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slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 67 of 458 (509703)
05-24-2009 1:36 AM
Reply to: Message 65 by Percy
05-23-2009 6:10 AM


Ok, well next time I'll use more concrete examples such as dinosaur to bird so that it won't be confusing for anyone.
And you'll have to tell me how I advocated an old earth on the cosmology thread, since I do remember only saying that Carmeli was advocating an old earth, not me

This message is a reply to:
 Message 65 by Percy, posted 05-23-2009 6:10 AM Percy has replied

Replies to this message:
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slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 69 of 458 (509705)
05-24-2009 2:14 AM
Reply to: Message 66 by Dr Adequate
05-23-2009 6:13 AM


What was it?
The phrase was about the no selection zone.
Er ... what? This doesn't appear to mean anything. "Quasi-inexistent due to low noise"?
noise is what determines the range of the 'no-selection zone' in Kimura's mutation distribution. Bacterias have have a very high signal-to-noise ratio because there noise is very, very small. So even nearly-neutral deletirious mutations in bacteria have an impact on the phenotypic level on which natural selection can happen. Likewise, beneficial mutations are rapidly fixed in a population, and the fast accumulation of such mutations makes the optimization of bacteria populations to new conditions very fast (sometimes in a matter of days) Thus, there is no muller's ratchet in those populations.
And what do your statements about bacteria have to do with yeast, which is a eukaryote?
And what evidence do you have for anything you're saying?
There is not much difference between the noise in yeast and in bacterias, and so again no muller's ratchet.
The difference I could see would be in their mutations rates. Eukaryotic (if I'm not mistaken) have more efficient mutation-correcting mechanisms which would slow down any adaptation compared to bacterias.
But it has changed in such a manner. A defining characteristic of the species has been altered. Anyone who had found something that behaver like Lenski's bacteria in the wild who checked to see if they were E. coli would have found that they weren't and would have announced the discovery of a new bacterial species.
Funny how E.Coli capable of feeding on citrate had already been identified in the past, but were nonetheless recognized as mutant E.Coli: (both cited in Lenskis work, BTW)
- Hall, B.G. 1982. Chromosomal mutation for citrate utilization by Escherichia coli K-12. J. Bacteriol. 151:269-273.
- Pos, K.M., Dimroth, P., and Bott, M. 1998. The Escherichia coli citrate carrier CitT: a member of a novel eubacterial transporter family related to the 2-oxoglutarate/malate translocator from spinach chloroplasts. J. Bacteriol. 180:4160-4165.
In the first reference, the mutation was never identified. In the second one, the gene citT was overexpressed. Lenski didn't really innovate, he simply redid the experiment hoping to get a different mutation. He hasn't yet tracked his mutation down, but I suspect it will be similar.
You would not find Lenski's bacteria in the wild if 'the wild' would be in oxygen rich conditions. You have to remember that it was known before Lenski's experiment that E.Coli could ''feed'' on citrate in anaerobic conditions. Lenski put his E.Coli in a very citrate-rich environnment, with very little glucose, keeping them in some sort of starvation mode so that if a mutation could get the citrate inside the cell, it would be beneficial due to a high concentration of citrate.
Although the fitness of the bacteria has increased, it has come at a cost: all lines lost the ability to catabolize ribose, and some lines lost the ability to repaire DNA.
If you take Lenski's E.Coli, and give them an abundance of glucose, they will not only regain their ability to feed on it, they will also loose their citrate-feeding capability. This is simply a showing of the vast adaptation capability of baterias, because of what I've said earlier (it took 20 years in lenskis experiment because it needed 2 or more mutations). Put them in different environnments, and they will develop different 'new traits' accordingly. But all in all, they will always remain E.Coli.

This message is a reply to:
 Message 66 by Dr Adequate, posted 05-23-2009 6:13 AM Dr Adequate has replied

Replies to this message:
 Message 72 by Dr Adequate, posted 05-24-2009 2:54 AM slevesque has replied

  
slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 70 of 458 (509706)
05-24-2009 2:16 AM
Reply to: Message 68 by Dr Adequate
05-24-2009 1:43 AM


Is it false to say that birds could become the ancestors of some horse animal in the future ?
Be careful with the arrogance, it was an example of something that, if evolution is true, could happen in the future! And so even if has a very remote chance of happening, it is nonetheless true, not false

This message is a reply to:
 Message 68 by Dr Adequate, posted 05-24-2009 1:43 AM Dr Adequate has replied

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slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 73 of 458 (509713)
05-24-2009 3:29 AM
Reply to: Message 72 by Dr Adequate
05-24-2009 2:54 AM


"Noise"?
Phenotypic noise. It is the simple concept that factors other then the genome influence natural selection. Mostly enviromental factors such as nutrition,chance etc.
Signal-to-noise ratio is often expressed in terms of heritability. a heritability of 1 means the trait is 100% heritable (such as blood type). As an example, height has a heritability of 0.3
If you propose that in eukaryotes deleterious mutations have no effect on the phenotype, I should be fascinated to know in what sense they are deleterious.
They are not neutral, they are nearly-neutral (neutral mutations don't exist, see kimura). This means they do have an effect, but it is so small that it can't be selected because of the noise.
You might want to look up the term: "Muller's ratchet".
It is, by definition, a mechanism which causes the accumulation of deleterious mutations in asexually reproducing organisms. Such as bacteria.
Maybe a quote from Muller will make it a little more clear:
quote:
There comes a level of advantage,however, that is too small to be effectively seized upon by selection, its voice being lost in the noise, so to speak. This level would necessarily differ greatly under different circumstances (genetic,ecological,etc.), but this is a subject which has as yetbeen subjected to little analysis ... although deserving it
I hope this makes it clearer. For the mutations to accumulate in the population, they most be selectable. In order for them to be selectable, signal-to-noise ratio most be high. So bacterias (and yeast), due to very small noise, have practically no accumulations of deletirious mutations.
I won't come back on the Lenski experiment, as I think my explanation was pretty clear. You say its evolution, fine, as long as your showing it as simple descent with modification, and not as one of the steps of bacteria-to-man evolution.
Edited by slevesque, : No reason given.

