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Author Topic:   Reduction of Alleles by Natural Selection (Faith and ZenMonkey Only)
Blue Jay
Member (Idle past 2698 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 36 of 87 (554463)
04-08-2010 12:25 PM
Reply to: Message 33 by Faith
04-08-2010 12:06 AM


Re: You can't make a healthy allele out of a sick mutation
Hi, Faith.
I don’t really pay that much attention to subtitles (except when I want to write one of my own), and I rarely (if ever) respond to them.
Faith writes:
I have no problem at all understanding the difference between the mechanism of mutation and the product...
...Simple traits such as eye color and hair color and body type come from normal genes; genetic diseases come from diseased genes...
... If you are insisting on equating disease with health and that I accept this as proof that mutations produce alleles, I'm very sorry, I consider this to be a staggeringly glaring case of where science goes wrong.
See, this shows that, despite your claims, you do not understand the difference between mechanism and phenotype.
Diseases and handicaps are phenotypes: it has not been demonstrated that such a thing as a diseased gene or diseased allele exists. For this reason, intellectual honesty requires scientists to disregard the notion of diseased genes until somebody steps up and shows that this is actually a meaningful way to categorize genes.
Until such time as diseased genes are shown to be meaningfully distinguished from normal genes on grounds other than phenotype, you are making the same error you have been harping on evolutionists for making: that is, you are claiming to be talking about genotype, when, in fact, you are only talking about phenotype.
-----
Faith writes:
Bluejay writes:
(1) Demonstrate that mutations create new alleles.
(2) Observe that no other means of creating alleles has been demonstrated.
(3) Disregard these undemonstrated means of creating alleles.
(4) Conclude that, to the best of our knowledge, all alleles come from mutations.
You really think I've been missing this obvious progression of how you all think?
Yes, Faith, I do think you have been, and still are, missing it. And, you proved it when you wrote the very next sentence:
Faith writes:
It is the ToE that leads you to even have to have a means of creating alleles.
When you write stuff like this, what choice do I have but to conclude that you completely missed this obvious progression of how we all think?
Even under creationism, there would need to be a means of creating alleles.
Otherwise, how did any of us ever end up possessing alleles?
The creationist means of creating alleles is whatever design process was used by the Designer.
Because no such process has been demonstrated to exist, scientists are required to exclude it from our models. If you want it to be considered in scientific models, demonstrate that it exists.
In science, we can only use those means of creating alleles that have been demonstrated to exist, and, so far, mutation is all we’ve got. We are literally---literally---out of options, Faith. We don’t really have a choice but to conclude that mutations are all there is. In religion, we have the luxury of tossing around indemonstrable processes, but the standards in science are such that we can only base our models on things we can demonstrate.
This is why it is up to you, the person who thinks some other means of creating alleles needs to be invoked, to demonstrate that mutation cannot explain normal or beneficial alleles, or to demonstrate that this other means of creating alleles actually exists.
-----
Faith writes:
AND none of this in any way justifies calling it FACT. It's all still an unconfirmed hypothesis at best. To call it FACT is really to commit a fraud.
I think these are the first two times the word fact has appeared in this conversation.
There is no use throwing around libel about fraud when the conditions you cite for fraud have not been met and show no indication of being met in the near future.

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
 Message 33 by Faith, posted 04-08-2010 12:06 AM Faith has replied

Replies to this message:
 Message 37 by Faith, posted 04-08-2010 1:17 PM Blue Jay has replied
 Message 38 by Faith, posted 04-08-2010 7:13 PM Blue Jay has not replied

  
Blue Jay
Member (Idle past 2698 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 39 of 87 (554629)
04-09-2010 11:13 AM
Reply to: Message 37 by Faith
04-08-2010 1:17 PM


