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Author Topic:   Quality Control the Gold Standard
U can call me Cookie
Member (Idle past 4982 days)
Posts: 228
From: jo'burg, RSA
Joined: 11-15-2005


Message 79 of 238 (285156)
02-09-2006 9:38 AM
Reply to: Message 59 by Evopeach
02-08-2006 5:37 PM


mutation rate
Yet in life the error rate in replicating the DNA molecule is about one mistake in a billion base pairs.
It seems you've been operating with a little bit of a straw-man here.
The estimate you give as a mutation rate i.e. 10E-9, is not only outdated, but is also specific only to single nucleotide polymorphisms (SNPs).
Nowadays, a working estimate is taken to be around 10E-8. This also fluctuates depending on location (eg. areas of high recombination) and sequence content (eg. GC islands). NB. this is only for SNPs.
SNPs, however, are not the only forms of mutation out there.
The mutation rates for microsatellites (STRs) are much higher, ranging from 10E-3 to 10E-4. The mutation rates for Chromosomal rearrangements also fall within this range.
Thus, on average, mutation rate is substantially HIGHER than the estimate you provided.
It might also be (though I could be wrong, here) that lethal mutations - ones who cause spontaneous abortions - are not even reflected in the above estimates, making them lower estimates.
While i don't know much (if anything) about the sigma system, it seems biological systems do not have sigma 7 status.
PS. Dude, the acid-spitting, to me, is pretty unecessary. People don't agree with you; so what? It doesnt, override the duty to one's self to maintain civilty.
EDIT: Lower changed to HIGHER. stupid mistake.
This message has been edited by U can call me Cookie, 02-10-2006 01:16 AM
This message has been edited by U can call me Cookie, 02-10-2006 03:53 AM

"The good Christian should beware the mathematician and all those who make empty prophecies. The danger already exists that the mathematicians have made a covenant with the devil to darken the spirit and to confine man in the bonds of hell." - St. Augustine

This message is a reply to:
 Message 59 by Evopeach, posted 02-08-2006 5:37 PM Evopeach has not replied

Replies to this message:
 Message 98 by NosyNed, posted 02-09-2006 1:14 PM U can call me Cookie has replied

U can call me Cookie
Member (Idle past 4982 days)
Posts: 228
From: jo'burg, RSA
Joined: 11-15-2005


Message 114 of 238 (285387)
02-10-2006 1:14 AM
Reply to: Message 98 by NosyNed
02-09-2006 1:14 PM


Re: mutation rate
OMG!
Thanks Ned, what a Friggin stupid mistake on my part.

"The good Christian should beware the mathematician and all those who make empty prophecies. The danger already exists that the mathematicians have made a covenant with the devil to darken the spirit and to confine man in the bonds of hell." - St. Augustine

This message is a reply to:
 Message 98 by NosyNed, posted 02-09-2006 1:14 PM NosyNed has not replied

U can call me Cookie
Member (Idle past 4982 days)
Posts: 228
From: jo'burg, RSA
Joined: 11-15-2005


Message 115 of 238 (285390)
02-10-2006 1:32 AM
Reply to: Message 110 by Evopeach
02-09-2006 9:57 PM


Re: Getting back on topic
The evolutionist insist that a seven sigma quality process can be developed by random muation of a string of sequenced molecules and supporting entities also developed by the same processes.
Hmmm...seems u choose to ignore posts that refute your claims, EP.
As stated previously, biological mutation rate is not at sigma 7 levels

"The good Christian should beware the mathematician and all those who make empty prophecies. The danger already exists that the mathematicians have made a covenant with the devil to darken the spirit and to confine man in the bonds of hell." - St. Augustine

This message is a reply to:
 Message 110 by Evopeach, posted 02-09-2006 9:57 PM Evopeach has replied

Replies to this message:
 Message 116 by Evopeach, posted 02-10-2006 8:56 AM U can call me Cookie has replied

