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nylonase refuted?

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nylonase refuted?

Postby adkinsjr » Sat Dec 19, 2009 10:43 am

I came across an anti-evolution paper about novel genes from duplication. I don't know much about genetics, so I thought that perhaps someone on this forum could help me understand this. From what I'm reading, the paper claims that gene duplication and frame-shift mutation are not sufficient to account for new genes. Nylonase is an example frame-shift mutation which was believed to have created a new gene. The paper claims to refute this.

http://talkrational.org/showthread.php?t=20043

Is any of this information correct?
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Postby JackBean » Sun Dec 20, 2009 11:32 pm

not available
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re: nylonase refuted?

Postby robsabba » Mon Dec 21, 2009 4:24 pm

adkinsjr wrote:I came across an anti-evolution paper about novel genes from duplication. I don't know much about genetics, so I thought that perhaps someone on this forum could help me understand this. From what I'm reading, the paper claims that gene duplication and frame-shift mutation are not sufficient to account for new genes. Nylonase is an example frame-shift mutation which was believed to have created a new gene. The paper claims to refute this.

http://talkrational.org/showthread.php?t=20043

Is any of this information correct?

You need to log in . Can you cut and paste it here?
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Re: nylonase refuted?

Postby adkinsjr » Mon Dec 21, 2009 11:45 pm

Sorry about that. The file is pdf, so I can't attach it. I uploaded it to megaupload. It only takes a second to download and open.

http://www.megaupload.com/?d=SQ362L1I

This is the thread where I found the paper on talk rational:

http://talkrational.org/showthread.php?t=20043

If you register, you can download it straight from the talkrational forum.
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Re: nylonase refuted?

Postby adkinsjr » Tue Dec 22, 2009 12:19 am

Browsing the paper, I don't understand the duplicate analysis. However, the main argument seems to be that the duplicates don't sufficiently diverge to produce novel genes. Mutations only result in "variations within a kind" of gene.

I always thought that evolution occured when genes vary. How do we determine a point that a gene is "NEW" and not just a variation of the ancestrial gene?
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Postby MrMistery » Sat Jan 02, 2010 5:11 pm

this article is stupid. It claims that when a gene is duplicated, both copies are ALWAYS under purifying selection. That cannot be true. If it were, then:
1. pseudogenes wouldn't exist
2. down syndrome wouldn't be bad - if two copies of a gene were better than one because one copy would be just a backup, then having down syndrome would result in a better adapted individual. Obviously that doesn't happen

That's what happens when you read crap that wasn't subjected to peer review and that has the users of an internet forum under acknowledgements. Anyone can write some crap and put it on the internet.
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Re: nylonase refuted?

Postby Phydeaux » Sun Jan 03, 2010 2:30 am

Hmmm, well while the subject is up. I'm curious of what you guys think of this:

http://aslodge.tripod.com/id89.htm

According to him:

"...if only 6 of these 47 mutations were essential for the evolution, the probability of achieving it in 30 years is about 3 x 10^-35. So, if the evolution could not be random, then it would have to be nonrandom..."

This was put up in 2002 so it is possible he did have all of the data, but really, what are the chances of this occurring? Is it really plausible? Would this be the extreme and very unlikely case or perhaps a nonrandom cause could be the answer as this guy suggests?
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Postby MrMistery » Sun Jan 03, 2010 7:52 pm

that is not an error in the data, it is an error in using probability. Probability can only be used forward, not backward. Let me give you a couple of easy examples to make my point.

1. Take a deck of cards and deal them between you and your friend. After that ask yourself "What is the probability of dealing this hand of 26 cards? How improbable! Considering those odds, if I play cards all my life i won't get the same hand!". But nevertheless you dealt the cards, and nevertheless you got the hand that you got.

2. Take the Harvard Class of 2009 - 1600 people. The probability that student #1 being born on the exact day he was actually born on is 1/365. Now take student #2. The probability that she was born on her birthday is also 1/365. The probability that both of them were born on their birthdays is (1/365)^2. In fact the probability that the entire class was born on their birthday is (1/365)^1600, much smaller than the probability calculated by he person in that article. There is nothing non-random in the distribution of those birthdays, and the people exist for sure: they graduated last summer.
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Re:

Postby Phydeaux » Sun Jan 03, 2010 8:27 pm

MrMistery wrote:that is not an error in the data, it is an error in using probability. Probability can only be used forward, not backward. Let me give you a couple of easy examples to make my point.

1. Take a deck of cards and deal them between you and your friend. After that ask yourself "What is the probability of dealing this hand of 26 cards? How improbable! Considering those odds, if I play cards all my life i won't get the same hand!". But nevertheless you dealt the cards, and nevertheless you got the hand that you got.

2. Take the Harvard Class of 2009 - 1600 people. The probability that student #1 being born on the exact day he was actually born on is 1/365. Now take student #2. The probability that she was born on her birthday is also 1/365. The probability that both of them were born on their birthdays is (1/365)^2. In fact the probability that the entire class was born on their birthday is (1/365)^1600, much smaller than the probability calculated by he person in that article. There is nothing non-random in the distribution of those birthdays, and the people exist for sure: they graduated last summer.


Well, in your examples you could have said that about any combination. In the case of beneficial mutations it is a bit different. Any mutation will not be beneficial, but I suppose his assumptions here are that 6 of the mutations must have happened, no other combination could end up with the same result, and different beneficial result with a gain of information could occur. Whether that is a safe assumption or not I doubt we really know enough about beneficial mutations to know. I do think the nonrandom idea is silly (although I wouldn't ignore it as a possibility), but perhaps one could argue that this was the extreme case.
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Postby bellyjelly » Tue Jul 12, 2011 7:51 am

As I understand nylonase refuted is a type of gene mutation wherein the addition or deletion of (a number of) nucleotide(s) causes a shift in the reading frame of the codons in the mRNA, thus, may eventually lead to the alteration in the amino acid sequence at protein translation.
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Re:

Postby Vanessa13 » Mon Aug 01, 2011 7:35 am

MrMistery wrote:this article is stupid. It claims that when a gene is duplicated, both copies are ALWAYS under purifying selection. That cannot be true. If it were, then:
1. pseudogenes wouldn't exist
2. down syndrome wouldn't be bad - if two copies of a gene were better than one because one copy would be just a backup, then having down syndrome would result in a better adapted individual. Obviously that doesn't happen

That's what happens when you read crap that wasn't subjected to peer review and that has the users of an internet forum under acknowledgements. Anyone can write some crap and put it on the internet.


fully agree with all arguments, the article does't go for sure
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Re:

Postby merv » Mon Oct 03, 2011 4:52 am

MrMistery wrote:this article is stupid. It claims that when a gene is duplicated, both copies are ALWAYS under purifying selection. That cannot be true. If it were, then:
1. pseudogenes wouldn't exist
2. down syndrome wouldn't be bad -


duuuude....what the f are you saying? next you'll be saying having slanty eyes is bad, and blond hair, and so on. Down's syndrome is a challenge, sure, but no man is an island- we all need help here and there, and Down's syndrome help too - stop being so politically incorrect, especially in a genetics forum. I am sure it was just a innocent slip, right? :cry:


MrMistery wrote:if two copies of a gene were better than one because one copy would be just a backup, then having down syndrome would result in a better adapted individual. Obviously that doesn't happen

That's what happens when you read crap that wasn't subjected to peer review and that has the users of an internet forum under acknowledgements. Anyone can write some crap and put it on the internet.


no kidding. what about short people, how do you get on with them? are they ok or do they need to adapt better too? Jeeeez Louise.
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