Re: You can't make a healthy allele out of a sick mutation
Hi, Faith.
Faith writes:
Why is it so hard to come up with a real example of an actual mutation you can point to that produces a genuine normal trait in the organism?
As long as you believe that there are such things as diseased genes, this will not help you. It would be a bit like casting my pearls before swine.
I’m trying to dispel your notion that disease is genotypic, and not just phenotypic. I thought the best way to do this was to appeal to something we both agreed on (i.e. neutral mutations, which are clearly not pathogenic, but are of the same kind as deleterious mutations).
But, since that's not going to work, I present you with a beneficial mutation: here and, for good measure, here.
These papers were done in 1991 and 1989, respectively. They document the genotypes and phenotypes of, collectively, 26 mutations to the gyrA and gyrB genes that confer resistance to a type of antibacterial drug called quinolone. All were confirmed as mutations, because they were induced in populations of bacteria whose genotype for the gene in question was known beforehand.
If mutation is a pathological process, common sense should tell us that it cannot possibly produce something that is useful to an organism. Yet, I just presented 26 examples of proven, documented mutations that confer a beneficial phenotype on bacteria (13 each from two different genes).
-----
I’m sure Wounded King or some other geneticist could provide a longer litany of these.
You should concede the point that mutations are relevant to your model, given that I have demonstrated that beneficial mutations exist, and have demonstrated the massive potential for new mutations to have been introduced into a growing population, such as the northern elephant seal.
If you do, we can then proceed to discuss the implications of this for your model of bottleneck speciation.
Edited by Bluejay, : Edited content for civility, as per Admin's request. My apologies.

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
 Message 37 by Faith, posted 04-08-2010 1:17 PM Faith has replied

Replies to this message:
 Message 41 by Faith, posted 04-10-2010 5:26 AM Blue Jay has not replied
 Message 42 by Faith, posted 04-10-2010 3:20 PM Blue Jay has replied

  
Blue Jay
Member (Idle past 2698 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 43 of 87 (554877)
04-10-2010 5:14 PM
Reply to: Message 42 by Faith
04-10-2010 3:20 PM


Re: You can't make a healthy allele out of a sick mutation
Hi, Faith.
Faith writes:
I asked a long time ago that bacteria not be used in this discussion...
What reason could you possibly have for making that request?
If bacteria prove my point, I'm going to use them. I see no reason to agree to such arbitrary conditions.
-----
Faith writes:
I doubt that example is of a mutation that produced an allele, but probably just knocked out another allele.
How can you say this? The papers I cited even identify the sequences of the new alleles!
By definition, a new allele replaces an old one when a mutation occurs: this is because all mutations are alterations to old alleles. So, in "knocking out" an allele, these mutations produced a new allele.
You cannot deny that this created a new allele, and you cannot deny that it had a beneficial effect for the organism. Both of these are documented, observed facts. And, in this case, I used the word "fact" intentionally, because these are things that have been witnessed directly.
You are now officially denying facts.
----
Faith writes:
Bluejay writes:
I thought the best way to do this was to appeal to something we both agreed on (i.e. neutral mutations, which are clearly not pathogenic, but are of the same kind as deleterious mutations).
Perhaps you misspoke? Deleterious does mean pathogenic.
No, you misunderstood it.
"Deleterious" is not a kind of mutation: it is a kind of phenotype.
Kinds of mutation are, for example, substitution, insertion, deletion, etc.
Substitution-type mutations (such as those in the papers I cited) can produce deleterious, neutral and beneficial phenotypes.
-----
Faith writes:
But if you will, then in my accepting for the sake of argument that mutations produce alleles, how about if you now give me some numbers to work with: Just how many new alleles should I have to take into account and at what point(s) in the life cycle? Not math, just numbers.
I already provided the numbers: 0.6 new alleles per individual, at the moment the individual is born.

