Natural Selection or Luck

Lucaspa: Look at the equation, DNAunion. Even the slightest positive selection value will result in fixation.

DNAunion: Your original statement that I addressed, when taken in complete isolation, was incorrect.

However, I did not bother to follow the discussion, or even read that whole post, so it is quite possible that I missed one or more things that made your statement correct within the discussion's overall context. If so, I apologize.

Lucaspa: Now, since you say that loss of beneficial mutations from a population is a common event, you should give us examples of this happening.

DNAunion: Genetic drift is driven by chance so selection really has no say in the matter. Consequently, alleles lost from a population by genetic drift can be deleterious, neutral, or beneficial ones.

Anyway, I'll drop out of this thread (assuming no one tries to argue against the correctness of my original point).

PS: I didn't say it was common, I said it often times occurs: there's a slight difference.
 
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lucaspa

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Today at 06:39 PM DNAunion said this in Post #81

DNAunion: Your original statement that I addressed, when taken in complete isolation, was incorrect.

You should not have taken it in complete isolation.  You picked one statement out-of-context from within a long and complex discussion and addressed that.  If this were thermodynamics, you looked only at a system and ignored the surroundings. :)

However, I did not bother to follow the discussion, or even read that whole post, so it is quite possible that I missed one or more things that made your statement correct within the discussion's overall context. If so, I apologize.

Thank you. That is what you did.

Anyway, I'll drop out of this thread (assuming no one tries to argue against the correctness of my original point).

Since your original point was a strawman of your own making, congratulations in your correctness concerning the strawman.

DNAunion: Genetic drift is driven by chance so selection really has no say in the matter. Consequently, alleles lost from a population by genetic drift can be deleterious, neutral, or beneficial ones.

We weren't discussing genetic drift (and this only really occurs when the effective population size is less than 10 or so).  Micaiah also had a misconception of "chance" in the survival of individuals.
 
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lucaspa

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Today at 06:39 PM DNAunion said this in Post #81


Lucaspa: Now, since you say that loss of beneficial mutations from a population is a common event, you should give us examples of this happening.

DNAunion: Genetic drift is driven by chance so selection really has no say in the matter. Consequently, alleles lost from a population by genetic drift can be deleterious, neutral, or beneficial ones.

I ask for specific examples and you give me a glittering generality of genetic drift!!  Where's the beef?  How many examples of genetic drift are there?  Is genetic drift a common event?

Aren't there any studies looking at populations undergoing genetic drift and watching the disappearance of "beneficial mutations"?

You often ask me for references and material.  I'm asking you for that same. Sauce for the goose.
 
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lucaspa

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Micaiah, you are concerned with deaths not directly related to the trait under selection.

Futuyma addresses that (which is one reason people should really read an evolutionary biology textbook).

"Thus much, perhaps most, of the mortality suffered by a population may be random with respect to this locus or character [hoofs in horses, for example]  These nonselective deaths may be contrasted with selective death, those that contribute to the difference in fitness between genotypes.  Even if most mortality is nonselective, the selective deaths that do occur can be a potent source of natural selection.  For instance, genetic differences in swimming speed in a small planktonic crustacean might well not affect the likelihood of being eaten by baleen whales, which might be the major source of mortality.  But if swimming speed affects escape from another predator species, even one that accounts for only 1 percent of the deaths, there will be an average difference in fitness, and swimming speed may evolve by natural selection." Futuyma, Evolutionary Biology, pg 368.
 
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Yinlowang

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LucasPA, have a question for ya, trying to understand more about this stuff.

If you have a population of say 100,000 critters and 20% or 20,000 have the slightly bigger middle toe. If 70% of the population dies to things not related to that feature, then 6,000 of the individuals with the big toe are remaining on average, right?

OK, then of the remaining population of 6,000 big toes and 24,000 small toes, 100% of the big toes reproduce and say 90% of the small toes live long enough to reproduce then the next generation (assuming a litter of 5) you end up with 30,000 big toes and 108,000 small toes. Now 21.7% of the population have the big toe. Is that how it works?

And then in the population of big toes, you have a certain percent that have even bigger toes, and of those some even bigger, etc where they are gaining "market share" so to speak. :) Is that anywhere close to right?
 
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lucaspa

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Today at 11:29 AM Yinlowang said this in Post #85

LucasPA, have a question for ya, trying to understand more about this stuff.

