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Author Topic:   Is there any proof of beneficial mutations?
ProtoTypical
Member
Posts: 1792
From: Ontario Canada
Joined: 08-04-2010


Message 106 of 166 (580600)
09-10-2010 8:14 AM
Reply to: Message 105 by ProtoTypical
09-10-2010 8:12 AM


Re: Cause of mutation?
Is that true?

I guess not. Thanks Percy.


This message is a reply to:
 Message 105 by ProtoTypical, posted 09-10-2010 8:12 AM ProtoTypical has not yet responded

Replies to this message:
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greyseal
Member (Idle past 2144 days)
Posts: 464
Joined: 08-11-2009


Message 107 of 166 (580601)
09-10-2010 8:16 AM
Reply to: Message 103 by Omnivorous
09-10-2010 8:01 AM


Re: Cause of mutation?
Do those numbers represent the incidence of the AIDS-resistant mutation?

A quick check on google tells me that the mutation in humans actually blocks a crucial pathway for all current AIDS strains - regardless of variant.

Until or unless the AIDS virus mutates itself away from needing these blocked pathways, those who are immune will continue to be immune.

Apparently, the partner of one of the first people to ever knowingly die of aids didn't catch it himself purely because he was lucky enough to have this mutation.

If you were talking about the prevalence of the mutation in human populations (and not talking about mutated strains of aids) then yes, those numbers (admittedly pulled out of my foggy memory, so they may be incorrect) are of the numbers of the population with that mutation.

Edited by greyseal, : No reason given.


This message is a reply to:
 Message 103 by Omnivorous, posted 09-10-2010 8:01 AM Omnivorous has responded

Replies to this message:
 Message 111 by Omnivorous, posted 09-10-2010 10:10 AM greyseal has responded

    
greyseal
Member (Idle past 2144 days)
Posts: 464
Joined: 08-11-2009


(1)
Message 108 of 166 (580603)
09-10-2010 8:32 AM
Reply to: Message 106 by ProtoTypical
09-10-2010 8:14 AM


Re: Cause of mutation?
Dogmafood, if you want to start talking about "adverse mutations" then I think you'll need a different thread. In short, mutations are mutations. Some are slightly good, some are slightly bad. Some are drastically bad, some very, very good. In general, a really bad mutation will result in death for either the organism or it's offspring. slightly negative won't affect things much, neither will slightly positive.

The aids-resistant mutation, for example, does very little good most of the time...but it does very little bad either. On it's own, it tends to randomly re-occur relatively often and has been found in historical remains going back 4000-5000 years at least.

The key becomes when that mutation does something useful - then those with it are at an immediate advantage. It wasn't put there on purpose, it didn't happen for a reason (other than blind chance and probability) but because it DID do something good under certain conditions (yes, it took a change to find that good result) then it becomes advantageous.

Now, that mutation can mutate back in any subsequent generation, or change again into something else, or get altered by some other genetic mutation - it's really very, very far from simple - and there may come a day when something else will occur and that mutation will be bad for you...

survival of the fittest is survival of populations, not so much individuals. Sometimes it comes down to individuals, but there's a very fuzzy-wuzzy line that a single post to a message board like this can't very well deal with, especially when I am just a layman.


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Bolder-dash
Member (Idle past 1912 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 109 of 166 (580605)
09-10-2010 9:06 AM
Reply to: Message 95 by greyseal
09-10-2010 3:01 AM


Re: Cause of mutation?
Greyseal,

Do you know specifically what does the mutation that makes one immune to Aids do?

My understanding is that there is not even a clear definition of what Aids actually is, so I think to say that one mutation can make someone resistant to something we can't define seems a little unclear.