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
 Message 42 by Faith, posted 04-10-2010 3:20 PM Faith has replied

Replies to this message:
 Message 45 by Faith, posted 04-10-2010 5:29 PM Blue Jay has replied

  
Blue Jay
Member (Idle past 2698 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 47 of 87 (554898)
04-10-2010 7:34 PM
Reply to: Message 45 by Faith
04-10-2010 5:29 PM


The men who witnessed evolution
Hi, Faith.
Faith writes:
Just because you see a series of codons in the place where an allele should be does NOT mean it's a functioning allele. It may simply be gobbledygook, and it MAY simply have knocked out a functioning allele that was sensitive to the antibiotic, thus providing the resistance. This is NOT proof of mutations making viable alleles!
Here is a link to the first abstract again (Hallet and Maxwell 1991).
Let me review what they did:
  1. Acquired a colony of bacteria with known genotype for the gyrA gene. This bacterium is known to be susceptible to to the antibacterial quinolone.
  2. Induced random misrepair mutations in the gyrA gene.
  3. Applied quinolone to the colony.
  4. Discovered that some of the bacteria were not killed by the quinolone.
  5. Sequenced the gyrA gene of some of the bacteria that survived the quinolone.
  6. Discovered that one resistant bacterium had a gyrA genotype that was different from the original colony’s genotype (where the original genotype’s 317th nucleotide was an A, the resistant genotype’s 317th nucleotide was a G)
  7. Discovered that the protein produced by the mutant allele was also different from the original protein of the colony.
  8. Isolated the gyrase protein that was produced by the mutant gyrA allele
  9. Tested the function of this protein under varying levels of quinolone.
  10. Discovered that the mutant protein could tolerate 10 times more quinolone than the original protein, and still function properly.
They saw a beneficial new phenotype, and demonstrated that it correlated with a change in a nucleotide, a change to the protein made by the mutant gene, and an improvement in function over the wild-type protein. They demonstrated that an undirected mutation, a mistake---a disease process, as you like to call it---can produce a product that outperforms what you would call a "normal allele.
In this case, the mutation involved was changing an A to a G. This can be classified as a point mutation, also called a substitution, and, more specifically, as a transition. In other cases---this one, for example*--- it has been shown that changing an A into a G can cause a loss of functionality or some other deleterious effect.
*I think this one is free for the public to access. Scroll down to the Results section, Molecular Genetics Analysis subsection, and you’ll see that 3 of 5 mitochondrial myopathy patients had adenine-to-guanine (A-to-G) mutations that caused the disease.
This is what I mean when I say that mechanism and phenotype are different: the same mechanism of mutation can result in either deleterious, neutral or beneficial phenotypes in different cases. There is no diseased process involved: it is just a process of change, and disease is only one of several possible outcomes.
Edited by Bluejay, : opening quote mark around "normal"

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
 Message 45 by Faith, posted 04-10-2010 5:29 PM Faith has replied

Replies to this message:
 Message 49 by Faith, posted 04-10-2010 9:03 PM Blue Jay has replied

  
Blue Jay
Member (Idle past 2698 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(2)
Message 50 of 87 (554917)
04-10-2010 9:11 PM
Reply to: Message 45 by Faith
04-10-2010 5:29 PM