This message is a reply to:
 Message 72 by Dr Adequate, posted 05-24-2009 2:54 AM Dr Adequate has replied

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 Message 75 by Dr Adequate, posted 05-24-2009 10:16 AM slevesque has replied

  
slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 83 of 458 (510329)
05-30-2009 3:15 AM
Reply to: Message 75 by Dr Adequate
05-24-2009 10:16 AM


Now I'll try to make things clearer on here.
Find Kimura's mutation distribution graphic, you will see that 0 (neutrality) is an asymptote.
Also on Muller ratchet, notice that it was never observed to cause the extinction of bacteria species. It was, in fact, very, very, very seldom observed. Remember that at the time Muller thought of this, technology wasn't good enough for him to test it. It is still much more hypothetical than experimental, exactly because of what I was saying earlier.
The only experimental documentation of muller's ratchet I found is this:
- Chao, 1990, Fitness of an RNA virus decreased by Muller's ratchet, Nature 348: 454 - 455
Muller ratchet has not yet been falsified. The vast majority of geneticist agree that it exists. You question why we do not see it causing the extinction of bacterias ? It is because of what I have explained (noise, etc.). Ask a geneticist and he will give you aproximately the same answer. Its existence in bacteria populations is not questioned by evolutionist or creationist.
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

This message is a reply to:
 Message 75 by Dr Adequate, posted 05-24-2009 10:16 AM Dr Adequate has replied

Replies to this message:
 Message 86 by Dr Adequate, posted 05-30-2009 4:06 AM slevesque has replied

  
slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 84 of 458 (510330)
05-30-2009 3:24 AM
Reply to: Message 76 by Taq
05-26-2009 6:37 PM


I agree some mutations account to multiple variations in nucleotides. But the ''representing at least 40 million mutations fixed'' include all types of mutations.

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slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 85 of 458 (510332)
05-30-2009 3:45 AM
Reply to: Message 62 by Dr Adequate
05-23-2009 4:54 AM


Ok, I'll try to follow you here.
According to your calculations, how many mutations would be fixed in a single generation ? Your equation is gMs if I'm not mistaken.
Now 1 generation means g=1. M=1.7 ~ 10^-8 and s=3 000 000 000
So, according to you, there is 510 mutations fixed per generation, am I correct on this ?
If so, why the part on ‘ ?

This message is a reply to:
 Message 62 by Dr Adequate, posted 05-23-2009 4:54 AM Dr Adequate has replied

Replies to this message:
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slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 88 of 458 (510337)
05-30-2009 4:29 AM
Reply to: Message 87 by Dr Adequate
05-30-2009 4:21 AM


I recalculated and got 51 also
that last character didn't come out well, it was supposed to be the u

This message is a reply to:
 Message 87 by Dr Adequate, posted 05-30-2009 4:21 AM Dr Adequate has replied

Replies to this message:
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slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 89 of 458 (510338)
05-30-2009 4:36 AM
Reply to: Message 86 by Dr Adequate
05-30-2009 4:06 AM


I thought you were asking why muller's ratchet didn't provoke the extinction of bacterias ?
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.
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 like an extension of Muller's ratchet, if you like.

This message is a reply to:
 Message 86 by Dr Adequate, posted 05-30-2009 4:06 AM Dr Adequate has replied

Replies to this message:
 Message 91 by Dr Adequate, posted 05-30-2009 4:49 AM slevesque has replied
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slevesque
Member (Idle past 4640 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

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slevesque
Member (Idle past 4640 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.

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 Message 91 by Dr Adequate, posted 05-30-2009 4:49 AM Dr Adequate has replied

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

  
slevesque
Member (Idle past 4640 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.

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slevesque
Member (Idle past 4640 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.

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slevesque
Member (Idle past 4640 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.

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 Message 97 by Dr Adequate, posted 05-31-2009 5:04 AM Dr Adequate has replied

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slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 106 of 458 (511091)
06-06-2009 2:23 AM


advancement in this debate. Sanford developped along with Baumgardner a computer program named 'Mendel's accountant' which ''is a user-friendly biologically realistic simulation program for investigating the
processes of mutation and selection in sexually reproducing diploid populations''.
(on a side note, Baumgardner is the one who developped the 'Terra' program, used by geophysicists)
Sanford says in an interview that this program has been reported in two secular journals. I'm trying to find the articles in question.
EDIT:
John Sanford, John Baumgardner, Wes Brewer, Paul Gibson, and Walter ReMine, Mendel’s Accountant: A biologically realistic forward-time population genetics program, Scalable Computing: Practice and Experience 8(2):147—165, June 2007.
John Sanford, John Baumgardner, Wes Brewer, Paul Gibson, and Walter ReMine, Using computer simulation to understand mutation accumulation dynamics and genetic load, in Y. Shi et al. (eds.), Computational ScienceICCS 2007, Part II, Lecture Notes in Computer Science 4488, Springer—Verlag, Berlin, Heidelberg, pages 386—392.
They has made simulations using this program that confirmed what Sanford was advancing in his book Genetic entropy.
This is the description of the program, I'm reading it right now. (http://www.scpe.org/vols/vol08/no2/SCPE_8_2_02.pdf)
Edited by slevesque, : No reason given.

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