U can call me Cookie
Member (Idle past 4982 days)
Posts: 228
From: jo'burg, RSA
Joined: 11-15-2005


Message 152 of 238 (286062)
02-13-2006 1:45 AM
Reply to: Message 116 by Evopeach
02-10-2006 8:56 AM


Re: Getting back on topic
As i said, your numbers are out of date...
you want refs...I got refs...
SNP mutation rate:
quote:
Many previous estimates of the mutation rate in humans have relied on screens of visible mutants. We investigated the rate and pattern of mutations at the nucleotide level by comparing pseudogenes in humans and chimpanzees to (i) provide an estimate of the average mutation rate per nucleotide, (ii) assess heterogeneity of mutation rate at different sites and for different types of mutations, (iii) test the hypothesis that the X chromosome has a lower mutation rate than autosomes, and (iv) estimate the deleterious mutation rate. Eighteen processed pseudogenes were sequenced, including 12 on autosomes and 6 on the X chromosome. The average mutation rate was estimated to be approximately 2.5 x 10(-8) mutations per nucleotide site or 175 mutations per diploid genome per generation. Rates of mutation for both transitions and transversions at CpG dinucleotides are one order of magnitude higher than mutation rates at other sites. Single nucleotide substitutions are 10 times more frequent than length mutations. Comparison of rates of evolution for X-linked and autosomal pseudogenes suggests that the male mutation rate is 4 times the female mutation rate, but provides no evidence for a reduction in mutation rate that is specific to the X chromosome. Using conservative calculations of the proportion of the genome subject to purifying selection, we estimate that the genomic deleterious mutation rate (U) is at least 3. This high rate is difficult to reconcile with multiplicative fitness effects of individual mutations and suggests that synergistic epistasis among harmful mutations may be common.
Estimate of the mutation rate per nucleotide in humans.
STR mutation rate:
quote:
We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9x10-4 per 25 years, with a standard deviation across loci of 5.7x10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria.
The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time.
Chromosomal rearrangement mutation rate:
quote:
The gametic mutation rates of human structural chromosome rearrangements have been estimated from rearrangements ascertained from systematic surveys of live births and spontaneous abortions. The mutation rates for rearrangements that survive long enough to give rise to clinically recognized pregnancies are 2.20 X 10(-4) for balanced rearrangements, 3.54 X 10(-4) for unbalanced Robertsonian translocations, and 3.42 X 10(-4) for unbalanced non-Robertsonian rearrangements. These estimates give a mutation rate for all detectable structural chromosome rearrangements of approximately 1 X 10(-3). The most common single rearrangement, the Robertsonian translocation involving chromosomes 13 and 14, has a mutation rate of 1.5 X 10(-4).
Mutation rates of structural chromosome rearrangements in man.
As mentioned previously by myself, crashfrog, and many others, the substitution rate on its own is inadequate.
Rather than quoting your one favorite source that enables you to post a cynical swipe why not do a wider review .. if you had it would have saved you embarrassment and me some time.
Be wary of the assumptions you jump to, and of your words... I have have been civil to you, I would expect the same treatment from you.

"The good Christian should beware the mathematician and all those who make empty prophecies. The danger already exists that the mathematicians have made a covenant with the devil to darken the spirit and to confine man in the bonds of hell." - St. Augustine

This message is a reply to:
 Message 116 by Evopeach, posted 02-10-2006 8:56 AM Evopeach has replied

Replies to this message:
 Message 155 by Evopeach, posted 02-13-2006 11:41 AM U can call me Cookie has not replied
 Message 158 by Evopeach, posted 02-13-2006 4:05 PM U can call me Cookie has replied

U can call me Cookie
Member (Idle past 4982 days)
Posts: 228
From: jo'burg, RSA
Joined: 11-15-2005


Message 183 of 238 (286767)
02-15-2006 4:58 AM
Reply to: Message 158 by Evopeach
02-13-2006 4:05 PM