Loose Ends
Hi, Faith.
I didn't address that entire post in my last response, because I didn't want that response (which I consider more important) to become too cluttered with other things.
Still, I'd like to address a few other comments you made in your last couple of posts. This is kind of scrambled mishmash of stuff that loosely ties in with the topic. You can completely disregard this post if you don't feel like responding to it.
Faith writes:
YOU are... possibly not playing with a full deck yourself.
I think you're mistaken, but I certainly won't deny it outright.
-----
Faith writes:
Thirteen mutations to a SINGLE gene? Two genes with 26? What kind of "mutation" could that possibly be? What sort of random process changes the same gene thirteen times all toward the same result and another at the same rate yet? Something very weird about this idea. Sorry, this gets curiouser and curiouser. It may superficially look like a mutation but anything that behaves with such consistency has to be built into the organism somehow or other. No way I can concede anything with such a strange example.
They were only able to report beneficial mutants because their method for determining whether beneficial mutations happened was to apply a lethal substance and see if any bacteria could survive it. So, all the deleterious and neutral mutants perished during the process. There were probably a good number of non-beneficial mutations in the pool, as well, but we’ll never know that for sure, because they’re all dead.
-----
Faith writes:
"Deleterious" used to desribe the phenotype is new to me, but whether it can be used that way or not, the word is CERTAINLY used to describe mutations...
As I just explained, when one says "deleterious mutation," one is not saying that the process that produced the mutation is inherently deleterious: one is saying that the phenotype that results from the mutation is deleterious to the organism.
You quoted from the Wiki article on "Mutation." From that same article:
quote:
A deleterious mutation has a negative effect on the phenotype, and thus decreases the fitness of the organism.
You are classifying mutations by their phenotype, and not by their mechanism. A more mechanistic classification is provided in that article under the heading By effect on structure. There is a disconnect between this classification and the phenotypic classification: any one of the mutation types listed under By effect on structure could feasibly produce deleterious, neutral or beneficial phenotypes.
-----
Faith writes:
But apart from that, whatever happens in bacteria is a pretty sorry example for answering the glaring fact that there are thousands of known disease-causing mutations in human beings, which has been my example here. There is NO reason you can’t produce a normal allele from a mutation in human beings unless they don’t do what you think they do. Sorry, that’s what you need, not bacteria.
It is completely unfair to shrink the goal after I’ve taken my shot. It’s like changing where the bullseye is after I’ve thrown all my darts!
Nevertheless, there is a good reason why I can’t produce a normal allele from a mutation in human beings: think about the process that was needed to identify beneficial mutations in that bacterium.
Would you suggest we apply a lethal substance to an entire population of humans to see which, if any, are resistant to that lethal substance, and then sequence the relevant genes of the survivors to determine if the resistance is due to a mutation?
Of course you wouldn’t. Neither would I. So, we rely on people to volunteer for genetics studies in humans. Most people who volunteer are people who know they have a problem, and hope that the research will uncover the cause of the problem.
Furthermore, what if there were a beneficial mutation in your genome? Would you even notice it? Think of something about yourself that you are better at than anybody else you know. Did you ever not catch a cold when everyone else in your family caught it? Are you more attractive than other people in your family? Does everybody in your family except you need glasses? Do you have more natural talent for basketball than your sister or mother? Etc.
Did it ever occur to you to wonder whether or not these sorts of things were due to beneficial mutations? Of course not: nobody ever considers that. And, those who do consider it rarely (if ever) feel the desire to go get their genomes sequenced to find out. So, naturally, our sample is skewed towards deleterious mutations, because there is more motivation to work with deleterious mutations.
By the way, why do I have to provide an example from humans, anyway? I thought we were talking about cheetahs and elephant seals.
-----
Faith writes:
One new allele per individual at birth? Or half an allele? I can't work with .6
Why not? I already did the math back in Message 24.
Use one-half: it’s more friendly to your argument, and will prove my point better that way.

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
 Message 45 by Faith, posted 04-10-2010 5:29 PM Faith has replied

Replies to this message:
 Message 51 by Faith, posted 04-10-2010 10:36 PM Blue Jay has replied

  
Blue Jay
Member (Idle past 2698 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 52 of 87 (554933)
04-10-2010 10:38 PM
Reply to: Message 49 by Faith
04-10-2010 9:03 PM


