I'm going to show off my genius by not touching this topic with a ten foot pole. It's simply beyond my brain power.

(I think you would need to be an expert across many other fields before you even thought about dabbling in immunology)
:D

It is a difficult topic, but EM's textbook is well-written and not difficult to read. Unfortunately, it's not browsable, but it is searchable.
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
—Lazarus Long, from Time Enough for Love, by Robert A. Heinlein

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Re: Stupid mutants.

Postby Nikki Nyx » Wed Jul 19, 2017 6:09 am

ElectricMonk wrote:An essay about immunology without the key component of the preimmune antibody repertoire?
No thanks.

He still has it wrong six ways from Sunday. Maybe if he actually, I don't know, read the textbook? :roll:
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
—Lazarus Long, from Time Enough for Love, by Robert A. Heinlein

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Re: Stupid mutants.

Postby Lance Kennedy » Wed Jul 19, 2017 6:16 am

Nikki

Quoting verbatim from a textbook is not an argument. A sign that someone understands a subject is that they are able to paraphrase it. You have shown no sign of such understanding.

And once more you got my position wrong. And yes, EM, was definitely arguing that the immune system was non adaptive. You would know this if you had properly read the thread. The whole reason he quoted that textbook was to use the concept of the preimmune antibody repertoire to suggest that the immune system did not have to change.

By the way, the word 'adaptive ' has a range of meanings depending on context, as my degree in biology has informed me. I am still seriously disappointed in you. Why does a smart woman support EM's scientific bull-shit?

If you had actually read EMs comments you would realise that he truly meant that the immune system was non adaptive. If you had actually read my comments, you would realise that I had not denied that textbook. My actual comments were that EM had misinterpreted what it said, not that it was wrong.

And as far as antibody modification is concerned, of course they are bloody modified. The fact that the modification is of the population of antibodies rather than one at a time does not change the fact that the antibodies are modified to suit the antigens. Sheesh!

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Re: Stupid mutants.

Postby ElectricMonk » Wed Jul 19, 2017 7:32 am

Lance, stop hiding the goalposts by stuffing them up your arse.
The textbook is the best knowledge, and you don't have to argue about it, you just have to accept it or provide more up-to-date alternatives. How can I misinterpret it when I quote verbatim, but you are right without mentioning the text even once?

The preimmune antibody repertoire is the ONLY critical thing in the entire process, which is why it is much older, evolutionarily speaking, than its sub-system, refinement via hypermutaion: only vertebrates have the latter, but all animals have the former. It is basic evolution that organisms genetically adapt to pathogens, and the pre-immune repertoire IS that adaption - without it, you have no way to inherit resistances across generations.

You simply have no clue of molecular biology if you think it is possible for an organism to generate a "mold" from any "key", and no true grasp of immunology, either:
- how does the body know which bit is human and which is not? Do they have labels on them that an antigen could read?
- why wouldn't antigens of a kind trigger ALL lymphocytes at the same time, if they all could respond to it?
- how, exactly, can the lymphocyte even "catch" the antigen, if it can't specifically bind it?`
- and why can't some ethinc groups make antibodies against (for them) novel diseases?

Your explanation of "adaption is enough" fails on so many levels, and your best argument is E30, which we all know is based on cheap maths, not biology.

Why TF don't you ask your class-mates or professors instead of trying to twist Nikki's or my words in a futile attempt to save face?
Until you accept the pre-natal genetic antibody generation as the central feature of the specific immune system, you are simply wrong.
I've come up with a set of rules that describe our reactions to technologies:
Spoiler:
1. Anything that is in the world when you’re born is normal and ordinary and is just a natural part of the way the world works.
2. Anything that's invented between when you’re fifteen and thirty-five is new and exciting and revolutionary and you can probably get a career in it.
3. Anything invented after you're thirty-five is against the natural order of things.
- Douglas Adams

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Re: Stupid mutants.

Postby Lance Kennedy » Wed Jul 19, 2017 9:36 am

EM

Stop telling lies.

I have not ONCE argued against the textbook. I have told you that you misunderstood what it was saying, which is true.

The preimmune antibody repertoire is not what actually does the job of dealing with pathogens. It is a start, but it is not till the beta lymphocytes undergo modification and selection , leaving those lymphocytes that produce the antibodies specific to the antigens on the problem pathogen as the majority, that the disease is effectively dealt with.

Mostly an individual does NOT inherit resistant to disease across generations. That is true only for a small set of illnesses. For most illnesses, resistance is developed AFTER the pathogen invades. If we inherited widespread resistance, we would never get sick. The lack of pre existing resistance is why we need vaccines, for Finagles sake ! I am immune to measles because I caught the disease as a child. Not because I inherited it across generations.

Hypermutation occurs at the antigen binding sites on the antibodies. Do you actually understand what this means ? I seriously doubt it

How does the body know which is human and which is not ? The fact that you ask this question means you do not know the answer. The answer is that the antibodies 'recognise ' certain sequences of amino acids, which are human. It is alien sequences which are recognised as non human. They do not adapt to human sequences, and thus do not form antibodies against those proteins (except in certain auto immune illnesses).

Why do not all lymphocytes respond ? In fact, all beta lymphocytes of the correct type do. They undergo change after contact with an antigen. This happens due to the movement of the beta lymphocytes in the body, which causes them by normal motion, to bounce off everything around them. When they contact a pathogen, they react to the antigen. It does not "catch " the antigen till it has formed suitable antibodies.

Why can some ethnic groups not respond to certain diseases ? I have not researched this point. I will just say that they do respond. Just not as quickly, which can lead to tragic results, like African children not responding quickly enough to the measles virus and dying. The genetic differences that lead to slower responses I cannot comment on.

Why don't you stick to discussing something you know about.

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Re: Stupid mutants.

Postby ElectricMonk » Wed Jul 19, 2017 10:20 am

Lance Kennedy wrote:How does the body know which is human and which is not ? The fact that you ask this question means you do not know the answer. The answer is that the antibodies 'recognise ' certain sequences of amino acids, which are human. It is alien sequences which are recognised as non human. They do not adapt to human sequences, and thus do not form antibodies against those proteins (except in certain auto immune illnesses).


This is no answer at all.
The question is:
HOW do they know?
WHEN did they learn?
WHY don't they adapt to human sequences?
Do antibodies have a look-up table installed?


you are big at claiming to explain things, but then don't. You haven't thought this through, and it is obvious in all of your posts. You just regurgitate Kindergarten-level immunology without actual understanding that biomolecules aren't small robots.


Lance Kennedy wrote:Why do not all lymphocytes respond ? In fact, all beta lymphocytes of the correct type do. They undergo change after contact with an antigen. This happens due to the movement of the beta lymphocytes in the body, which causes them by normal motion, to bounce off everything around them. When they contact a pathogen, they react to the antigen. It does not "catch " the antigen till it has formed suitable antibodies.


what do you means by "correct type" ?
Also, you know {!#%@} about a little thing called "binding affinity".
Bounce around the body but stick for no reason to lymphocyctes?
Good Grief!
You are totally clueless.

Please, just please pick up an introduction textbook on biology....
Last edited by ElectricMonk on Wed Jul 19, 2017 4:41 pm, edited 2 times in total.
I've come up with a set of rules that describe our reactions to technologies:
Spoiler:
1. Anything that is in the world when you’re born is normal and ordinary and is just a natural part of the way the world works.
2. Anything that's invented between when you’re fifteen and thirty-five is new and exciting and revolutionary and you can probably get a career in it.
3. Anything invented after you're thirty-five is against the natural order of things.
- Douglas Adams


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