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Replies to this message:
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Wounded King
Member (Idle past 2377 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(3)
Message 110 of 166 (580613)
09-10-2010 9:58 AM
Reply to: Message 109 by Bolder-dash
09-10-2010 9:06 AM


Re: Cause of mutation?
There are a number of mutations which have been identified as conferring some resistance to HIV-1 infection and/or AIDS progression, one is a 32bp deletion in the gene for the CCR5 chemokine receptor protein which confers almost complete resistance to infection in homozygotes (Struyf, 2000) and slows progression in heterozygotes, other chemokine receptor variants also retard progression and some variants have been identified which seem to accelerate progression (Rana et al.,1997; Parczewski et al., 2009 PDF). The molecular basis for many of these is well understood and centers around the way the HIV virus utilises receptors of the immune cells to infect the cell (Venkatesan et al., 2002).

My understanding is that there is not even a clear definition of what Aids actually is, so I think to say that one mutation can make someone resistant to something we can't define seems a little unclear.

I think your understanding is wrong, try the scientific literature there really is quite a lot about HIV and AIDS.

TTFN,

WK


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Omnivorous
Member (Idle past 1250 days)
Posts: 3808
From: Adirondackia
Joined: 07-21-2005


(1)
Message 111 of 166 (580615)
09-10-2010 10:10 AM
Reply to: Message 107 by greyseal
09-10-2010 8:16 AM


Re: Cause of mutation?
I've been googling the subject for the past hour as well.

You'll find I am not averse to online research; it was not your numbers but your syntax I was unsure of, and it seemed more civil to ask than to research and assert.

It's a fascinating subject: your numbers hold up. The resistance could also partially explain the greater impact of HIV on the African-American community

It appears homozygosity of the allele confers nearly complete immunity, heterozygosity, greater resistance to both infection and progression; fortunately, neither appears to confer any deleterious effect.

The more recent study abstracts I've been able to view confirm the immunity/resistance, but question the bacterial/bubonic cause, hypothesizing instead a virus, perhaps a hemorrhagic fever like Ebola, or even smallpox.

From a 2007 popular account:

quote:
The source of that genetic pressure is still being debated by scientists. The early favorite was the Black Death, the Bubonic plague that swept through Europe in the Fourteenth century.

Other researchers have hypothesized that the period of selective pressure created by the Bubonic plague, roughly 400 years, was not
long enough for the overwhelming presence of the gene to appear.

These researchers suggest that smallpox, which has killed as many people as the plague over a much longer time period, could have provided sufficient selective pressure.

To support this conclusion, it is proposed that the continued presence of the mutated gene...is due to the fact that smallpox was only eradicated recently while the plague hasn't been a serious problem in 250 years. Indeed, a cousin of the smallpox virus has been shown to use CCR5 to enter host cells. Thus, CCR5-32 may provide resistance to smallpox.


Since I enjoy an apparent immunity to chickenpox and smallpox, perhaps survival of my wayward youth had more to do with lucky genes than anything else.


Have you ever been to an American wedding? Where's the vodka? Where's the marinated herring?!
-Gogol Bordello

Real things always push back.
-William James


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Dr Jack
Member (Idle past 387 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


(2)
Message 112 of 166 (580617)
09-10-2010 10:37 AM
Reply to: Message 109 by Bolder-dash
09-10-2010 9:06 AM


Re: Cause of mutation?
Do you know specifically what does the mutation that makes one immune to Aids do?

Wounded King has alluded to the CCR5 Δ32 variant in his reply. I am not sure whether this is the mutation that Greyseal referred to, but having just finished a course on how genetic variation effects HIV susceptibility and performed lab experiments specifically into the Δ32 mutation in human cell lines it's one I happen to know quite a bit about.

The HIV-1 virus enters human immune cells by binding to two surface receptors, one is called CD4, the other is either CCR5 or CXCR4. CCR5 binding is usually involved in the initial infection and early stages of the disease, CXCR4 binding in the late stages. CCR5 is a cell surface receptor involved in immune system signalling, and part of a family of receptors referred to as 7TMs because the protein crosses the plasma membrane that forms the cell surface seven times.

In the CCR5 Δ32 variant a 32 base pair section of the CCR5 gene has been deleted. As you'll doubtless be aware, DNA is "read" in codons of 3 base pairs at a time, each coding for an amino acid. Because 32 is not a multiple of 3, this deletion produces what is called a frame shift meaning that the codons after the deletion are read in a different fashion. In the particular case of the CCR5 Δ32 variant this frame shift produces a stop codon shortly after the deletion. A stop codon being, of course, one of the three codons that does not code for an amino acid but instead triggers translation of the protein to stop.