If you have a population of say 100,000 critters and 20% or 20,000 have the slightly bigger middle toe. If 70% of the population dies to things not related to that feature, then 6,000 of the individuals with the big toe are remaining on average, right?

OK, then of the remaining population of 6,000 big toes and 24,000 small toes, 100% of the big toes reproduce and say 90% of the small toes live long enough to reproduce then the next generation (assuming a litter of 5) you end up with 30,000 big toes and 108,000 small toes. Now 21.7% of the population have the big toe. Is that how it works?

And then in the population of big toes, you have a certain percent that have even bigger toes, and of those some even bigger, etc where they are gaining "market share" so to speak. :) Is that anywhere close to right?

Very, very close.  Right idea but wrong details :)

It looks like you are using an asexually reproducing population, so you have each of 6,000 big toes making 5 offspring for your 30,000 and each of 0.9 x 24,000 =  21,600 smaller toes having 5 offspring, right?  That would give you the 108,000 small toes.

Instead, the situation is based on sexual reproduction, so we have 21,600 total breeding animals for 11,800 breeding pairs, each  pair producing 5 offspring for a total of 59,000 offspring.  Now, assuming that each of the 6,000 big toes chose a small toed partner and assuming that big toe shows up in all 5 offspring (both not realistic but close enough for government work), that means 30,000 big toe offspring and only 29,000 small toed offspring. The market share has increased not from 20% to 21.7% but from 20% to nearly 50%.  A much bigger jump than you calculated!

Now, being realistic is going to lower that 50% some.  To find out the real number, go back to the delta p equation and put in 0.1 for s, 0.25 for p, and 0.75 for q and see what you get for delta p. Add that to 20% to get the new market share.

And you are absolutely right that in the next generation, some will have even bigger toes than the first generation.  That is the beauty of cumulative selection.  Very good!
 
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Lucaspa: Now, since you say that loss of beneficial mutations from a population is a common event, you should give us examples of this happening.

DNAunion: Genetic drift is driven by chance so selection really has no say in the matter. Consequently, alleles lost from a population by genetic drift can be deleterious, neutral, or beneficial ones.

Lucaspa: I ask for specific examples and you give me a glittering generality of genetic drift!!

DNAunion: I gave you what I needed to in order to support my position. The logic is really quite simple and I am sure everyone here - even those with no formal education in biology - grasped it quite easily.

Do you reject the fact that beneficial alleles can be lost from a population through genetic drift?
 
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DNAunion: And here's some supporting material (from my personal notes).

Most Beneficial Mutations Fail to become Fixed in the Population and Many are Lost

Sticking with the topic of population genetics for a minute, one more important point should me made concerning mutant alleles.

“[Random genetic] Drift and differential survival operate at cross purposes, and the net result can be counter-intuitive. For example, most beneficial mutations never reach fixation, but are eliminated from the population by drift, despite the advantage they confer. This tends to occur
within the first ten generations after the entrance of the beneficial mutation into the population.


***************************
“Only a small fraction of the beneficial mutants are lucky enough to escape accidental loss in the first few generations of their existence. The fortunate few eventually attain a frequency high enough to protect them from further risk of chance extinction … (Kimura and Ohta, 1971, p3)”
***************************

Let s be the selection coefficient of a beneficial mutation. For small values of s (said to be typical of evolution) the chance of the mutant eventually reaching fixation is 2s. For example, a mutant with a one-percent advantage (s = 0.01) has only one chance in fifty that it will eventually
spread to the entire population [reference pointing to supporting materials: Kimura and Ohta, 1971, p3; Maynard Smith, 1989, p161-162]. Likewise, for every mutant gene having a selective advantage of 1/2 percent, that becomes fixed in a population, 99 equally advantageous mutants have been lost, without ever being used in evolution [reference pointing to supporting material: Kimura and Ohta, 1971, p10-11]. This result is based on the assumption that the population is extremely large (approaching infinity).

In a smaller population the outlook is less hopeful. The smaller the population, the smaller is the chance of receiving a beneficial mutation in the first place. A population one tenth as large must wait ten times longer for a beneficial mutation.

Also, the smaller the population, the more genetic drift dominates over differential survival.

