Register | Sign In


Understanding through Discussion


EvC Forum active members: 65 (9162 total)
4 online now:
Newest Member: popoi
Post Volume: Total: 915,817 Year: 3,074/9,624 Month: 919/1,588 Week: 102/223 Day: 0/13 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Evolving New Information
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 91 of 458 (510340)
05-30-2009 4:49 AM
Reply to: Message 89 by slevesque
05-30-2009 4:36 AM


I thought you were asking why muller's ratchet didn't provoke the extinction of bacterias ?
I'm asking why bacteria don't go extinct as a result of these mysterious, impossible mutations which cause extinction but are invisible to natural selection, when they are more vulnerable to the accumulation of deleterious mutations and breed much faster. If we don't observe it in them, why should it affect anything else?
I think it is gonna be very difficult to discuss this with your aggressive behavior ...
You mean, I point out where you're wrong, ask you for evidence, that sort of thing?
... coupled with the fact that you haven't read the book.
Feel free to reproduce his arguments.
Incidentally, have you read Kimura?
Dr. Sanford doesn't simply apply Muller's ratchet on sexual species, he ellaborates the concept of mutation accumulations to sexual species. This is very different.
It is. Muller's rachet specifically applies to asexual organisms; the idea was put forward as one reason why sex is biologically advantageous. Calling some putative process that affects sexually reproducing organisms by the name "Muller's rachet" is sheer obfuscation.

This message is a reply to:
 Message 89 by slevesque, posted 05-30-2009 4:36 AM slevesque has replied

Replies to this message:
 Message 94 by slevesque, posted 05-31-2009 3:15 AM Dr Adequate has replied

  
Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 92 of 458 (510341)
05-30-2009 6:49 AM
Reply to: Message 89 by slevesque
05-30-2009 4:36 AM


From Message 83:
slevesque in Message 83 in reply to Dr Adequate writes:
The interpretation creationist do of it is debatable, but for that you'll have to read the book instead of just reading the critics on amazone.com
From Message 89:
slevesque in Message 89 in reply to Dr Adequate writes:
I think it is gonna be very difficult to discuss this with your aggressive behavior coupled with the fact that you haven't read the book.
If someone actually reads the book that will be a nice bonus for you, but don't expect it to happen. The Forum Guidelines require that you make your arguments in your own words:
  1. Bare links with no supporting discussion should be avoided. Make the argument in your own words and use links as supporting references.
You're referencing a book instead of a link, but the same principle applies. Make the argument in your own words. The purpose of debate is so you can assess how effectively *you* can construct and support an argument, not someone else.
About the funny characters, were you trying to say ‘(μ) or something like that?
--Percy

This message is a reply to:
 Message 89 by slevesque, posted 05-30-2009 4:36 AM slevesque has not replied

  
slevesque
Member (Idle past 4641 days)
Posts: 1456
Joined: 05-14-2009


Message 93 of 458 (510417)
05-31-2009 2:52 AM
Reply to: Message 90 by Dr Adequate
05-30-2009 4:38 AM


Now, a new neutral variation thrown up by mutation is one of 2N versions (some identical) of the site, where N is the size of the population (the 2, of course, is there because we are dealing with diploid organisms). Because the variation is neutral, this means that it has no better nor worse chance of going on to fixation in the gene pool than the other 2N-1 versions of the site. It follows that when it first arises, its probability of fixation is 1/2N. A more detailed version of the proof will be found here.
Now, let the probability of the mutation in an individual be . Then the probability of it arising in a generation will be 2N. So the probability, in any generation, that such a mutation will arise and eventually go on to fixation is 2N/2N; and since we can cancel the 2N on the top and bottom of this fraction this works out to be just equal to .
I was talking about that part, with the u
The 51 mutations fixed per generation, is that threw genetic drift ?
Edited by slevesque, : No reason given.

