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jerrywickey

Threshold for evolutionary advancement

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The only evolutionary imperative is replication. Any characteristics thought to have arisen by evolutionary process must do so by augmenting replication in some manner, since robustness of replication is the only characteristic which can be tested for adaptive success.

 

Nature tests replicative success when a species either succeeds and thrives or fails to thrive. Success validates a new characteristic's augmentation to replication, while replicative failure deselects the characteristic.

 

Replicative success is effected my many random factors at once. Any new characteristic effecting replication by some insignificant amount relative to the many other random factors, is lost in the "noise." That is to say, there exists a threshold of replicative augmentation below which a new characteristic can not have a lasting effect on replication and therefore can not be tested by natural selection.

 

An index of replicative augmentation can be derived for any new characteristic. Finding this index may be more complicated for some characteristics than for others, as its effect on replication may be complicated. A threshold value for this index can also be derived, values above which indicates testing by natural selection is possible and below which indicates testing by natural selection is voided by the random "noise" of other events effecting replication.

 

This threshold value will fall as the robustness of replication of any species rises because small effects of any new characteristic is amplified by each replication. That is to say, the effects of any new characteristic become more significant to replication.

 

This threshold value rises when a specie's rate of replication is slow. That is to say, the effects of any new characteristic must be greater to have significant enough effect to consistently overcome random effects on replication.

 

This threshold value falls if the specie's environment is deplete of other random influences to replication.

 

In a perfect evolutionary world, random mutation would produce a new characteristic, then randomness would turn off, to allow that characteristics to be tested by natural selection. While, in the real world, randomness does not switch off. Which means that any new characteristic must overcome the same randomness which spawned it.

 

This was suggested by playing with the robustness of replication and the probability of mutation parameters in First Colony early evolution simulation software.

 

http://www.satellitemagnet.com/firstcolony

 

I observed successful colonies of organisms if the ratio of replicative success and probability of mutation was higher than 1.4 Lower ratios resulted in dwindling populations and ultimate extinction. This suggests a threshold value less then but near 1.4.

 

Curiously, static populations are likely impossible. A species either thrives or dies. There seems to be no equilibrium to maintain a midway point. Only rapid growth which feeds on itself or inevitable deterioration, rapidly leading to extinction.

 

I will refine this threshold index further. 0.4 over unity is statistically very very high. Should this prove to be the threshold, creationists could easily develop a successful argument that the same probability of random mutation required to spawn mutation is just as likely to kill an organism before replication.

 

The argument would suggest that random mutation and natural selection could only simulate successful evolution in controlled simulations like First Colony.

 

The threshold must actually lie much closer to one to account for the assumptions of evolution.

 

Jerry

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The only evolutionary imperative is replication. Any characteristics thought to have arisen by evolutionary process must do so by augmenting replication in some manner, since robustness of replication is the only characteristic which can be tested for adaptive success.

 

A bit too simplistic. A characteristic needs to improve the organisms ability to earn a living. The result of that is differential reproductive success. Notice that. It's not that the individual replicates more than other individuals, it's that the individual's offspring contribute more to the next generation than the offspring of other individuals. Fitness is defined as the frequency of trait/allele observed divided by the frequency of trait/allele as predicted by Hardy-Weinberg.

 

Nature tests replicative success when a species either succeeds and thrives or fails to thrive.

 

The unit of selection is the individual, not the species. The individual either thrives or fails to thrive. Any "species" success is simply the cumulative success of the individuals, not something unique at the species level.

 

Replicative success is effected my many random factors at once. Any new characteristic effecting replication by some insignificant amount relative to the many other random factors, is lost in the "noise."

 

Define "insignificant". Actually, it's not. The equations of population genetics are very clear: a trait that has any positive fitness will be selected for and will, eventually, become fixed in the populatoin.

 

The "threshold" is fitness = 1. Any value greater than 1 is going to result is selection and eventual fixation.

