Evolution and the Human Immune System

Introducing a new topic here...Do any of you creationists out there know how the human immune system works? Any takers? The number of variants of bacteria out there are staggering. Since to create a specific protein requires a specific DNA sequence, how on earth could any animal at all possibly be able to produce proteins designed to selectively bond to these incredibly varied bacterial surfaces? Only about 1,000 active genes had the possibility of being involved in the process, and yet there are countless antibodies that our body can produce.This was a long standing question in the scientific community, and was finally solved by Susumu Tonegawa, leading to a Nobel Prize in 1987. He discovered that not all of the genes in a person's body are identical, at least when it comes to lymphocytes. When a lymphocyte is produced, it randomly activates one element in each of six "families" of genes.Now, if you were to inject a mouse with a specific antigen, and were to sample the DNA of its different B lymphocytes, you would find that none of them produce an antibody that has much of an affinity to the antigen. However, if you kept taking regular samples, you would find that the cells' DNA in this region steadily converges on a specific pattern. The changes in the DNA (and consequently, the antibody) steadily decrease, until the body is left with as near-perfect of an antibody for bonding to the specific antigen as possible - and that antibody is being produced en masse. In fact, if you follow the progression of the DNA, it follows a "family tree" structure, with branches and inheritance, that steadily migrates towards fitness for bonding to the antigen.What could be causing this? It turns out that at specific stages in their lifecycle, B lymphocytes increase the mutation rate of specific genes by more than 1000-fold ("hypermutation"). In the body, when the lymphocites produce an antibody that can bond, even weakly, to an antigen, they begin to produce large numbers of antibodies and to multiply quickly; this suppresses the production and multiplication of other types of B lymphocytes. The better the bond, the faster they multiply and produce antibodies (and thus, suppress the less effective lymphocytes more). However, with their rapid mutation rate, many of their copies have the antibody that they're producing slightly vary. This reshapes and restructures the protein by small amounts in different places. Most of these changes make it bond worse than the original, but a few will bond better. These in turn produce more antibodies and reproduce more quickly, and suppress their poorer competitors.This discovery has enabled much of the progress that has been seen in medical research involving the immune system in the past few decades.Oh, but my mistake - natural selection can't work... Right?------------------
"Illuminant light,
illuminate me."

quote:

---

Natural selection has long been an important feature of the creation model (as has allopatric speciation), and in fact was proposed by a creationist several years before Darwin (we suspect he 'borrowed' the idea from Blyth).

---

Well, seing as most scientists were creationists then, that's no real shock Nonetheless, I have seen many creationists try and argue against natural selection. It's good for you that you accept it.

quote:

---

Since NS can only work with pre-existing genes, NS generally promotes loss of genetic information; the evolutionary model on the other hand argues that NS is capable of promoting genetic information gain over time.

---

Are you trying to change this into a discussion about "information" as opposed to natural selection?

quote:

---

Rei, through your lens you see evolution, through my lens I see incredible design. How did such a complex program evolve?

