Random mutations

[CabVet]

No thats wrong. I believe in random mutations, yeah I believe. From time to time anyway. But whether I know them to be randon is another thing. And why should a belief be sure if it is not a knowing belief? So therefore I ought not be sure they are random. That would be inappropriate sureness, certainty out of place. Hence "I'm not sure they are" is the right attitude for me.

I believe in various things from day to day. First its regular theism, then reincarnation, next I'm in a multiverse, then I'm a computer programme, next some sort of dream and then back to square one. With such an inconsistent set of habits and a carefree attitude I am not sure I can actually know that much because my general principles of approach are hardly that disciplined. So even if you teach me random mutation, I wouldn't suppose, and don't you suppose I know it or can surely believe it because such knowledge or rational confidence takes a certain type of psychological and behavioural attitude towards the world.

Plus there's the regular arguments like "science changes" etc.

Yeah, when you compare something that you can actually observe in nature (random mutation) to something not only never confirmed, but also impossible to observe even if it happened (reincarnation), there is not much I can do. Might as well not believe in gravity, magnetism, relativity, etc.

 

[Zaius137]

(sfs)…

“Since we are, once again, talking about the deleterious mutation rate and not Haldane's Dilemma, and since the two have next to nothing to do with one another, why do you keep bringing up Haldane? Could you at least try to keep straight the argument you're making?”

Actually I am getting around to that matter of Haldane and the “U”. All in good time.

Again you want to ease the effects of a high “U” value and avoid paying the needed price for population purification.

“Exactly. And soft selection does precisely that -- as noted in that piece of the Nachman and Crowell paper you keep ignoring, and by Wallace who introduced the term soft selection, whom I have quoted to you, and by many others. So let's see how you respond to the quite simple fact that soft selection mitigates genetic load . . .”

No it does not…

“Thus, contextual analysis finds that soft-selection constitutes a form of group selection (Goodnight et al. 1992), contrary to the conclusion of the Price approach. Below, I demonstrate that the Price approach, when the population is subdivided into regulation groups, also reveals that soft-selection includes a group-component of selection, independently supporting the conclusion of Goodnight et al. (1992).”

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3151721/

Being a form of group selection or truncation selection it can not ease a deleterious mutation rate approaching (U=5) or about 297 offspring needed per female. Now all you need to do is to show how a form of group selection can mitigate a high genetic load when the ratio of bad mutations to good mutations is about 1000/1.

Yes… Sorry but that is just another case of the evolutionist not wanting to face the consequences of there own theory.

“So there we have your detailed response: nothing.”

You have not adequately addressed the “U” paradox. Given the common consensus of average mutation rate of ~175 mutations, 3 and maybe more (5) deleterious. There can not be a chimp human divergence just because of the unsupportable birth rates of our ancestors.

If deleterious mutations are not purged immediately they are just carried over and add to the genetic loading. The population cannot undergo purification without purging deleterious mutations no matter what the selective pressure is.

“Since that's what I just wrote, I'm not likely to disagree. Deleterious mutations are indeed purged. So what? Try to understand this fact: purging deleterious mutations only imposes a genetic load if the selection is hard.”

You need to show how a form of group selection (soft selection) in a small population (evolution dogma) helps your case.

I disagree with the above analysis… Do you have a basis given the serious nature of those deleterious mutations? No matter hard/soft or what ever...

“Deleterious silent mutations (including noncoding mutations and synonymous coding mutations) have been known and studied for decades. (Detecting and characterizing disease-causing mutations is a significant chunk of what our research institute does, as it happens.) “

Can you comment on silent mutations adding to the deleterious accounting? Synonymous mutations and non coding mutations in introns leading to exon skipping seem to be very important.

 

[Zaius137]

CabVet…

Yeah, when you compare something that you can actually observe in nature (random mutation) to something not only never confirmed, but also impossible to observe even if it happened (reincarnation), there is not much I can do. Might as well not believe in gravity, magnetism, relativity, etc.

Yes random mutation is observed in nature. It does not lead to evolution. All accounting of the mutational approach to a chimp human divergence proves evolution is wrong. Random mutations degrade overall fitness.