 

An index of replicative augmentation can be derived for any new characteristic. Finding this index may be more complicated for some characteristics than for others, as its effect on replication may be complicated.

 

It's very simple. Mendelian genetics makes it simple. Basically, Hardy-Weinberg states that the frequency of an allele/trait in a population will remain constant. In fact, most alleles/traits are in Hardy-Weinberg equilibrium most of the time.

 

In a perfect evolutionary world, random mutation would produce a new characteristic, then randomness would turn off, to allow that characteristics to be tested by natural selection.

 

LOL! It isn't necessary for "randomness" to be turned off. Remember, natural selection is a two step process:

1. Variation (of which mutations are a part)

2. Selection.

 

Selection is ALWAYS non-random. So it doesn't matter how many "random" variations there are in a population, selection will sort thru them all and pick the best one.

 

Curiously, static populations are likely impossible.

 

Static populations are the norm! This is the basis of natural selection. An environment has only so many individuals that it can support. More individuals are born in a generation than the population can support. This is the basis for selection. Since only X number can be supported, and X + Y are born, then Y must be eliminated by competition.

 

From your website:

"You can watch this replicator organism turn the field red as it consumes all the available nutrients then turn the field dark green as it takes on its first advantageous mutation and passes it to all of its offspring. "

 

No wonder your simulation led you to erroneous conclusions. You don't have selection. What you have is a phenonmenon called "boom and bust". This is when a population is in a limited area and limited food supply but there is no competition, no selection. It happens to deer on isolated islands with no predators. The population expands until it eats all the food supply, then collapses. You don't have competition or selection, but simply a program to see which can replicate the fastest.

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"A bit too simplistic. "

 

Actually no. Evolutionary selection can not operate on any mutation which has no direct or indirect effect on replication. The effect it has on replication may be very complex. A mutation which makes getting food easier effects replication probabilities pretty directly.

 

 

 

 

"The unit of selection is the individual,"

 

Of course.

 

 

 

 

"Define insignificant."

 

That is the point of my post. I do not know exactly what that value is. But it must exist.

 

This is true because evolutionary selection can not operate on any mutation which indirectly effects replication to a lesser degree than random variations in replications.

 

For example. If a given mutation effects replication advantageously such that any organism with that mutation replicates 1% more often than the average for that organism, but the average replication rate for that organism is 10% per month, and random environmental activity kills 9% per month, the 1% increase over 10% base rate will have a measurable effect if the population is 1000s but if the population is 300, you will find that the statistical variation negates an appreciable effect.

 

Now if we use realistic figures of billions of organisms and replication rates of 100 million +-10 million per 20 minutes, and random deaths of 100 million +- 10 million per 20 minutes, a mutation endowing less than a 0.1% advantage to replication no longer retains the statistical likelihood for selection. Not a little bit. Not at all. The advantage falls to less than 1% of the statistical variation.

 

This is the "threshold" in this case.

 

 

 

 

"LOL! It isn't necessary for "randomness" to be turned off"

 

Who is suggesting it is? Perhaps, you misunderstood.

 

 

 

 

"you have is a phenomenon called boom and bust. "

 

Now I know you misunderstood. My simulation is of EARLY evolution. Any first replicator must "boom" otherwise random nucleotide assembly would destroy it. It has no cell wall to protect it.

 

These are fundamental principles. Their application to evolution is to understand the process. Many studies, perhaps even such as the one you cite, attempt to use real world examples of processes we see today, to extrapolate evolutionary fundamental principles. The fault in this is that we can never know all the variables. The results may seem universal, when in fact they are applicable only to the small set of variables present in the observed real world example.

 

The only way to know all the variables is to make them our selves. By using this simulation, I can state every assumption and set every variable.

 

Jerry

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"A bit too simplistic. "

 

Actually no. Evolutionary selection can not operate on any mutation which has no direct or indirect effect on replication. The effect it has on replication may be very complex. A mutation which makes getting food easier effects replication probabilities pretty directly.