********************************
“The fact that the majority of mutants, including those having a slight advantage, are lost by chance is important in considering the problems of evolution by mutation, since the overwhelming majority of advantageous mutations are likely to have only a slightly advantageous effect. …

In our opinion, this fact has not fully been acknowledged in many discussions of evolution. It is often tacitly assumed that every advantageous mutation that appears in the population is inevitably incorporated. Also, it is not generally recognized that this fact can set an upper limit to the speed of adaptive evolution, because the frequency of
occurrence of advantageous mutations must be much lower than that of deleterious mutations. (Incidentally, this fact gives a great evolutionary advantage to a large population.)” (Kimura and Ohta, 1971, p11 [italics by quoting author]).
*****************************

Kimura and Ohta correctly point out the great evolutionary advantage of large population sizes.

They note that small population size can limit the speed of evolution. This conflicts with the claims of many paleontologists who (based on fossil gaps) assert that the small population is where rapid evolution occurs.” (Walter James ReMine, The Biotic Message: Evolution Versus Message Theory, St. Paul Science, 1993, p180-181)

DNAunion: Some may object to the above lengthy quote, claiming that the author is biased (the book is after all an “anti-evolution” text). However, note that a good portion of the quote is actually from a respected evolutionist: not from ReMine himself. In addition, the following long quote from a recent evolutionary text confirms the most important points that ReMine made.

“The probability that a new mutant allele will become fixed in a population (i.e. the mutant gene completely substitutes the original wild-type allele) depends on its selective advantage, disadvantage or neutrality, as well as the population size. According to the calculations of Kimura (1962) for a neutral allele the fixation probability (P) equals its frequency in the population. This plausible conclusion reflects the fact that in the case of neutral alleles, fixation occurs by random genetic drift, where neutral alleles have an equal probability of fixation, the outcome of the competition depends only on their frequency. It could also be shown that if an advantageous mutation arises in a large population and its selective advantage (s) over the rest of the alleles is small then the probability of its fixation is P [is about equal to] 2s. In other words, if a mutant has 1% selective advantage, it has about 2% chance of fixation. An important consequence of this conclusion is that an advantageous mutation does not always become fixed in the population but may be lost by chance. The results of Kimura’s work are of great theoretical importance, since they show that the earlier views that saw evolution as a process in which advantageous mutations are always fixed and only advantageous mutations are fixed are oversimplified. In fact, the calculations show that neutral and even slightly deleterious mutations may have a definite probability of becoming fixed in a population.” (emphasis added, Laszlo Patthy, Protein Evolution, Blackwell Science, 1999, p40-41)
 
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DNAunion: Always willing to support my position (unlike some people we know who post here), here's another quote.

"The production of random evolutionary changes in small breeding populations is known as genetic drift. Genetic drift results in allele frequency changes in a population from one generation to another. One allele may be eliminated from the population by chance, regardless of whether that allele is beneficial, harmful, or of no particular advantage or disadvantage." (emphasis added, Eldra Pearl Solomon, Linda R. Berg, & Diana W. Martin, Biology: Fifth Edition, Saunders College Publishing, 1999, p393)
 
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lucaspa

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26th March 2003 at 06:47 PM DNAunion said this in Post #87

DNAunion: I gave you what I needed to in order to support my position. The logic is really quite simple and I am sure everyone here - even those with no formal education in biology - grasped it quite easily.

Do you reject the fact that beneficial alleles can be lost from a population through genetic drift?

You said it had been observed.  Where are the observations?
 
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lucaspa

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27th March 2003 at 06:27 PM DNAunion said this in Post #88

“Only a small fraction of the beneficial mutants are lucky enough to escape accidental loss in the first few generations of their existence. The fortunate few eventually attain a frequency high enough to protect them from further risk of chance extinction … (Kimura and Ohta, 1971, p3)”
***************************

Let s be the selection coefficient of a beneficial mutation. For small values of s (said to be typical of evolution) the chance of the mutant eventually reaching fixation is 2s. For example, a mutant with a one-percent advantage (s = 0.01) has only one chance in fifty that it will eventually
spread to the entire population[/I]

This formula applies only to large populations, where N is too large for genetic drift.  Care to give us the formula for small populations?

"In a smaller population the outlook is less hopeful. The smaller the population, the smaller is the chance of receiving a beneficial mutation in the first place. A population one tenth as large must wait ten times longer for a beneficial mutation."

This does not follow.  This assumes that "beneficial mutations" are rate limiting.

I don't see any references to observations yet, DNAunion. And that is what you promised.

You are also ignoring that Kimura is promoting a falsified theory here: that speciation occurs by mutation first followed by natural selection.  That has been disproved.  Speciation is the result of natural selection.

"It is often tacitly assumed that every advantageous mutation that appears in the population is inevitably incorporated. Also, it is not generally recognized that this fact can set an upper limit to the speed of adaptive evolution, because the frequency of
occurrence of advantageous mutations must be much lower than that of deleterious mutations."