Re: Getting back on topic
It’s almost amusing that you think you’ve defeated my arguments, if it wasn’t so . so sad.
All you’ve done is show, quite vehemently, that your understanding of DNA replication and repair is, at best, surface orientated.
Again, the 10** -09 was always in the context of defining the inherent dna copying mechanism in the human cell over huge populations and long time periods as in the Genome Project.
More accurately, it is in the context of the inherent DNA copying mechanism for point mutations.
STR mutations ARE due to the inherent DNA copying mechanism. Look it up .
You introduced all the other sources of mutation rates which are variant depending on a lot of variables that are difficult to isolate.
Could you explain this statement . it just sounds like an excuse to me. All cellular processes have variables including DNA replication and repair. Nothing occurs in isolation.
Hey I know an even better straw mand and red herring (you can do both simultaneously.. remarkable), IS TO USE THE RATE FOR 1,000 GENERATIONS IN RADIATED FRUIT FLYS.. THTA'S MUCH HIGHER.
Not one of your examples is apples to apples .. pitiful.
All my ref’s were based on observations of human DNA, so I have been comparing ”apples to apples’ . unless you don’t really know what that means .
Where did irradiated fruit flies come up in my words? Talk about apples with apples .
You do raise an interesting point here though; many organisms have a naturally occurring mutation rate that is substantially higher than in humans. How do you account for those? Or do you believe that people have been arguing over human evolution only, these past 150 years.
You know, I really wouldn’t have that much of a problem with the figure you’ve supplied had DNA replication and repair occurred solely in isolation . They Do Not.
Cells are not closed systems; substances enter and leave all the time, some of which are responsible for mutagenesis. Even substances produced by cells themselves can cause mutations. As such any practical mutation rate is a function of both the causation of mutation (whether extrinsic or intrinsic) and the adequacy of repair mechanisms (which themselves often result in the fixation of a mutation). Organisms live in the real world, not in test tubes.
It is now known that mutation rate differs depending not only on location in the genome, but also on the gene itself. The mutation rates of certain genes, for point mutations, can reach levels of 10E-5, rivaling even STR mutation rate.
You see, EP, there’s a lot more to mutation than a single number. If you actually knew anything about genetics . no, make that biology . you would realize this.
When one comes down to it, if mutations really were that rare, genetic disease would also be a rarity. Yet, do you know that there are more people living, and dying, of genetic disorders, than there are people living and dying of AIDS. Still, barring those, living and dying, of cancer.
Maybe one day, when you’re not blinded by your own ego, you might actually acknowledge that you live in the real world.

"The good Christian should beware the mathematician and all those who make empty prophecies. The danger already exists that the mathematicians have made a covenant with the devil to darken the spirit and to confine man in the bonds of hell." - St. Augustine

This message is a reply to:
 Message 158 by Evopeach, posted 02-13-2006 4:05 PM Evopeach has replied

Replies to this message:
 Message 185 by Evopeach, posted 02-15-2006 5:45 PM U can call me Cookie has replied

U can call me Cookie
Member (Idle past 4982 days)
Posts: 228
From: jo'burg, RSA
Joined: 11-15-2005


Message 188 of 238 (287188)
02-16-2006 1:18 AM
Reply to: Message 185 by Evopeach
02-15-2006 5:45 PM


Re: Getting back on topic
As i understand it, the book you are refering to is a popularization; something for public consumption. As such, you gotta expect a fair bit of dumbing down, in order to keep things simple and interesting.
The point i was trying to make is that such a number is almost meaningless in the real world.
To say that the rate of mutation in actual organisms is unaltered by intrinsic and extrinsic factors is simply unrealistic.

"The good Christian should beware the mathematician and all those who make empty prophecies. The danger already exists that the mathematicians have made a covenant with the devil to darken the spirit and to confine man in the bonds of hell." - St. Augustine

This message is a reply to:
 Message 185 by Evopeach, posted 02-15-2006 5:45 PM Evopeach has not replied

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