 

I think we're having a communication problem. Remember, it's differential reproduction. And it's not "evolutionary selection", but natural selection. Our conversation will go better if we use the terms used by evolutionary biologists. It seems like you are trying to use "replication" as "differential reproduction" but replication doesn't mean that in biology. In your post you talked about "augmenting replication" and "robustness of replication". To any biologist, this means that the individual produces more offspring; that the number of offspring increases. This is different from differential reproduction. A variation can hold replication (number of offspring per individual) either the same or even lower it, as long as more of those offspring survive to reproduce. For instance, look at the number of offspring of salmon and humans. Salmon lay thousands of eggs. They have a replication rate much higher than humans, who have -- at maximum -- 12 -15 kids per woman. Yet what matters is the number that survive and have their own kids. For salmon, this rate is very low. Thus, any variation in salmon that lowers the mortality between egg and reproduction will increase differential reproduction. The individual could lay many LESS eggs (lower replication) and still increase differential reproduction.

 

So, are we on the same page now?

 

"The unit of selection is the individual,"

 

Of course.

 

Good, but can you see how you threw me off with phrases like "Nature tests replicative success when a species either succeeds and thrives or fails to thrive."? Species are not individuals. Species are populations of individuals.

 

"Define insignificant."

 

That is the point of my post. I do not know exactly what that value is. But it must exist.

 

This is true because evolutionary selection can not operate on any mutation which indirectly effects replication to a lesser degree than random variations in replications.

 

OK, here is the problem. What are those "random variations in replication" going to do? IOW, what do we mean by "random"? Random here = effect on differential reproduction. So, in your system any "random" variation that increases the number of offspring per unit time is going to be selected for. Even if that variation increases the replication rate even 1% Keep reading, because there is another problem with how you are using the numbers:

 

For example. If a given mutation effects replication advantageously such that any organism with that mutation replicates 1% more often than the average for that organism, but the average replication rate for that organism is 10% per month, and random environmental activity kills 9% per month,

 

Replication rate is not going to be in percentages. It is going to be in number offspring per unit time per individual. So, you can have a mean replication rate of 100 offspring per month per individual. A 1% increase of THAT is going to mean 101 offspring per month per individual. Now, "random environmental activity kills 9% per month" doesn't make sense, either. Instead, you can say that 90% of the individuals per generation die. That is the meaningful number.

 

So:

Individual A has 100 offspring per month (the mean) and 90% of them die. That leaves 10 individuals left.

 

Individual B has 101 offspring per month and 90% of them die. That leaves 11 individuals left. So then we start again with the next generation:

 

Generation 2:

 

All A individuals have 1000 offspring total, of which 100 survive.

All B individuals have 1100 offspring total, of which 110 survive. You can see that generation 2 has a net increase of 9 individuals over generation 1. And it will continue.

 

Now, this is your setup. In it, the number of individuals per generation can increase. In the real world the total number of individuals of both A and B would be fixed. Instead of actual numbers, we would be looking at the frequency, or proportion of individuals with the trait. So let's do some of those numbers:

 

Total population = 1,000

Fitness = 1.01 (a 1% increase in fitness). s = 1 - fitness. It is general to use "p" and "q" for frequency. p + q = 1.

Frequency of q = 0.999 (999 individuals out of 1,000 have the original variation = A)

Frequency of p = 0.001 (a new mutation appears in 1 individual = B)

 

The equation is: delta p = (1/2)spq/(1-sp). Where delta p is the change in frequency of p.

 

delta p = .000495/.999 = 0.0005.

 

For the next generation:

p' = p + delta p = 0.0015

q' = q - delta p = 0.9985

 

So, out of 1,000 individuals, there will be 1.5 with B and only 998.5 with A. Since you can't have a half individual, that means either 1 or 2. But let's continue this another generation:

 

delta p = (1/2) (0.99 x 0.0015 x 0.9985) / (1 - 0.99 x 0.0015)

delta p = 0.0015

 

so p" = 0.0015 + 0.0015 = 0.003

q" = .997

 

Now you have 3 individuals with B and only 997 with A.