This message is a reply to:
 Message 90 by Dr Adequate, posted 05-30-2009 4:38 AM Dr Adequate has replied

Replies to this message:
 Message 98 by Dr Adequate, posted 05-31-2009 5:11 AM slevesque has not replied

  
slevesque
Member (Idle past 4641 days)
Posts: 1456
Joined: 05-14-2009


Message 94 of 458 (510418)
05-31-2009 3:15 AM
Reply to: Message 91 by Dr Adequate
05-30-2009 4:49 AM


I'm asking why bacteria don't go extinct as a result of these mysterious, impossible mutations which cause extinction but are invisible to natural selection, when they are more vulnerable to the accumulation of deleterious mutations and breed much faster. If we don't observe it in them, why should it affect anything else?
We don't observe it in them because the no-selection zone is quasi inexistant for them, and so even nearly-neutral mutations can be detected by natural selection. hence they are not really nearly-neutral. I think Kimura uses the term 'effectively neutral' for the mutations that are not subject to natural selection, Dr. Sanford uses the term nearly-neutral, but he is talking about the same mutations (cannot be selected for).
There is much more 'effectively neutral' mutations in humans then in bacteria, because of the difference in noise.
You mean, I point out where you're wrong, ask you for evidence, that sort of thing?
I have no problem with that. But I have to say that the very first of your comments I read (on other threads) were not of that kind which you are speaking of. Much more arrogant and aggressive.
It is. Muller's rachet specifically applies to asexual organisms; the idea was put forward as one reason why sex is biologically advantageous. Calling some putative process that affects sexually reproducing organisms by the name "Muller's rachet" is sheer obfuscation.
You have to remember two things: Muller developped his idea of ratchet in asexual species, but he was aware that the same could happen in sexual species. He was a leading adovcate of eugenics, and had a deep concern for human genetic deterioration (hence the eugenism).
He thought mutations were extremely rare, and so could be dealt with one at a time threw selection. Obviously, his concern was that with the arrival of medecine etc. Natural selection would be much less efficient in the human species, and so mutations would accumulate.

This message is a reply to:
 Message 91 by Dr Adequate, posted 05-30-2009 4:49 AM Dr Adequate has replied

Replies to this message:
 Message 96 by Dr Adequate, posted 05-31-2009 4:57 AM slevesque has replied

  
slevesque
Member (Idle past 4641 days)
Posts: 1456
Joined: 05-14-2009


Message 95 of 458 (510419)
05-31-2009 3:55 AM


The accumulation of mutations in sexual species is not a farfetched idea either. Take a look at the abstract of this paper:
Loewe, L. 2006. Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA. Genet. Res., Camb 87:133-159
Abstract:
The observation of high mitochondrial mutation rates in human pedigrees has led to the question of how such an asexual genetic system can survive the accumulation of slightly deleterious mutations caused by Muller's ratchet. I define a null model to quantify in unprecedented detail the threat from extinction caused by Muller's ratchet. This model is general enough to explore the biological significance of Muller's ratchet in various species where its operation has been suspected. For increased precision over a wide range of parameter space I employ individual-based simulations run by evolution@home, the first global computing system for evolutionary biology. .After compiling realistic values for the key parameters in human mitochondrial DNA (mtDNA) I find that a surprisingly large range of biologically realistic parameter combinations would lead to the extinction of the human line over a period of 20 million years — if accepted wisdom about mtDNA and Muller's ratchet is correct.. The resulting genomic decay paradox complements a similar threat from extinction due to mutation accumulation in nuclear DNA and suggests evaluation of unconventional explanations for long-term persistence. A substantial list of potential solutions is given, including compensatory back mutations, mutation rate heterogeneity and occasional recombination in mtDNA. Future work will have to explore which of these actually solves the paradox. Nonetheless, the results presented here provide yet another reason to minimize anthropogenic increase of mutation rates..
Article Abstract
Mitochodrial DNA is an asexual system, and so subject to Muller's ratchet. However, Loewe makes it abundantly clear that nuclear DNA (which is not asexual) can also be subject to mutation accumulation. This is exactly what Dr. Sanford is talking about, an arguing for.
You can ask, if mutations are accumulating in the human genome, why aren't we seeing its effects ? Sanford does not talk about this in his book, but personnally I think we can see repercussions in this accumulation.
From a personnal experience, the region where I live, saguenay-lac-saint-jeanthat are unique to the region. These are not near-neutral by any means, because each of them are very serious . But because they are recessive (as are most mutations I believe) they have been accumulating in the region at an alarming rate. Of course none have become fixed in the population yet, but it is a very alarming situation, to the point that there has been a lot of research money invested to 'fight' this.
Another example I can think of is the recent trend to ban marriage between cousins in Europe, which is becoming a hot topic I think over there. It seems that similar mutations are becoming more and more frequent, to the point that even cousins inter-marriage are having an increasing probability of birth defects. This is in stark contrast to the culture of even 200 years ago, where marrying a cousin was common but was not known as a source of child defects. If it is now seen as a problem, it is because mutations have become more widespread in the population.
Edited by slevesque, : No reason given.
Edited by slevesque, : No reason given.
Edited by Admin, : Shorten long link.