Re: The men who witnessed evolution
Hi, Faith.
Faith writes:
I refuse to accept it because a good thing for bacteria is not a good thing for higher living things, in which it has been made only too clear to me that mutations are NEVER beneficial.
DNA is DNA, Faith. It may be organized differently in different groups of organisms, but the underlying chemistry, and thus, the underlying mechanisms for mutation, are the same throughout the Tree of Life.
And, beneficial mutations are always defined with respect to the organism in which they occur, so your anthropocentric reasoning here is pretty pathetic.
-----
Faith writes:
Yes, you proved your point but you also so thoroughly confirmed for me the nonexistence of useful mutations for the rest of creation, I have to assume that bacteria simply have a superior system for protecting themselves that is long since lost to us. They must have some kind of chemical process that can recreate useful alleles in a way that seems out of the blue, not mutations but alleles that are part of their repertoire chemically speaking such that rare ones can appear under special conditions. For the rest of creation you get disease causing mutations and junk where the lowly bacterium gets new ways of killing us and making us sick.
I’m glad: now it is patently obvious to everybody that your intention is not to understand reality, but to rationalize your own silly beliefs at any cost. That bacteria can be benefited by mutation is proof positive of the principles behind the Theory of Evolution, but it is somehow also proof positive that nothing else can be benefited by mutation.
I wish I could have convinced you to listen to reason, but, instead, I’ll have to be content knowing that it was me who finally got you to reveal to the world your obvious idiocy.
Look, I realize how depressing it is to be faced with unequivocal evidence that the worldview you have held and defined yourself by all your life is actually inferior to some other worldview. I’m facing it myself, and it hurts like nothing I’ve ever experienced before: my family are all very disappointed in me (I’m scared of even going near my grandfather anymore), I don’t fit in with any of the communities I associate with anymore, I live in perpetual fear of my next ecclesiastical interview, and I have utterly failed to convince myself that I am not deeply saddened by the prospect of disappearing into oblivion after I die, which I now regard as a very real possibility.
It sucks, but I have never been good at deluding myself. You do not seem to have this problem.
-----
Faith writes:
Thanks for the example and I see that a useful allele was created from the point of view of the bacterium.
Great! At least I’ve accomplished something for all my effort.
-----
Faith writes:
But again, since the vast majority of mutations are not useful, and since you haven't a single one in human beings despite many opportunities to find one if it ever occurred, I'm still going to refuse to accept this.
And now I'm not even going to accept mutations AS IF they can produce alleles. I don't believe it and don't see the point any more.
So if we're going to discuss my claim that the processes that lead to and include speciation also involve decreased genetic diversity we're going to do it without that assumption.
I think it’s safe to say we are done here. I suspect that this was your intention: to say something like this that you knew would make me back out instead of you, so it would look and feel to you like you won. But, I think you're the only person who is fooled by this.
Good bye.

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
 Message 49 by Faith, posted 04-10-2010 9:03 PM Faith has replied

Replies to this message:
 Message 53 by Faith, posted 04-10-2010 10:40 PM Blue Jay has not replied
 Message 57 by Faith, posted 04-10-2010 10:51 PM Blue Jay has not replied

  
Blue Jay
Member (Idle past 2698 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 54 of 87 (554936)
04-10-2010 10:41 PM
Reply to: Message 51 by Faith
04-10-2010 10:36 PM


Re: Loose Ends
Hi, Faith.
Faith writes:
I'll send you some cookies if it would make you feel better...
...Chocolate chip?
It would make me feel better, actually.

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
 Message 51 by Faith, posted 04-10-2010 10:36 PM Faith has replied

Replies to this message:
 Message 55 by Faith, posted 04-10-2010 10:43 PM Blue Jay has seen this message but not replied

  
Blue Jay
Member (Idle past 2698 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 61 of 87 (555125)
04-12-2010 9:13 AM
Reply to: Message 60 by Admin
04-11-2010 6:10 AM


Re: The Road from Here
Hi, Admin.
Obviously, I've completed my part of this debate, but it feels like it just ended without any real closure.
So, if the thread is going to be closed, I would like to post a summation message before it closes. If someone else is going to pick up where I left off, a summation may not be necessary.
Ultimately, the thread's fate should be Faith's choice, since I won't be participating anymore, either way.