 

You can keep this up generation by generation and you will see that, eventually, all the individuals will be B and none will be A.

 

"LOL! It isn't necessary for "randomness" to be turned off"

 

Who is suggesting it is? Perhaps, you misunderstood.

 

Perhaps I did. But you said "In a perfect evolutionary world, random mutation would produce a new characteristic, then randomness would turn off, to allow that characteristics to be tested by natural selection." How did I misunderstand that? What did you intend to say? As I said, even in "perfect evolutionary world" randomness doesn't need to be turned off. The conceptual mistake you have is that "randomness" will destroy an individual or an individual RNA molecule. See below.

 

Now I know you misunderstood. My simulation is of EARLY evolution. Any first replicator must "boom" otherwise random nucleotide assembly would destroy it. It has no cell wall to protect it.

 

1. You are working with RNA world. There are other scenarios for early evolution. And no, random nucleotide assembly in this scenario does not destroy the RNA replicator. Random RNA sequences are not going to destroy other RNA sequences. The random sequences simply use resources (the nucleotides) that the replicator would use. So the calculation would be the frequency of the replicator (p) vs the frequency of the sum of all the random sequences (q).

 

Many studies, perhaps even such as the one you cite, attempt to use real world examples of processes we see today, to extrapolate evolutionary fundamental principles. The fault in this is that we can never know all the variables. The results may seem universal, when in fact they are applicable only to the small set of variables present in the observed real world example.

 

You have it backwards. The math for population genetics was derived from the universal of Mendelian genetics. So the math is universal. What was then done was look at many real world populations (at random) to see if they conformed to the universals of the math. And yes, they do.

 

The only way to know all the variables is to make them our selves. By using this simulation, I can state every assumption and set every variable.

 

But this leaves you open to GIGO. And I think this is what happened to you, for the reasons I've tried to outline above.

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The things which my simulations have brought to my attention are not inconsistent with anything you have said. I suspect you are not understanding the simulation. Be careful to not OVER think the problem, and don't underestimate my skill.

 

 

Let me rephrase the post.

 

We all know that any mutation which is acted upon by natural selection must to a greater or lesser degree effect reproduction. Any mutation which has absolutely no effect on reproduction of the organism is a mutation which can not be acted upon by natural selection.

 

My simulation suggested that there is a lower limit to the degree of effect. If a mutation has less effect on reproduction than the random effects of environment and other temporary and random external effects on reproduction, natural selection can not operate on it.

 

So, a mutation which endows an unspecified slight advantage to reproduction, but less then that of random statistical variation (math term not biologic term,) is a mutation upon which natural selection can not operate.

 

You actually touch on this when you point out that an organism can not half reproduce. Just imagine an advantage which endows 0.0001 increased reproduction when natural variation in reproduction by random environmental conditions which might, alter reproduction at any given time by perhaps as high as 0.001.

 

Now you probably see what I mean. Natural selection can not operate on that advantageous mutation. Now, you probably realize that all the things that raised flags in your head were miscommunications. All that I am saying is that 0.00000000000....1 equals zero. I am applying that to limitations of natural selection operating on advantageous mutations.

 

Until I saw it in my very controlled simulations, I was unaware of this limitation to advantageous mutations. It appears you also were unaware of this limitation. Finding such as these are difficult or impossible to observe in vivo. And...

 

We have to be careful what we take from simulations and of what we have to be suspicious instead. I am very good at identifying the difference. Perhaps, better than you are, considering it took this long to explain my post to you.

 

Jerry

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We all know that any mutation which is acted upon by natural selection must to a greater or lesser degree effect reproduction. Any mutation which has absolutely no effect on reproduction of the organism is a mutation which can not be acted upon by natural selection.