Replies to this message:
 Message 97 by Dr Adequate, posted 05-31-2009 5:04 AM slevesque has replied
 Message 103 by Theodoric, posted 05-31-2009 9:37 PM slevesque has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 96 of 458 (510424)
05-31-2009 4:57 AM
Reply to: Message 94 by slevesque
05-31-2009 3:15 AM


We don't observe it in them because the no-selection zone is quasi inexistant for them, and so even nearly-neutral mutations can be detected by natural selection.
Saying this is no substitute for evidence.
You have to remember two things: Muller developped his idea of ratchet in asexual species, but he was aware that the same could happen in sexual species.
Quotes, please?

This message is a reply to:
 Message 94 by slevesque, posted 05-31-2009 3:15 AM slevesque has replied

Replies to this message:
 Message 99 by slevesque, posted 05-31-2009 6:50 AM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 97 of 458 (510425)
05-31-2009 5:04 AM
Reply to: Message 95 by slevesque
05-31-2009 3:55 AM


Mitochodrial DNA is an asexual system, and so subject to Muller's ratchet. However, Loewe makes it abundantly clear that nuclear DNA (which is not asexual) can also be subject to mutation accumulation.
Where does he make it "abundantly clear" that mutations in nuclear DNA, invisible to natural selection, can accumulate to cause extinction?
From a personnal experience, the region where I live, saguenay-lac-saint-jeanthat are unique to the region. These are not near-neutral by any means, because each of them are very serious . But because they are recessive (as are most mutations I believe) they have been accumulating in the region at an alarming rate. Of course none have become fixed in the population yet ...
The reason that they are unique to the region is because of the founder effect, and the reason that they will never become fixed is heterozygote equilibrium.
Another example I can think of is the recent trend to ban marriage between cousins in Europe, which is becoming a hot topic I think over there.
I've never heard of such a movement.
It seems that similar mutations are becoming more and more frequent, to the point that even cousins inter-marriage are having an increasing probability of birth defects.
Evidence?
This is in stark contrast to the culture of even 200 years ago, where marrying a cousin was common but was not known as a source of child defects. If it is now seen as a problem, it is because mutations have become more widespread in the population.
No, it's because now people know about it.
Mutations which cause birth defects are, in any case, not invisible to natural selection and so have nothing to do with Sanford's fantasies.

This message is a reply to:
 Message 95 by slevesque, posted 05-31-2009 3:55 AM slevesque has replied

Replies to this message:
 Message 100 by slevesque, posted 05-31-2009 7:01 AM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 98 of 458 (510426)
05-31-2009 5:11 AM
Reply to: Message 93 by slevesque
05-31-2009 2:52 AM


I was talking about that part, with the u
Ah, I see. That's a mu (μ) not a u.
That represents the probability of any particular single nucleotide substitution occurring.
The 51 mutations fixed per generation, is that threw genetic drift ?
Yes.
Edited by Admin, : Fix special character so it doesn't become a smiley.

