Pete's Quite Thread post

[Pete Harcoff]

Mark, I'm not going to bother anymore. We're going around and around in circles again and again. You appear to have several fundamental misunderstandings which is preventing this discussion from going anywhere.

First, you continue to ignore the very concept of natural selection and differential reproductive success. The basic definition of an adaptive or beneficial mutation is one that is going to increase the probability of successful survival and reproduction in a given environment (and the latter point is key). Likewise, deleterious mutations are the ones that are going to decrease the probability of successful survival and reproduction. So you can't argue that all these deleterious mutations are going to be fixed in a population because by definition they are the ones that won't. Likewise, the beneficial mutations are going to be the mutations favored for fixation. You can't do a 1-to-1 comparison, because they're not the same thing.

Now, obviously it is possible for deleterious mutations to become fixed or even accumulate in a population. But this is based on specific circumstances (i.e. small populations, inbreeding). And in such cases where deleterious mutations accumulate too fast, you can wind up with a population crash and/or extinction.

You appear to have also misread some of the abstracts you quote. I urge you to go back and re-read those papers, because I think you are missing a lot. In particular, you claimed that the fitness effects of beneficial mutations was an assumption. Then you missed the rest of the paper where they experimentally verified this. You appear to have misunderstood the abstract regarding deleterious mutation rates. It's not 1.6 deleterious mutations per generation. It's 1.6 deleterious mutations per diploid per generation. And in the Rates of Spontaneous mutation paper, you missed the part I was talking about (the 1/300 cell divisions). It's right there in the abstract, not buried somewhere in the paper.

You also claimed that beneficial mutations would have to be fixed in every generation, or that the number of beneficial mutations would equal the number of deleterious mutations. I have no idea where you pulled any of that from.

You further completely misunderstood how I calculated my numbers. I never derived the number of beneficial mutations by comparing it to the delterious mutation rate. I can see now how you made that mistake. I took the number 1.6 from a different paper, where it suggested that number the total mutation rate (per effective genome). The paper you keep citing pegs that number as higher (4.2 mutations per diploid per generation). So it's 1 in 625000 mutations is beneficial, NOT 1 in 625000 deleterious mutations is beneficial.

I compared it to the total mutation rate and figured a conservative estimate of 64000 beneficial mutations appearing in the population over 5 million years. I have no idea how many would need to be fixed or even would be fixed. But likewise, I have no idea how many beneficial mutations it even takes to evolve a human. And neither do you, so it's premature to suggest the rate of beneficial mutations is too small.

I understand what you are looking for. You want all the specifics. But I never intended to even discuss the specifics. In fact, modern science isn't even at the point where we can know all the specifics. I wish you luck in searching for what you seek, but it's beyond the scope of what I even intended to discuss.

 

[gluadys]

What is there to know, the fit survive and the less fit die. I don't know what deep esoteric meaning you see in natural selection but it is actually nothing more then a pedantic clutch phrase in absense of a demonstrated mechanism for evolution.

Carry that principle through 100 generations Mark. What are the implications for the species?

I can't believe you asked me how many desendants there would be with a lethal mutation over a hundred generations. I think you should consider the meaning of the word lethal, when there is a lethal mutation offspring don't make it past the zygote stage. You might want to think about that get back to me when you are actually interested in looking for a Malthusian parameter.

So why do you continue to insist that lethal mutations are a problem for evolution? Do you not see the internal contradiction in your own hypothesis?

The number and impact of them. Come on Glaudys, you know so much about natural selection, just name me one beneficial mutation directly observed or demonstrated in human chromosome 21, just one.

And what is the evolutionary impact of deleterious mutations? And what is the evolutionary impact of beneficial mutations?

Remember to keep in mind the biological definition of fixation which I gave you earlier from Mark Ridley.

 

[Tomk80]

It keeps on occurring to me that Mark doesn't have a good grip on one central question, namely what the difference is between what a harmful mutation does to the individual and what a harmful mutation does to the population. I've noticed this in earlier threads, and it seems that the same thing comes up here again. He seems to be doing this on a lot of things that have both an effect on the individual and an effect on the population.

 

[mark kennedy]

Mark, I'm not going to bother anymore. We're going around and around in circles again and again. You appear to have several fundamental misunderstandings which is preventing this discussion from going anywhere.

I don't know what is more fundamental then a mutation being a transcript error. They are a problem for evolution because around ~80% don't do anything at all. Apparently you wanted to demonstrate that given present mutation rate to presense of 68,000 indels, split evenly between the chimpanzee and human lineages are no problem for evolution. You forget the 1 to 2% of the genome consisting of single base substitutions and the effects of mutations on fittness.