 

We still have that communication problem. You are placing the effect on natural selection on reproduction. Instead, natural selection increases the ability of the individual to do better in competition for scarce resources. A consequence of doing better in the competition is that the indivuals will have relatively more offspring than other individuals.

 

I keep hearing you say that natural selection has a direct effect on reproduction.

 

And let's talk "variation", since mutations are only one form of variation. Recombination in sexually reproducing organisms introduces a lot more variation than mutation does.

 

If a variation is neutral in the competition, then we will not see a difference in the frequency of that variation in the population. Well, not quite true, since genetic drift will also alter frequency over a very long time. But for our purposes, "neutral" variations will not change the frequency of the variation in the population.

 

My simulation suggested that there is a lower limit to the degree of effect.

 

And this is where I question the simulation. It goes against quite a bit of mathematics and observation. That's why I suspect GIGO for the reasons I stated. I add another one: you seem to have skewed your simulation only to look at "reproduction". Now, an issue we are going to have is how emotionally attached you are to your simulation. Are you truly interested in it accurately mimicking evolution or are you going to defend your simulation as "right" and instead label evolution as "wrong"? IOW, are you really interested in seriously considering criticisms of the simulation based upon other data in evolution or are you only interested in using your simulation to challenge evolution? If the latter, then our discussion goes nowhere.

 

So, a mutation which endows an unspecified slight advantage to reproduction, but less then that of random statistical variation (math term not biologic term,) is a mutation upon which natural selection can not operate.

 

Then your simulation is not mimicking natural selection correctly. What you call "random statistical variation" are instead individuals with advantages to reproduction that are better than the mutation (let's call it A). When we get to statistics we are talking about populations. This is what evolution deals with. It selects among the individuals of the population.

 

In the example above, natural selection is operating. It is selecting the variation (call it B) that gives the best advantage to reproduction. Apparently your population has variation that are already B because you introduced them initially. Therefore, if you introduce A, it is not going to replace B because B is already better than A. What you have to do is find a variation C that is better than B.

 

Just imagine an advantage which endows 0.0001 increased reproduction when natural variation in reproduction by random environmental conditions which might, alter reproduction at any given time by perhaps as high as 0.001.

 

Now you probably see what I mean. Natural selection can not operate on that advantageous mutation.

 

Back to what we are talking about before. Yes, if you have a variation with s = 0.001 but there is already in the population a variation with s = 0.01, then of course the variation with the lower s is not going to succeed. It can't compete with a better variation.

 

However, what do you mean by "random environmental conditions"? Are you referring to something outside the genome? If so, what?

 

All that I am saying is that 0.00000000000....1 equals zero. I am applying that to limitations of natural selection operating on advantageous mutations.

 

What you overlooked was the competition part of natural selection. Natural selection has the variations (individuals) competing against each other. Part of your GIGO was introducingt an "advantageous mutation" that was not as good as a variation already in the population. Of course it did not do well. What you are looking for is a variation better than any variation already in the population. Do that in your simulation. Pick a "mutation" that is only 0.1% better than the best variation in your "statistical variation" and see what happens over the course of many generations.

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CONTENTS

 

compliment to your ability

 

discussion of your error

 

MOST IMPORTANT a logical progression describing my post

organized in such a manner as to make your critique as easy as possible.

 

(don't be afraid to say, "I see what you mean now. It was just communication.")

 

 

 

 

It is important never to allow something that feels comfortable to overshadow observations. This applies not only to my software but also to currently accepted interpretation of observations. We also have to remember that the correct answer is usually very illusive. But attempts to answer the questions help us both to learn.

 

Observations are king. However, most of the things we are talking about are not actually observations. They are interpretations of observations. Neither of us nor the large community of researchers have actually observed the mechanisms of variation and natural selection.

 

What we have observed are the end results. Interpreting the observations in an attempt to understand the mechanisms is what you and I are doing right now.

 

You are much more proficient than most posters. I appreciate discussing this with you. As we each explain our points of view, we learn as much as we are teaching.