This message is a reply to:
 Message 93 by slevesque, posted 05-31-2009 2:52 AM slevesque has not replied

  
slevesque
Member (Idle past 4641 days)
Posts: 1456
Joined: 05-14-2009


Message 99 of 458 (510434)
05-31-2009 6:50 AM
Reply to: Message 96 by Dr Adequate
05-31-2009 4:57 AM


the evidence is that bacteria species do not go extinct because of Muller's ratchet
For the quote:
Muller, HJ. 1950. Our load of mutations. Maer. J. Human Genetics. 2:111-176 (page149-150)
quote:
...the open possibility that the deterioration consequent on the present relaxationof selection may after all be a good deal more rapid than has commonly been imagined ... it is evident that the natural rate of mutation of human is so high, and his natural rate of reproduction so low, that not a great deal of margin is left for selection ... if u has the minimal value of 0.1 ... an average reproductive rate of 2.4 children per individual would be necessary ... without taking any account whatever of all the death and failures to reproduce for non-genetic causes ... it becomes perfectly evident that the present number of children per couple cannot be great enough to allow selection to keep pace with a mutation rate of 0.1 ... if, to make matters worse, u should be anything like as high as 0.5 ...,our present reproductive practises would be utterly out of line with human requirements.
Thus why he was a proponent of eugenics.
Note also that, if I'm not mistaken, we now know that the mutation rate is at least 1000-fold higher, and that fertility is on the decline, which in itself is compelling.
Edited by slevesque, : No reason given.
Edited by slevesque, : No reason given.

This message is a reply to:
 Message 96 by Dr Adequate, posted 05-31-2009 4:57 AM Dr Adequate has replied

Replies to this message:
 Message 101 by Dr Adequate, posted 05-31-2009 8:51 PM slevesque has not replied

  
slevesque
Member (Idle past 4641 days)
Posts: 1456
Joined: 05-14-2009


Message 100 of 458 (510437)
05-31-2009 7:01 AM
Reply to: Message 97 by Dr Adequate
05-31-2009 5:04 AM


Where does he make it "abundantly clear" that mutations in nuclear DNA, invisible to natural selection, can accumulate to cause extinction?
"The resulting genomic decay paradox complements a similar threat from extinction due to mutation accumulation in nuclear DNA "
Its is as clear as you can get
No, it's because now people know about it.
People would have known of birth defects caused by sister-brother marriage, but would have been ignorant of cousins marriage birth defect ?
It seems more logical to me that it was less of a problem in those days.
Mutations which cause birth defects are, in any case, not invisible to natural selection and so have nothing to do with Sanford's fantasies.
Of course, if we are talking about a dominant gene, then it cannot accumulate. But if the birth defect comes fro ma recessive gene, then it can accumulate, and as it accumulates, it becomes more frequent that two individuals have the gene and give birth to sick children.
I've never heard of such a movement.
It isn't a movement (yet, I suppose) but it is being talked, especially in England. It is because of the Islam, in which cousins marriage is encouraged I think (Mohammed married his cousin). And so the problem is more evident.
Here in North America it is no longer popular to marry our cousins (thankfully lol), but my intuition would tell me that if it would still be, then we would be facing the same problems as in europe.

This message is a reply to:
 Message 97 by Dr Adequate, posted 05-31-2009 5:04 AM Dr Adequate has replied

Replies to this message:
 Message 102 by Dr Adequate, posted 05-31-2009 8:56 PM slevesque has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 101 of 458 (510501)
05-31-2009 8:51 PM
Reply to: Message 99 by slevesque
05-31-2009 6:50 AM


the evidence is that bacteria species do not go extinct because of Muller's ratchet
That would be my point.