This one has actually been refuted by data on studying the rate of "deleterious mutations". The rate of such mutations is actually about 2.6 per thousand mutations.  PD Keightley and A Caballero, Genomic mutation rates for lifetime reproductive output and lifespan in Caenorhabditis elegans.  Proc. Natl. Acad. Sci. USA 94: 3823-3827, 1997

Note that the data comes 28 years after Kimura's paper and replaces the statements.

DNAunion, when quote mining, you have to be sure that the quotes are addressing the topic at hand. Kimura and Ohta's paper addressed a different issue.

Finally, the quotes weren't long.  Most of it seems to be your words outside the quotation marks but included in the quote box.
 
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lucaspa

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I happen to own Protein Evolution, so I can check the quote.  Once again, DNAunion, you have taken a quote out of context.  What the text is doing is describing Kimura's writings, not endorsing them as true, as you imply.  If you go to the previous page (pg 40) you find Patthy describing natural selection:  "Significantly, even a minor difference in fitness value (s = 1%) may eventually lead to elimination fo the allele with lower fitness and fixation of the allele with higher fitness."

Now, go to the bottom of page 41: "As may be clear from this bried summary, the dispute between neutralists and selectionists is essentially centred around the frequency distribution of fitness values of mutant alleles.... The key difference between neutralists and selectionists is in their assesment of the relative proportion of neutral vs advantageous mutations.  Selectionists claim that that very few mutations are selectively neutral, neutralists maintain that most nondeleterious mutations are neutral and very few are advantageous."

Now, the equations of delta p show that fixation is inevitable given any selective advantage.  Now, if you noticed Pratthy, Kimura's equations work based on two "ifs".  "It could also be shown that if an advantageous mutation arises in a large population and its selective advantage (s) over the rest of the alleles is small then the probability of its fixation is P [is about equal to] 2s."

So, the equation of the probability of fixation is based on s being small. That's part of the "if".  Now, in Futuyma on page 394 he gives the data from a study by Endler of fitness values gathered in natural populations up to 1986.  It turns out that instances of s  is less than 0.2 represents less than 20% of total instances of s. That is, 80% of the time s is greater than 0.2 which means that the equation doesn't apply.

Futuyma doesn't give any citation to a study where beneficial mutations were actually observed to be lost.  You have posted Kimura's equations, but no data that the equations represent reality.
 
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Lucaspa: You said it had been observed.

DNAunion: No I didn't.

Tell you what - why don't you go ahead and give us the quote and the post #.


Where are the observations?

DNAunion: Don't need them. I didn't say it had been observed - I said it occurs. And the quotes I provided from two mainstream sources and the logic I presented support that position. That's it...that's all I need to do.

So let me ask you again - do you deny that a beneficial allele can be lost from a population by genetic drift?
 
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Lucaspa: I don't see any references to observations yet, DNAunion. And that is what you promised.

DNAunion: Repeating a lie doesn't make it true.

So Lucaspa, why don't you go ahead and FOR ONCE support your assertions. Show us the quote of me saying that along with the post #.
 
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DNAUnion: [quoting material]: "It is often tacitly assumed that every advantageous mutation that appears in the population is inevitably incorporated. Also, it is not generally recognized that this fact can set an upper limit to the speed of adaptive evolution, because the frequency of occurrence of advantageous mutations must be much lower than that of deleterious mutations."

Lucaspa: This one has actually been refuted by data on studying the rate of "deleterious mutations".

DNAunion: Which "one"? You quoted multiple statements that make different points. Do you mean the statement, "the frequency of occurrence of advantageous mutations must be much lower than that of deleterious mutations"? Clarity please.

Lucaspa: The rate of such mutations is actually about 2.6 per thousand mutations. PD Keightley and A Caballero, Genomic mutation rates for lifetime reproductive output and lifespan in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 94: 3823-3827, 1997

DNAunion: And the rate of advantageous mutations is....?

And would you be so kind as to provide us with that actual statement that supports your position from that source?

Finally, let us assume for the moment that it is true that advantageous mutations occur more often than deleterious ones...how does that "prove" that an advantageous allele can't be lost from a population by genetic drift?
 
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Lucaspa: Finally, the quotes weren't long. Most of it seems to be your words outside the quotation marks but included in the quote box.

DNAunion: Seems that way only to a retard! :D

Look again at the reference at the end of the quote.