---

Incredibly simply. The more possible genes that can be selected from in each family of genes, the better the organism can fight off disease. Likewise, the more families there are, the better. There are many sequences in DNA which are quite clearly analogues of each other, cut and shifted up or down the chromosome - a good example is the piece of DNA that contains the genes for red and green color vision, for which not only the gene, but the whole section of DNA around it is nearly identical except for scattered mutations (which, on the gene, change the target wavelength for the cone). There are rare cases in which there is yet another copy - a third copy - which codes for yet another wavelength, and people with this tend to have a very slightly better ability to distinguish colors in the red/green range. Note that the gene for recognizing blue is unrelated.If possible proteins to select from in developing immunity were duplicated, and then slight mutations occurred, the proteins would fold and bond differently with different antigens, and provide a distinct advantage in the number of possibilities.In the original case, you have a simple multicellular organism, perhaps something no larger than daphnia, running into the problem that bacteria are able to out-adapt them due to their faster reproductive rate. We'll look at a starting timeframe here in which the organism has only the basic ability to code for a simple set of antibody proteins, and reproduces from the possibilities based on how well they're bonding (we can go back further if you want). The organism would have trouble still at keeping up with bacteria - there's only so many cell receptors that they can have to test how well each antibody that they have the ability to code for bonds to an antigen, only so much DNA that they can have for producing the proteins, etc. But, if one of these simple creatures, due to a mutation, began coding for a slight mutagen that targets that region of the DNA, it would immediately gain an advantage for at least increasing how different the immune systems of the child organisms were from their parents. Stronger, more targetted mutagens, and mutagens which are produced more often when antigens are more common, are in turn more likely to be selected. If another protein develops that even slightly changes the cell's reproductive timing based on how good of a bond its antibodies are getting with the antigen - even through throwing off one of the cell's many timing feedback mechanisms - the cell can reproduce more quickly. A similar development can occur for the level of antibody production. And yet another similar development can occur for apoptosis of ineffective lymphocytes.Note that none of these stages need to have multiples steps occur at the same time. In fact, it is fairly irrelevant as to what order these steps go in, or if they're simultaneous. And, you'll note, no step requires a *particular* mutation. There are many, many ways each feedback system could be altered. Lastly, the first "step" in each stage needs to only have a slight effect, which is, through natural selection (which you accept the occurrance of), made more common.------------------
"Illuminant light,
illuminate me."

quote:

---

I must say, that was one grandiose tale! This is called a just-so story.

---

Hey now, that's completely unfair. You presented the situation as if it were impossible. I quite clearly demonstrated a lineage in which an organism with an immune system that cannot do this mutation/selection of genes gets to one which can. Then you criticize me for a "grandiose tale"!No more childishness. If you wish to defend your argument, you need to explain what is unreasonable about the line of progression presented occurring. And again, if your argument sums up to "there are other ways it coud have occurred than this", then you're actually helping my case. So, please explain what is flawed with this.

quote:

---

Do you know how many different antigens there are out there? That is the reason for the ingenious design of the immune system to handle a number far greater than the number of proteins that can be programmed for them in the DNA. In your example, the odds of extinction would be astronomical but you conveniently ignore this.

---

My god, did you completely ignore my post? Please, answer honestly. Because I just showed that *any* improvement in the number of antibodies that the organism can produce increases the odds of survival. Now, I ask a direct question:Do you acknowledge that any increase in the number of antibodies that the organism can produce increases its odds for survival?From there, I went on to discuss how a mutagen that effects this region of the organism's genetics increases the variance in the population when it comes to resistance to organisms, without raising the overall mutation rate and thus risking genes that have been working well and should be mutating at a much lower rate.Do you acknowledge that it would be an advantage to increase the diversity in the population when it comes to the ability to resist diseases, even if each organism can only produce the same total number of antibodies?From there, I went on to discuss how if that mutagen became more targetted and more powerful through successive changes to the protein, that's advantageous compared to a poorly targetted weak mutagen.Do you acknowledge this?(I can keep on going... in short - at what stage do you claim that there would be a problem with this line of progression?)I want serious debate, not your hand-waving dismissals. And you can say "it's been debated" all that you want, however, I have not seen any refutation for this line of progression conducted. Point me to one, do it yourself, or acknowledge that the evolution of this system is quite possible.------------------
"Illuminant light,
illuminate me."

Judge:If you'll recall, not once did I say that no creationist believes in natural selection. I never once attempted to set up a straw man. You, however, by implying that I did, are setting up a straw man, and I don't appreciate it.Regardless of your opinions, many of your ideological peers do not believe in it.------------------
"Illuminant light,
illuminate me."

Of course ------------------
"Illuminant light,
illuminate me."