This message is a reply to:
 Message 99 by slevesque, posted 05-31-2009 6:50 AM slevesque has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 102 of 458 (510502)
05-31-2009 8:56 PM
Reply to: Message 100 by slevesque
05-31-2009 7:01 AM


"The resulting genomic decay paradox complements a similar threat from extinction due to mutation accumulation in nuclear DNA "
Its is as clear as you can get
Ah, I see.
Nonetheless, he seems convinced that this does not actually happen.
People would have known of birth defects caused by sister-brother marriage ...
Would they?
It's not like it happens that often. What with being illegal, and all that.
Of course, if we are talking about a dominant gene, then it cannot accumulate. But if the birth defect comes fro ma recessive gene, then it can accumulate, and as it accumulates, it becomes more frequent that two individuals have the gene and give birth to sick children.
Up to heterozygote equilibrium.
It isn't a movement (yet, I suppose) but it is being talked, especially in England.
I'm English, I've never heard of this.

This message is a reply to:
 Message 100 by slevesque, posted 05-31-2009 7:01 AM slevesque has not replied

Replies to this message:
 Message 105 by bluegenes, posted 06-01-2009 6:19 PM Dr Adequate has not replied

  
Theodoric
Member
Posts: 9076
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 3.7


Message 103 of 458 (510505)
05-31-2009 9:37 PM
Reply to: Message 95 by slevesque
05-31-2009 3:55 AM


slevesque writes:
where marrying a cousin was common but was not known as a source of child defects. If it is now seen as a problem, it is because mutations have become more widespread in the population.
Ok do you have any evidence for the things you say. Cousin/cousin is not huge cause of birth defects.
Here is some real science on the issue
quote:
Contrary to widely held beliefs and longstanding taboos in America, first cousins can safely have children together, without a great risk of birth defects or genetic disease, scientists are reporting today. They say there is no biological reason to discourage cousins from marrying[
Here is the original.
quote:
There is a great deal of stigma associated with cousin unions in the United States and Canada that has little biological basis.

Facts don't lie or have an agenda. Facts are just facts

This message is a reply to:
 Message 95 by slevesque, posted 05-31-2009 3:55 AM slevesque has not replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 104 of 458 (510607)
06-01-2009 5:41 PM


Muller's Ratchet
Three points.
1. Muller's ratchet can be overcome through recombination. While bacteria are considered asexual they do exchange DNA on occasion.
2. Beneficial mutations can compensate for deleterious mutations. This is exactly what was found in this study:
quote:
However, we also observed the accumulation of putative compensatory mutations (DRSeq2) in temperate-clade C. briggsae lineages (Figure 4) that likely reduce ND5 deletion levels. The DRSeq2 mutations can only be considered beneficial, however, in the context of the preexisting deleterious ND5-2 insertion mutation — in fact, virtually any mutation in ND5-2 that reduces its homology to ND5 is likely to be beneficial to some extent.
In other words, mutations that compensate for the deleterious mutations will be selected for.
3. A genome can only handle a certain amount of deleterious mutations. At some point new deleterious mutations will be face strong selective pressures. This appears to be the case in the primary endosymbiots of lice (this study).
quote:
A decrease in nucleotide substitution rates over time suggests that selection may be limiting the effects of Muller's ratchet by removing individuals with the highest mutational loads and decreasing the rate at which new mutations become fixed. This countering effect of selection could slow the overall rate of endosymbiont extinction.
So it would seem that there are at least 3 mechanisms by which asexual genomes can avoid the effects of Muller's Ratchet.

  
bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 105 of 458 (510613)
06-01-2009 6:19 PM
Reply to: Message 102 by Dr Adequate
05-31-2009 8:56 PM


Cousin marriage
Dr Adequate writes:
I'm English, I've never heard of this.
I have. It's not Muslims as such, but people from some areas of Pakistan (who happen to be Muslims) that have produced a lot of migrants. Here (link below), it says that the birth defect rate is thirteen times the average, which doesn't seem to fit the U.S. research for random cousin marriages Theodoric linked to above.
However, it may be a cumulative effect in communities that constantly do it (you're marrying your first cousin, second cousin and aunt/uncle once removed all at the same time!!!!).
BBC NEWS | Programmes | Newsnight | The risks of cousin marriage

This message is a reply to:
 Message 102 by Dr Adequate, posted 05-31-2009 8:56 PM Dr Adequate has not replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024