Now, human cells (like other eukaryotic cells) have a mechanism for detecting damaged protein transcripts and genes called nonsense-mediated decay in which gene transcripts that contain multiple stop codons are marked for destruction before they can be converted into proteins. It is thought that this mechanism means the CCR5 Δ32 protein is never produced (certainly none has been found). Even if it were produced, and transferred to the cell surface it would not bind HIV-1 because it lacks the section to which the virus binds since this occurs after the stop codon.

So, without the CCR5 protein on the surface, the HIV virus is unable to enter the cell, and thus unable to infect the person carrying the mutation. In people who are heterozygous for the wild type and Δ32 variants, they merely have fewer CCR5 receptors on the cell surface and are approximately 25% less likely to catch HIV than wild type homozygotes. Δ32 homozygotes are, while not quite totally immune (because it is just possible for the virus to enter via interaction with CXCR4) they are about a thousand times less likely to catch the disease.

(Oh, and BTW, whether the CCR5 Δ32 variant is actually a beneficial mutation depends on context because while it protects against AIDS, it makes the carrier more susceptible to West Nile Virus)

My understanding is that there is not even a clear definition of what Aids actually is, so I think to say that one mutation can make someone resistant to something we can't define seems a little unclear.

This is quite wrong. AIDS is well understood in terms of what it is, and what causes it. In fact, compared to most diseases, it is extremely well studied.

Edited by Mr Jack, : + bit about West Nile Virus

Edited by Mr Jack, : No reason given.


This message is a reply to:
 Message 109 by Bolder-dash, posted 09-10-2010 9:06 AM Bolder-dash has responded

Replies to this message:
 Message 113 by Omnivorous, posted 09-10-2010 10:51 AM Dr Jack has responded
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Omnivorous
Member (Idle past 1250 days)
Posts: 3808
From: Adirondackia
Joined: 07-21-2005


Message 113 of 166 (580619)
09-10-2010 10:51 AM
Reply to: Message 112 by Dr Jack
09-10-2010 10:37 AM


Re: Cause of mutation?
Mr Jack writes:

(Oh, and BTW, whether the CCR5 Δ32 variant is actually a beneficial mutation depends on context because while it protects against AIDS, it makes the carrier more susceptible to West Nile Virus.

Thanks for adding that; I had thought there were no deleterious effects of the CCR5 Δ32 variant.

I've had West Nile, subjectively experienced as a mild flu. Whether selected for by the bubonic plagues or by multiple viral outbreaks, the variant sounds like a winner.

Has there been any new work on clarifying the selective pressure which ramped up the variant in European populations?


This message is a reply to:
 Message 112 by Dr Jack, posted 09-10-2010 10:37 AM Dr Jack has responded

Replies to this message:
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Dr Jack
Member (Idle past 387 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 114 of 166 (580623)
09-10-2010 11:09 AM
Reply to: Message 113 by Omnivorous
09-10-2010 10:51 AM


Re: Cause of mutation?
Omnivorous writes:

I've had West Nile, subjectively experienced as a mild flu.

While West Nile is typically harmless, or only produces mild symptoms, it can also cause fatal encephalitis, so it's not as harmless as all that.

Whether selected for by the bubonic plagues or by multiple viral outbreaks, the variant sounds like a winner.

Has there been any new work on clarifying the selective pressure which ramped up the variant in European populations?

I'm personally sceptical that the variant is as completely harmless as thought because organisms don't usually carry around functional but pointless genes. However, if the Δ32 variant is as harmless as currently suspected, I'd point out that the incidence rate is within that explicable simply by genetic drift and other neutral factors. Especially as the trait is largely recessive.

I don't know specifically of any work done in this area, though.