 

 

 

 

Your point of view contains two errors. I understand well the temptation of these errors.

 

1) If two variations are present, where one is a much greater advantage than the other, the greater advantaged will not limit the lesser. Both variations will proliferate throughout the population over time. You state "if you have a variation with s = 0.001 but there is already in the population a variation with s = 0.01, then of course the variation with the lower s is not going to succeed. It can't compete with a better variation."

 

The variations only compete when they both are forced to compete for the same resources. I am sure you agree with that. We don't actually disagree.

 

2) This one is the important one. "natural selection increases the ability of the individual to do better in competition for scarce resources. A consequence of doing better in the competition is that the individuals will have relatively more offspring than other individuals."

 

Sounds good. But wording it this way makes it easy to misapply. Natural selection does not act on a variation at all. It acts only on individual organisms allowing reproduction of the organisms entire genome or not. There is no half way. That means that if a variation endows some advantage to gathering food or to escaping predators, that variation ultimately is an advantage to reproduction.

 

It is the variations effect on reproduction which the phrase natural selection is describing. Organisms well advantaged enjoy selection preference in that their genome proliferates through out the population.

 

 

 

My simulation does not contain any simulation engines which select anything. The eight sim engines do these things

 

1) In according with user parameters for, keep track of a large number of RNA sequences

2) In according with user parameters for, randomly alter a single nucleotide in a randomly selected RNA sequence

3) In according with user parameters for, randomly remove a single nucleotide in a randomly selected RNA sequence

4) In according with user parameters for, randomly add a random number of random nucleotides to a randomly selected RNA sequence.

5) In according with user parameters for, search each RNA sequence for constituent sequences which are arbitrarily assigned as endowing chemical activity which is fatal to the RNA sequence.

6) In according with user parameters for, search each RNA sequence for constituent sequences which are arbitrarily assigned as endowing chemical activity of unspecified advantage to replication to the RNA sequence.

7) In according with user parameters for, search each RNA sequence for constituent sequences which are arbitrarily assigned as endowing chemical activity of unspecified disadvantage to replication to the RNA sequence.

8) In according with user parameters for, search each RNA sequence for constituent sequences which are arbitrarily assigned as endowing replicative activity to the RNA sequence.

 

That's it. That is all of them. My simulation does nothing more. It does not message the RNA sequences. All results are an emergent resolution of these activities. No garbage in, simply because there is no garbage to be put in.

 

 

 

 

 

Here is how it works. Take a look at this section and comment on any errors here.

 

Every variation having arisen by mutation or activity of sexual reproduction or by any other means will either endow some, however small or great, advantage to replication or it will endow no advantage to replication.

 

This statement is true.

 

For the moment don't worry about what you feel I might be forgetting. You might be thinking "he is forgetting that some variations endow advantage but not to replication." Just follow the progression.

 

If the variation endows no advantage to replication what so ever, this variation will be replicated every time this organism reproduces. But since it does not endow any advantage to replication, this organism will reproduce with only the same robustness as all of its sisters. After a thousand generations, the number of organisms with this variation will remain the same percentage of organisms which the one in which it arose was of the entire colony. i.e. if there were ten organisms when the variation arose in a single organism, after 10 generations of reproduction unhindered by lack of resources. 1* repo_rate^10 organisms will contain the variation, while 10* repo_rate^10 will not contain the variation.

 

1/10 of the organisms contained the variation when the variation first arose, after 10 generations of unhindered reproduction still only 1/10 of the organisms contained the variation. The same proportion as when the variation first arose.

 

Natural selection does not operate on variations which do not effect replication. We understand that variation to be neutral.

 

A variation which endows no direct or indirect advantage to reproduction is simply not a variation which makes any difference at all. But there is more.

 

These paragraphs are true.