1) didn't even come close to addressing my original challengeYour original challenge was how such a mechanism could evolve. I presented a possible mechanism. It is impossible to show the *EXACT* mechanism that was used long ago, just like you can't show the design that Noah would have used in building the ark. Don't be ridiculous.2) you provided no evidence to back your tailAgain, I presented *a possibility*. If you claim that a single element of that possibility that I proposed is impossible - say so, or concede the point. You go off on this incredulity about how such a system could evolve, and then when I show a mechanism, you *fail to challenge it* beyond asking me to prove that this *was the exact mechanism*.you did not provide a mathematical explanationProvide a mathematical explanation for a tree germinating from a seed.It follows known chemical processes, certainly - but, unfortunately, mathematics is essentially possible in complex systems. Even the weather, which largely works in bulk operations (instead of fast, tiny reactions) becomes near impossible to predict after a few days.

quote:

---

something like "so-and-so- study showed that such a step-wise process, given condictions x,y,z....

---

You're asking for studies on precise chemical pathways which don't exist any more. You know very well that what you're asking for is impossible. We know how genes work. We know how mutations in genes work. We know that mutations in genes can alter proteins. We know that genes can be duplicated. That is all that is needed for what I suggested. We know that it is possible to have an immune system of the kind that we currently have. I'm sure you wouldn't argue the claim that it's possible to have an immune system which only has a preset number of antibodies that it can produce, but that such an organism with an immune system like that would have to be one that reproduces very quickly if it is to adapt at the same speed as bacteria. My argument doesn't require anything more complex than this.So, in short, please answer what I've been trying to get you to answer the whole time: Name A Part That You're Claiming Is Impossible, And Explain Why. Argument from incredulity always ticks me off, it's like talking to a brick wall.

quote:

---

"if a cow gets a good running start, and if it leaps successfully, it could jump over the moon...now Fred, don't you at least agree a cow can get better jump if it has a running start?"...

---

And if I had asked you that, would the proper thing for you to do be:
a) Incredulity
b) Respond with something to the effect of "the amount of energy needed to move a 1,000kg mass over the moon is X joules, which would be more than all of the energy in the chemical bonds of a cow."
c) Any other argument similar to (b)(here's a hint: the answer is either (b) or (c)).

quote:

---

And again? I *never offered* an alternative scenario

---

You don't get it. You're trying to claim that because there's no way to know the *specific* chemical pathways that were taken, than it's just hand-waving to suggest a possibility. But that's ludicrous; that's like, if you said "a person can't travel across the country in a week", and I said, "well, a person could get into a vehicle of some kind, and then either navigate it themselves or have someone else navigate it, and end up here in a week", and you got all incredulous by saying "You don't even know this person!". What I'm presenting is a possible method - now, please:-- Either Discuss Why You Feel That The Method That I Proposed Couldn't Happen, Or Concede That It Could. --

quote:

---

Yes.

---

So, you are acknowledging those first two points? Good. Now where do you claim that the possibility becomes impossible?

quote:

---

Do you acknowledge you have not provided any evidence or mathematical model to defend this claim?

---

1) I have provided a model. I have not provided a mathematical model - because this is not a mathematics problem. How would you feel if I asked you to present a mathematical model for the process of writing an essay on George Washington?2) I would love to be able to defend my claim, but you *haven't challenged a specific part of it yet*. That's what I'm trying to get you to do. And again, remember that the claim isn't that this is the specifics of how it happened - the claim is that this is a *possibility*. Refer back to the "person travelling cross-country" analogy.

quote:

---

Do you acknowledge that in the very least a beneficial mutation would be extremely rare?

---

Now we're getting somewhere. Yes. Do you acknowledge that there are about 5e30 prokaryotes on Earth? If we're dealing with a creature that is, say, 1000 times more massive than a simple bacteria, and assuming a ^2 reduction in population, that's still 5e24 of creatures the size that we're talking about here.Also, do you acknowledge that evolutionists accept a period of several billion years of development? Let's just assume for the sake of argument that we're talking about 100 million years of time, and that a creature of this size reproduces 100 times per year. That's 5e34 generations for what I proposed to evolve. *However*, this is the population of *adults* involved - remember that for later.

quote:

---

Do you acknowledge that even when one occurs there is still no better than 1 in 50 chance it will survive in the population, even given a high selective value of .1%?