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Taq
Member
Posts: 8081
Joined: 03-06-2009
Member Rating: 4.1


Message 115 of 166 (580625)
09-10-2010 11:38 AM
Reply to: Message 92 by dennis780
09-09-2010 11:57 PM


Re: Cause of mutation?
You are saying that ABR is not always a response to a hazardous environment, and mutation of this sort occurs randomly?

I am assuming that by ABR you are referring to anbiotic bacterial resistance. I apologize if you defined it elsewhere. With that said . . .

What I am saying is that mutations which confer antibiotic resistance are not triggered by the presence of antibiotics. This means that these mutations are random with respect to fitness. That last italicized part is important. Mutations are not random with respect to time because mutations rates can change. Mutations rates are not random with respect to each nucleotide in the genome because some areas of DNA are more prone to mutation than others. The randomness of mutations are random with respect to the needs of the organism, that is the important bit.

The game of craps is a great analogy for this. There are 11 possible outcomes for each roll of the dice which are 2 through 12 (we will ignore the specific dice combinations for now). However, in 100 rolls you will notice that there is not an even distribution between the numbers. There are very few 12's compared to 7's. So there is a much higher chance of rolling a 7 than there is a 12. This is the case with DNA. Certain DNA sequences have a higher chance of mutating due to their arrangement. So how is craps random? Well, it is random with respect to the bet. If I place my bet on the Pass Line (where a 7 or 11 is an automatic winner) the chances of rolling a winning combination is not increased. The outcome of the roll is random with respect to the bet in the same way that mutations are random with respect to the needs of the organism.

First, saying that God gave it to them would mean that they contracted the virus through no explainable way, a sort of opposite miracle.

I am not talking about an infection. I am talking about a genetic disease, a disease caused by a mutation. If you want to argue that mutations are designed into organisms then you have to also admit that this supposed designer designed this system to produce mutations that give children horrific genetic diseases.

Blaming a God for problems that could be solved is a blame-shift,

These genetic diseases are incurable, unless, of course, you are an omnipotent deity.

Ohhh, so you are not interested in being civil, even though my question is actually one that I am interested in.

You are asking me for the scientific outcome of a mythological story if the conditions were different. You are getting your wires crossed.

Give me a break. The fossil record is a joke, a 30 pieces to a million piece puzzle, a total lack of undisputed examples (fossilized or living) of the millions of transitional forms (“missing links”) required for evolution to be true. Radiocarbon dating methods that constantly contradict each other. The dating methods that evolutionists rely upon to assign millions and billions of years to rocks are very inconsistent and based on unproven (and questionable) assumptions, and an even worse explanation for the first living organism (abiogenesis) that would require a complexity that you couldn't devise if you spent your entire life on it, but it happened by chance. You are no more believer than I, other than your beliefs are naturalistic. If evolution were 100% true, then there would not be HUNDREDS of books published to the contrary, and this forum would be dead fuckin quiet.

All of this is off topic and covered in other threads. If you want, you can start a new thread on each of these topics. I would be most interested in your definition of transitional fossil, along with the criteria you use to determine if a fossil is transitional or not.

Edited by Taq, : No reason given.


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Bolder-dash
Member (Idle past 1912 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 116 of 166 (580626)
09-10-2010 11:44 AM
Reply to: Message 112 by Dr Jack
09-10-2010 10:37 AM


Re: Cause of mutation?
This is quite wrong. AIDS is well understood in terms of what it is, and what causes it. In fact, compared to most diseases, it is extremely well studied.

So what do you think when people such as Rebecca Culshaw (a PHD mathematical biologist, whose work involves mathematical models of HIV) and others say things like "phrases like "the AIDS virus" or "an AIDS test" have become part of the common vernacular despite no evidence for their accuracy."

and:

"The classification "AIDS" was introduced in the early 1980s not as a disease but as a surveillance tool to help doctors and public health officials understand and control a strange "new" syndrome affecting mostly young gay men. In the two decades intervening, it has evolved into something quite different. AIDS today bears little or no resemblance to the syndrome for which it was named. For one thing, the definition has actually been changed by the CDC several times, continually expanding to include ever more diseases (all of which existed for decades prior to AIDS), and sometimes, no disease whatsoever. More than half of all AIDS diagnoses in the past several years in the United States have been made on the basis of a T-cell count and a "confirmed" positive antibody test – in other words, a deadly disease has been diagnosed over and over again on the basis of no clinical disease at all. And the leading cause of death in HIV-positives in the last few years has been liver failure, not an AIDS-defining disease in any way, but rather an acknowledged side effect of protease inhibitors, which asymptomatic individuals take in massive daily doses, for years.