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
 Message 60 by Admin, posted 04-11-2010 6:10 AM Admin has seen this message but not replied

Replies to this message:
 Message 62 by ZenMonkey, posted 04-12-2010 4:23 PM Blue Jay has not replied

  
Blue Jay
Member (Idle past 2698 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 66 of 87 (555278)
04-12-2010 11:25 PM


Passing the Torch: End of the Bluejay Era
I've written up a brief synopsis of my arguments on this thread, as well as my assessment of Faith's arguments and where the debate sits at my departure. As always, I appear to have written too much, but I hope at least some people take the time to read it.
I entered this discussion trying to probe various points of Faith’s argument, looking for where miscommunication and misunderstanding came in. It didn’t take long before we were talking only about mutation: it's quite obvious to everybody that this is where Faith takes exception to the evolution paradigm.
However, we talked about mutation from two angles: (1) whether or not mutations can actually produce new alleles and (2) whether or not the production of new alleles by mutation would make a difference in Faith’s scenario anyway.
I attempted to explain the difference between the genotype and the phenotype of a mutation, and Faith claimed to understand this. In her defense, I think she did know the difference, but just hadn’t spent enough time considering it to realize that her arguments were failing to distinguish them. She repeatedly asked me to provide evidence of a beneficial mutation having occurred, but I initially resisted, because I thought it was more important to get her to accept the general concept of mutations being different from phenotypes before I got into discussing the data. In retrospect, I’m not sure I agree with my reasoning there.
I decided to first focus on the second angle: whether or not the existence of beneficial mutations would make a difference for Faith’s model. The combination of the paper about the human mutation rate and the data about the elephant seal populations was enough to show that: If each human has an average of 0.6 new alleles due to mutation, then the current population of elephant seals (100,000) should harbor somewhere in the neighborhood of 60,000 alleles that did not exist before the bottleneck (this math assumes that all seals living today are first-generation descendants of seals that survived the bottleneck, so it does not take into account all the seals that had lived and died between the bottleneck and now). From the standpoint of the population, that is a lot of new material to work with.
Since Faith continued to push for evidence of beneficial mutations, I presented her with a couple of papers showing the emergence of antimicrobial resistance in bacteria by random mutation. These were studies that really couldn’t be argued with: they started with a known allele, found variation in the population for the trait controlled by the gene, showed that the variation had was associated with genotypic variation, and demonstrated that the mutant allele outperformed the original allele. I was then able to compare it with other mutations that had happened the same way, but had had negative effects on the phenotype, and thereby, to finally show that a diseased phenotype is not necessarily tied to a diseased process.
Faith acknowledged that this was evidence of a mutation that was beneficial for the bacterium. This is the power of empirical evidence at work. This evidence actually caused Faith to make a re-evaluation of her argument. Unfortunately, she ultimately decided that the beneficial mutation was to be interpreted from an anthropocentric point of view.
She did not learn from her mistake of conflating the consequences of something with the nature of its cause, and has instead settled on a decision of pretty much the same fallacious logical formula. If anything, I have at least shown that this is no longer a safe assumption. Yet, Faith still wants it to be the null hypothesis, the one that we take as true when the evidence can be viewed as consistent with multiple explanations.
This is not how logic or science works: we take the safe routes, the paths of least resistance. This means our null hypothesis is always that what we have demonstrated in one organism applies equally well to any other organism, unless there is good reason to suspect that it doesn’t apply outside of the demonstration organism. Bacteria are very different from higher organisms, does not constitute a good reason. Nor does the relative amount of junk DNA. Yet, these are the only reasons that Faith could come up with for why we should work under the assumption that the data found in bacteria do not apply to higher organisms.
My assessment is that Faith needs to confront the math: because she has acknowledged that beneficial mutations can happen (even though she has decided that the word should be redefined to only refer to benefits to higher organisms), she can only challenge the idea by arguing that they are too infrequent to be of consequence to genetic diversity. She needs to show that there is no situation under which the rate of allele addition by mutation can outpace the rate of natural selection. Yet, convincing her that this is the case has been the entire thrust of the three threads she has participated in on this subject: I sincerely hope that ZenMonkey is able to accomplish what the rest of us have not been able to do.

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

Replies to this message:
 Message 68 by Faith, posted 04-13-2010 3:59 AM Blue Jay has not replied

  
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