---

I don't really get that statement of yours. You cite a number for the "selective value" (?) that is one in a thousand, and then say 1 in 50. I assume you mean "survive until reproductive age". A stable population of daphnia (an example modern species of about the size we're discussing) produces about 1000 eggs that hatch. In a stable population, that means about a 1 in 1000 chance of surviving to maturity if all offspring are equally fit. However, this also introduces 1000 brand new trials - it's 1000 times as likely that a given beneficial adaptation will occur. In short, while each organism competing with its siblings reduces its chance of making it to adulthood, the fact that there are so many siblings increases the likelyhood of a successful adaptation by the same amount.Do you accept the numbers? If not, which part do you challenge?

quote:

---

Do you acknowledge there is a speed limit on how soon such a mutation can fixate (related to the pop frequency at the time of mutation)?

---

"Fixate" according to the "pop frequency"? You're going to have to clarify yourself on that one. Perhaps you mean how quickly each trait can spread through the population as a whole? Well, thanks to sexual reproduction and the sharing of genes (another topic for debate, I'm sure, but out of scope of this one), the answer is "quite quickly". Since aquatic organisms have relatively little of a natural barrier to deal with, it would simply radiate outward. Given how quickly invasive species spread when *they* get to a habitat that they find easier to survive in than the native species, and thanks to oceanic conveyer belts which move quite quickly, I'd be surprised if it took more than a few decades to spread across all of the world's oceans - a blink of an eye by evolutionary standards.Your disagreement with this? (as specific of complaints as possible, please)

quote:

---

Given these facts, do you grant that your response was a just-so story

---

Not at all. And I encourage you to respond to what I posed above.

quote:

---

How does the immune program itself evolve?

---

I just showed you how the immune system evolves. What do you mean by "program"? Each mutation is a change in the DNA. If you are defining the DNA to be a "program", then the answer is right in front of you - if the stages that I described happen, then the "program" is evolved.

quote:

---

Can you explain how the whole antivody variable/constant region and hypermutation process that can pump out voluminous combinations of antibodies can evolve in a stepwise fashion?

---

If you read what I wrote, I listed it in steps, and no step was any sort of a jump, and most steps could occur in paralell. Mutagens exist. Duplication of genes with alteration occurs. A copied, but altered mutagen starts affecting the general region of the DNA in lymphocytes which is responsible for immune activity. Instant advantage: While the antibodies produced don't change real-time, the population becomes more diverse in the realm of antibody production, without damaging genes that need to be more stable. The production of the mutagen becomes tied in with the level of antigens in its environment. Instant advantage: the mutation is done when it is needed the most. Good binding of the cell's antibody activates the genes for reproduction. Instant advantage: Effective lymphocytes reproduce more often. The mutagen becomes more targetted at modifying only specific parts of the gene that activates the production of antibodies, causing it to activate production of the protein from multiple, separated segments of the DNA. Instant advantage: like the modern system.Now, can you explain why something along these lines *wouldn't* occur in 5e34 generations? I didn't count steps, but I'd imagine I listed around 5-10 steps - which means it has around 5e33 to 10e34 generations per step to make each one happen.

quote:

---

Evolution differs from a frog-to-prince fairytale only in the millions of years that were added to the story

---

I'll be the better person and not make an allusion to your invisible friend that lives in the sky, and simply comment on the fact that in the real-world case, the frog is breeding, and each of its offspring are slightly different from the last, moving into different niches, needing to adapt to those niches... and it's several hundred million years between amphibians and primates. ------------------
"Illuminant light,
illuminate me."