(Walter James ReMine, The Biotic Message: Evolution Versus Message Theory, St. Paul Science, 1993, p180-181)

DNAunion: DUH!!!

In addition, look at what I said immediately after that quote.

DNAunion: Some may object to the above lengthy quote, claiming that the author is biased (the book is after all an “anti-evolution” text). However, note that a good portion of the quote is actually from a respected evolutionist: not from ReMine himself.

DNAunion: Double DUH!!!!
 
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SLP

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31st March 2003 at 11:46 PM DNAunion said this in Post #96



In addition, look at what I said immediately after that quote.



DNAunion: Double DUH!!!!

ReMine has a history of, shall we say, not presenting the whole truth when it comes to quotes... Primary sources are much preferred, ESPECIALLY when the quotes come form creationists.
 
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lucaspa

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[31st March 2003 at 07:29 PM DNAunion said this in Post #93
DNAunion: No I didn't.

Tell you what - why don't you go ahead and give us the quote and the post
#.

Post #73: "DNAunion: WRONG!!! Beneficial mutations are often times lost from a population - those that do never become fixed. "

Where are the observations to back that statement up?  It's not stated as "equations indicate that" but rather "are often times lost". 

Now, I expect a long semantic, nit-picking argument from you.  But when you make statements of fact, like the one above, then you need facts -- data -- to back them.

The equations show that it is possible that this happens, but other equations show that fixation is assured. So where is the data to settle the issue?

DNAunion: Don't need them. I didn't say it had been observed - I said it occurs.

LOL!! In order to say "it occurs" then it has to have been observed.  What you have are equations that say it can occur, but in order for those equations to really describe what actually happens, you have to have observations.

Remember, Einstein's equations on General Relativity were just equations until Eddington made the observations. 

So let me ask you again - do you deny that a beneficial allele can be lost from a population by genetic drift

Can be?  No.  Those equations say it can be.  However, other equations say can not be lost.  So which equation is a correct description of what really happens? 
 
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Micaiah

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Notto - Post 72
Random Mutation throws 1000 coins. Selective pressure discards all except the 3 in a line. No intelligence needed.

Or, to look at your example another way, if I take three coins and throw them 1000 times, there is a chance that they would land separated a distance of 200mm. If I throw them a million times, the chance is higher. Of course, there is also a chance that I get it the first time. Again, no intelligence necessary, just selective pressure (what you are looking for in the results) to select when it is right.

Your example can be used to show how selective pressure can build on favorable results. You need to know what number of unsuccessful attempts were made to try to determine the probability of the outcome. Otherwise, any argument from probability fails. In your example, you are using only one attempt. This is not analgous to random mutation within a population.

Micaiah
The rate of mutations resulting from copying errors in animals is about 1 in every 10 billion (10^-10). This is also the chance of a copying error occuring.

The chances of multiple mutations of the same nucleotide occuring in a single generation is extemely low.

In a population of say 100 000, the chance of a point mutation occuring in a specific nucleotide in one generation is 100 000 * 10^-10 = 10^-5.

The chance of the same mutation occuring 5 times in a generation is
(10^-5)^5 = 10^-25.

The probability of 10 animals having the same mutation would be 10^-50.

The probability of 1000 animals in one generation with the same mutation would be 10^-5000. or 1 in 10^5000.

I estimate that if the world was made entirely of sand, the total number of grains of sand would be 8.78x10^27. Suppose our world was but a grain of sand in a giants world, and the giants world had 8.78x10^27 giant grains of sand. The chance of picking out a specific grain of sand from this would be 1 in 7.72^55, which is about the same as the chance of getting ten of the same mutations. This is practically impossible.

The chance all four players in a game of bridge will be dealt with one suit of 13 cards two times in a row is 1 in 4.84x10^54.

The chance of getting three coins to line up in a row as discussed above is 6.4x10^13. The chance of getting 10 coins to line up in a row is 1 in (40000)^20 or 1 in 1.05^46.

These events are considered impossible. It is clearly impossible that in one generation you could expect to get say ten of the same point mutations, let alone one thousand.

I want to investigate the chances of a change to a single nucleotide. These chances remain unaffected for calculation purposes by alternative nucleotide substitutions giving the same phenotypic changes.

How many animals do you think would need to have the same point mutation to be sure that the mutation survives?

It may be argued that the changes could occur in one animal and then get passed onto subsequent generations. In that case, the chances would need to include the chance of survival.
 
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