The epidemiology of HIV and AIDS is puzzling and unclear as well. In spite of the fact that AIDS cases increased rapidly from their initial observation in the early 1980s and reached a peak in 1993 before declining rapidly, the number of HIV-positive individuals in the U.S. has remained constant at one million since the advent of widespread HIV antibody testing. This cannot be due to anti-HIV therapy, since the annual mortality rate of North American HIV-positives who are treated with anti-HIV drugs is much higher – between 6.7 and 8.8% – than would be the approximately 1–2% global mortality rate of HIV-positives if all AIDS cases were fatal in a given year.

Even more strangely, HIV has been present everywhere in the U.S., in every population tested including repeat blood donors and military recruits, at a virtually constant rate since testing began in 1985. It is deeply confusing that a virus thought to have been brought to the AIDS epicenters of New York, San Francisco and Los Angeles in the early 1970s could possibly have spread so rapidly at first, yet have stopped spreading completely as soon as testing began. "

Do you think people who say this are lying?


This message is a reply to:
 Message 112 by Dr Jack, posted 09-10-2010 10:37 AM Dr Jack has responded

Replies to this message:
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Taq
Member
Posts: 8081
Joined: 03-06-2009
Member Rating: 4.1


Message 117 of 166 (580627)
09-10-2010 11:53 AM
Reply to: Message 116 by Bolder-dash
09-10-2010 11:44 AM


Re: Cause of mutation?
Bolder-dash,

Are you trying to say that HIV does not cause AIDS?


This message is a reply to:
 Message 116 by Bolder-dash, posted 09-10-2010 11:44 AM Bolder-dash has responded

Replies to this message:
 Message 118 by Bolder-dash, posted 09-10-2010 12:06 PM Taq has responded

  
Bolder-dash
Member (Idle past 1912 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 118 of 166 (580629)
09-10-2010 12:06 PM
Reply to: Message 117 by Taq
09-10-2010 11:53 AM


Re: Cause of mutation?
I am saying that there are people whose job it is to study these diseases who say that the links between Aids and HIV are not so simply defined, and that plenty of uncertainty exists-so I find it to be imprecise and misleading when Wounded King or Mr. Jack make these kind of blanket statements that the disease is perfectly understood.

This message is a reply to:
 Message 117 by Taq, posted 09-10-2010 11:53 AM Taq has responded

Replies to this message:
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 Message 121 by Wounded King, posted 09-10-2010 12:23 PM Bolder-dash has responded

  
Taq
Member
Posts: 8081
Joined: 03-06-2009
Member Rating: 4.1


Message 119 of 166 (580632)
09-10-2010 12:10 PM
Reply to: Message 118 by Bolder-dash
09-10-2010 12:06 PM


Re: Cause of mutation?
I am saying that there are people whose job it is to study these diseases who say that the links between Aids and HIV are not so simply defined, and that plenty of uncertainty exists . . .

Uncertainty as to what? That HIV can and does cause AIDS if left untreated in the vast majority of cases?


This message is a reply to:
 Message 118 by Bolder-dash, posted 09-10-2010 12:06 PM Bolder-dash has responded

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Bolder-dash
Member (Idle past 1912 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 120 of 166 (580633)
09-10-2010 12:21 PM
Reply to: Message 119 by Taq
09-10-2010 12:10 PM


Re: Cause of mutation?
I answered this in post 116, start by reading that and refute it is you wish.

I see a similar pattern of posting here, where people want to just say things like 'It is a known fact..." when the only fact is that people here like to say it is a known fact a lot.


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