 

However, if the variation endows even a small advantage to reproduction such as a slight increase in the number of foods it can metabolize or a slight advantage to predator evasion, such that any organism which contains this variation has a replication rate of repo_rate*1.1. After 10 generations of reproduction unhindered by limitation of resources or predators the variation will have proliferated through out the population at a much higher rate. The variation will exist in not 10% of the population as before but in 22% In a hundred generations the variation will exist in 99% of the population.

 

Natural selection acts on even a slight advantage exponentially but the advantage is only available to be acted upon by the emergent process of natural selection if it effects reproduction even in the slightest.

 

These paragraphs are true.

 

But the world does not provide environments with unlimited resources and with out predators. So repo_rate is always +- some amount.

 

The activity of predators and limitation of resources after adjusting for disadvantage and other calculable factors will still provide some random offset to reproduction for each organism.

 

If that random component is +-0.3 but the variation endowing advantage to replication endows only a statistically insignificant increase compared to the mean deviation of the random component to replication, that variation endowing advantage never has the opportunity to effect the emergent process of natural selection.

 

If you can, please point out the error in these paragraphs.

 

If these last paragraphs are with out error, the implication is that there exists a lower limitation of reproduction advantage, below which a variation endowing advantage is the same as a neutral variation. It does not proliferate through out the population.

 

Jerry

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Observations are king. However, most of the things we are talking about are not actually observations. They are interpretations of observations. Neither of us nor the large community of researchers have actually observed the mechanisms of variation and natural selection.

 

Yes, they have. Jerry, this is one area where you are ignorant of what has been done. First, remember that "variation" is a part of natural selection. Natural selection is a two step process:

1. Variation

2. Selection

 

Second, population geneticists have done numerous studies on natural selection both in the wild and in the lab. The place to start is RA Fisher's book The Genetical Theory of Natural Selection.

 

1) If two variations are present, where one is a much greater advantage than the other, the greater advantaged will not limit the lesser. Both variations will proliferate throughout the population over time. You state "if you have a variation with s = 0.001 but there is already in the population a variation with s = 0.01, then of course the variation with the lower s is not going to succeed. It can't compete with a better variation."

 

The variations only compete when they both are forced to compete for the same resources. I am sure you agree with that.

 

Yes, the greater advantage will limit the lesser. And, in any real population, they will always compete for the same resources. After all, they are in individuals and those individuals compete for the same resources.

 

2) This one is the important one. "natural selection increases the ability of the individual to do better in competition for scarce resources. A consequence of doing better in the competition is that the individuals will have relatively more offspring than other individuals."

 

Sounds good. But wording it this way makes it easy to misapply. Natural selection does not act on a variation at all. It acts only on individual organisms allowing reproduction of the organisms entire genome or not. There is no half way. That means that if a variation endows some advantage to gathering food or to escaping predators, that variation ultimately is an advantage to reproduction.

 

As Mayr notes, this is the confusion of "selection of" and "selection for" The unit of selection is indeed the individual. But what is being selected for is the allele. I'll let Mayr explain:

 

"Much confusion about this problem can be avoided by considering two separate aspects of the question: 'selection of' and 'selection for'. Let us illustrate this with the sickle cell gene. For the question 'selection of' the answer is the individual who either does or does not carry the sickle cell gene. In a malalrial region the answer to 'selection for' is the sickle cell gene, owing to the protection it gives to its heterogenous carriers." Ernst Mayr What Evolution Is, pg 126

 

And no, the variation is not "ultimately is an advantage to reproduction". It doesn't mean that the possessor (variation A) will have any more offspring than an individual with the other variation (B). It simply means that more of those offspring will survive. That's what we meand by "differential reproduction". You are focussing only on the absolute number of offspring. That is what your simulation does, but it is a special case because the entire "organism" is an RNA molecule and the only thing it is required to do is replicate. That's all your "environment" requires. You are speaking of your special case and calling it all of natural selection. I am looking at all of natural selection and saying that your special case is not representative.