 

[CabVet]

Being a form of group selection or truncation selection it can not ease a deleterious mutation rate approaching (U=5)

Oh, U=5 now? Since we are cherry-picking, what if we consider a family size of 50+ children per family?

“The number of Adam’s children, as says the old tradition, was thirty-three sons and twenty-three daughters.”

 

[CabVet]

Here, read this paper and let me know what you think. Also, the only place where I could find an explanation for the equation you posted is in a creationist website. Here is how they get those numbers:

So, to determine the reproductive impact, let
p = probability an individual's genome does not receive a new defect this generation
A female is required to produce two offspring, one to replace herself and her mate. So, she needs to produce at least 2/p to pay this cost and maintain the population. Let B represent the birth threshold:
B = 2/p
The probability p of an offspring escaping error-free is given by e^-U. Therefore, making the substitution,
B = 2e^U. For U=1.6, B = 9.9 births per female!

What I said in my point 4 was that this formula calculated the number of offspring that a female needs to have to produce one that is completely error-free. That's exactly what they say above.

Now, while searching for more information about this I found much more creationist pages than anything else (as expected). And most were just copies from each another, all of them also containing this statement:

Consider then that we humans have a 180,000,000 base pair difference from chimps, about 6% difference. Does one get the sense a problem is lurking somewhere? Let’s assume (very generously) that for every 3 desirable mutations fixed we need to purify out 3 unwanted mutations. For the chimp human divergence we would be dealing with 90,000,000 nucleotides (180,000,000 / 2 ). 90,000,000 /3 = 30,000,000 generations or about 600,000,000 years.

Can you spot the errors in the statement above? Here is the source.

 

[Zaius137]

Here is what I got out of this…

Let’s assume (very generously) that for every 3 desirable mutations fixed we need to purify out 3 unwanted mutations. For the chimp human divergence we would be dealing with 90,000,000 nucleotides (180,000,000 / 2 (two nucleotides in a base pair)). 90,000,000 /3 (90 million mutations/ U (3 deleterious mutations per generation) which gives 30 million generations) = 30,000,000 generations (20 years per generation) or about 600,000,000 years. What if U=100? Recall, U=3 was just pulled out of the air! U=100 has some experimental verification, and it may actually be far worse.

Yes this is an exaggeration/generalization but remember that for every one beneficial mutation there are about 1000 deleterious mutations. He forgot to do the following, 90 million divided by 1000 or 90,000 beneficial mutations and
(90,000,000 – 90,000) deleterious mutations. Then 8991000/U gives 29970000 generations or 59940000 years.

 

[Zaius137]

Oops that would be 599,400,000 years…. Dropped a zero.

 

[CabVet]

Oops that would be 599,400,000 years…. Dropped a zero.

Still not correct, for every 1,000 deleterious mutations there are 10,000 neutral ones. Yours (and his) calculations assume that all 90,000,000 mutations between human and chimps are beneficial, when the vast majority of them are neutral.

 

[Zaius137]

In the vein of intellectual honesty I need you to consider an objection raised to the formula 2e^U. The calculation could be reduced to 2e^U/2 if the sexual reproduction factor is considered. Come on sfs you need to follow the argument because I am not going to keep making your points.

 

[Zaius137]

Oops that would be 599,400,000 years…. Dropped a zero.

Still not correct, for every 1,000 deleterious mutations there are 10,000 neutral ones. Yours (and his) calculations assume that all 90,000,000 mutations between human and chimps are beneficial, when the vast majority of them are neutral.

In damaging a genome with random mutations what is considered neutral?

 

[Zaius137]

Try inserting random characters in a sentence and what do you get? You don’t get neutral meaning do you?

 

[Zaius137]

By the way CabVet that Cat is great. My wife and I have 11 of our own. I always say cat people are the most intelligent. With of course sfs as the exception to the rule.

 

[CabVet]

Oops that would be 599,400,000 years…. Dropped a zero.

Still not correct, for every 1,000 deleterious mutations there are 10,000 neutral ones. Yours (and his) calculations assume that all 90,000,000 mutations between human and chimps are beneficial, when the vast majority of them are neutral.

In damaging a genome with random mutations what is considered neutral?

Changing the third position of a codon does not change the amino-acid it codes for (in many amino-acids), therefore it's a silent (or neutral) mutation. Mutations in introns are also neutral. The number that you use (U=3) is only for deleterious mutations (mutations that change something in a negative way). Neutral mutations (which can be as much as hundreds per generation) are not included in the number and make up the vast majority of those 90,000,000 differences.

 

[CabVet]

Try inserting random characters in a sentence and what do you get? You don’t get neutral meaning do you?

Oh boy, DNA characters are not the same as words. Every amino-acid (building blocks of proteins) are coded by a three letter DNA code called a codon. Most codons are free to vary in the third position for redundancy, it is an adaptation to avoid too many changes in the DNA sequence. The amino acid leucine is specified by CUU, CUC, CUA, CUG codons (difference in the third position), so if there is a mutation in the third position of this codon, nothing happens to the protein this gene codes for, therefore a neutral mutation.

This is called degeneracy and can be observed in real time, even in humans. For example, if I were to sequence your DNA and your mother's DNA there would be hundreds of differences in those third positions. This is the basis for DNA forensic testing. If you don't think it's right, you might as well release everyone that was ever arrested based on DNA evidence (including a lot of people in death row).

 

[Zaius137]

Changing the third position of a codon does not change the amino-acid it codes for, therefore it's a silent (or neutral) mutation. Mutations in introns are also neutral. The number that you use (U=3) is only for deleterious mutations (mutations that change something in a negative way). Neutral mutations (which can be as much as hundreds per generation) are not included in the number and make up the vast majority of those 90,000,000 differences.

Actually CabVet I just showed how the new genetics is finding silent mutations in locations once thought to be harmless to actually be the reason for severe genetic dieses (50 now confirmed), Scientific American June 2009 volume 300 Number 6, A must read.

 

[CabVet]

By the way CabVet that Cat is great. My wife and I have 11 of our own. I always say cat people are the most intelligent. With of course sfs as the exception to the rule.

Haha, I know, right? I found this photo in one of those LOLCAT websites and thought it was hilarious. I love cats, but can't have one because of a deleterious, yet non-fatal mutation (I am allergic to them).

 

[CabVet]

Actually CabVet I just showed how the new genetics is finding silent mutations in locations once thought to be harmless to actually be the reason for severe genetic dieses (50 now confirmed), Scientific American June 2009 volume 300 Number 6, A must read.

They are finding those in areas previously considered "junk" DNA. That is not what I am talking about. I am talking about third position mutations, and mutations in introns, completely different.

 

[Zaius137]

Oh boy, DNA characters are not the same as words. Every amino-acid (building blocks of proteins) are coded by a three letter DNA code called a codon. Most codons are free to vary in the third position for redundancy, it is an adaptation to avoid too many changes in the DNA sequence. The amino acid leucine is specified by CUU, CUC, CUA, CUG codons (difference in the third position), so if there is a mutation in the third position of this codon, nothing happens to the protein this gene codes for, therefore a neutral mutation.

This is called degeneracy and can be observed in real time, even in humans. For example, if I were to sequence your DNA and your mother's DNA there would be hundreds of differences in those third positions. This is the basis for DNA forensic testing. If you don't think it's right, you might as well release everyone that was ever arrested based on DNA evidence (including a lot of people in death row).

Actually this proves the human race is young… You might as well get over it, The DNA is the most complex mechanism that we have ever undertaken. God created it and as He puts it “My ways are above your ways”.

 

[Zaius137]

They are finding those in areas previously considered "junk" DNA. That is not what I am talking about. I am talking about third position mutations, and mutations in introns, completely different.

You are completely wrong they mention exactly what you are talking about. Did you read that article? Please let’s stay honest here.

 

[CabVet]

Actually this proves the human race is young… You might as well get over it, The DNA is the most complex mechanism that we have ever undertaken. God created it and as He puts it “My ways are above your ways”.

No, it only demonstrates that we shared an ancestor with other apes approximately 6 million years ago

Don't take me wrong, I respect your belief, and I would be perfectly happy if every creationist told me "I don't accept evolution because it's against my religious beliefs". But instead, most creationists try to twist scientific evidence seeking support for their belief.

And in the end, even if you proved evolution was completely wrong, this still wouldn't give an ounce of support for creationism. All it would be was evidence against evolution.