 

It is the variations effect on reproduction which the phrase natural selection is describing. Organisms well advantaged enjoy selection preference in that their genome proliferates through out the population.

 

Close, but not quite.

1. The allele will become the dominant allele in the population, even eventually the only allele (fixed). But it doesn't mean the entire genome will become fixed.

2. The phrase "natural selection" is describing not the effects on reproduction but rather an process to give design. Here is Darwin's summary of natural selection:

 

"If, during the long course of ages and under varying conditions of life, organic beings vary at all in the several parts of their organization, and I think this cannot be disputed; if there be, owing to the high geometric powers of increase of each species, at some age, season, or year, a severe struggle for life, and this certainly cannot be disputed; then, considering the infinite complexity of the relations of all organic beings to each other and to their conditions of existence, causing an infinite diversity in structure, constitution, and habits, to be advantageous to them, I think it would be a most extraordinary fact if no variation ever had occurred useful to each beings welfare, in the same way as so many variations have occured useful to man. But if variations useful to any organic being do occur, assuredly individuals thus characterized will have the best chance of being preserved in the struggle for life; and from the strong principle of inheritance they will will tend to produce offspring similarly characterized. This principle of preservation, I have called, for the sake of brevity, Natural Selection." [Origin, p 127 6th ed.]

 

My simulation does not contain any simulation engines which select anything.

 

Then that is a problem right there. It's not "natural selection", is it? However, there is an implicit selection involved in steps 5-8.

 

Now, notice that you have a "large number of RNA sequences". You alter one of them and then see the effect on replication. Since you have a fixed number of nucleotides, in this situation the RNA sequence that reproduces the fastest will eventually come to dominate the population.

 

However, you have the problem that any one of those "large number of RNA sequences" may have replicative ability greater than the mutation you introduced.

 

The reason your results show that you have to get a value >1.4 times the original replication rate is because this represents a value that is at least 2 standard deviations away from the mean replicative rate of those "large number of RNA sequences". It's like I said, you have to get a fitness greater than the best fitness already in the population. Your basic assumption is that NONE of the RNA sequences replicate. Why should that be true?

 

My suggestion, Jerry, is to get an evolutionary biology textbook and look at the math on population genetics. When there are several alleles (forms of genes) in a population, what is calculated is the relative fitness of each of those to the others. The one with the highest relative fitness will end up being selected and becoming fixed. All the others, even if "advantageous" in the absolute sense, will be lost because it is not as good as the best. That is what is happening here.

 

No garbage in, simply because there is no garbage to be put in.

 

I'm sorry, but the GI is the assumption that there is no replication in any of those large number of random RNA sequences.

 

Every variation having arisen by mutation or activity of sexual reproduction or by any other means will either endow some, however small or great, advantage to replication or it will endow no advantage to replication.

 

And that is your selection criteria: replication. Now, what do you think is that "advantage to replication"? Is it allowing replication to go faster or is it at the same speed but ends up with a greater number of offspring because it doesn't stop? Either one means that mutation A will end up with more offspring than some of the others. Which is what you measure, right?

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This is getting frustrating.

 

You believe that I do not understand variation and selection.

 

You believe that my post is inconsistent with accepted findings.

 

You answer questions which have not been introduced.

 

However, you do not address the post. You have not yet made one comment germane to my argument.

 

My post is consistent with accepted findings.

 

I do understand variation and selection. You wrote a lot but at no point did you quote any thing I wrote under the heading "Here is how it works."

 

I clearly and slowly describe the process. Each statement is identified and it is true. Can you find a single error? You didn't comment on any of it.

 

Perhaps, you read a phrase and it triggers a recollection of an unrelated topic. Then you habitually spin off in that direction.

 

Try reading the explanation and finding the error there.

 

I have run into a lot of people who should understand evolution, but keep getting caught up in terminology which prevents them from understanding some of the basic principles. I am writing an evolution primer that addresses many of these misunderstandings.

 

I bet you are going to have fun with that.

 

Jerry

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