First, you continue to ignore the very concept of natural selection and differential reproductive success. The basic definition of an adaptive or beneficial mutation is one that is going to increase the probability of successful survival and reproduction in a given environment (and the latter point is key). Likewise, deleterious mutations are the ones that are going to decrease the probability of successful survival and reproduction. So you can't argue that all these deleterious mutations are going to be fixed in a population because by definition they are the ones that won't. Likewise, the beneficial mutations are going to be the mutations favored for fixation. You can't do a 1-to-1 comparison, because they're not the same thing.

Then why can't you identify a single beneficial mutation that improves fittness in this way. All anyone ever wants to refer to is anecdotal evidence that begs the question of proof and pithy syllogisms. Now I don't know where you get the idea that deleterious mutations do not become fixed in populations but they do. What is more the rare beneficial mutations, deluded darwinians think have some magical quality never contribute to major morophological change. That is a myth.

Now, obviously it is possible for deleterious mutations to become fixed or even accumulate in a population. But this is based on specific circumstances (i.e. small populations, inbreeding). And in such cases where deleterious mutations accumulate too fast, you can wind up with a population crash and/or extinction.

Due to the physiological costs of adaptation not all mutation can be purged. I don't know if you are actually saying that the deleterious mutations are expunged and the beneficial ones preserved but I am seeing the opposite in genetics.

You appear to have also misread some of the abstracts you quote. I urge you to go back and re-read those papers, because I think you are missing a lot. In particular, you claimed that the fitness effects of beneficial mutations was an assumption. Then you missed the rest of the paper where they experimentally verified this. You appear to have misunderstood the abstract regarding deleterious mutation rates. It's not 1.6 deleterious mutations per generation. It's 1.6 deleterious mutations per diploid per generation. And in the Rates of Spontaneous mutation paper, you missed the part I was talking about (the 1/300 cell divisions). It's right there in the abstract, not buried somewhere in the paper.

I understood the paper well enough but when you are talking about the effective genome the introduction of a mutation can effect enormous change. We know what those changes are and the 1.6 mutations per generation would be about all a population can handle, thats the Malthusian parameter but never mind. You emphasis that your going to focus on the effective genome so I brought up differences in the effective genome of humans and chimps are only about 80% simular after you said it was 99%, which is completly false. Let a creationist make a mistake like that and the evolutionists will have a feeding freenzy but being an evolutionist means never having to say your sorry, at least on CF.

You also claimed that beneficial mutations would have to be fixed in every generation, or that the number of beneficial mutations would equal the number of deleterious mutations. I have no idea where you pulled any of that from.

I know you don't understand but I have substantiated all of this over and over again. If you don't know by now, don't worry about it Pete, Im over it.

You further completely misunderstood how I calculated my numbers. I never derived the number of beneficial mutations by comparing it to the delterious mutation rate. I can see now how you made that mistake. I took the number 1.6 from a different paper, where it suggested that number the total mutation rate (per effective genome). The paper you keep citing pegs that number as higher (4.2 mutations per diploid per generation). So it's 1 in 625000 mutations is beneficial, NOT 1 in 625000 deleterious mutations is beneficial.

1 in 625000 mutations is beneficial and there are about 135 mutations in anyones overall genome. When you take into consideration that there are about 30,000 genes and only about 2% of our DNA actually does anything 1.6 mutations in the effective genome makes sense. The problem is that you did not take into consideration what these mutations actually do to these genes.

I compared it to the total mutation rate and figured a conservative estimate of 64000 beneficial mutations appearing in the population over 5 million years. I have no idea how many would need to be fixed or even would be fixed. But likewise, I have no idea how many beneficial mutations it even takes to evolve a human. And neither do you, so it's premature to suggest the rate of beneficial mutations is too small.

We are supposedly sharing a common ancestor with the chimpanzee, differences have been identified in the effective genome, they are supposedly the result of mutations and you have no idea why mutations have to be fixed.

I understand what you are looking for. You want all the specifics. But I never intended to even discuss the specifics. In fact, modern science isn't even at the point where we can know all the specifics. I wish you luck in searching for what you seek, but it's beyond the scope of what I even intended to discuss.

I can't believe how oblivious evolutionists are to things like transpositions, transversions, synergistic epistasis but I guess by now it shouldn't supprise me. Thanks for the exchange Pete, I really didn't intend to be critical of your post, I just wanted you to finish it. There are mutation rate estimations out there as they apply to human evolution, Bruce Lahn worked on one that claimed it would take hundreds, if not thousands of mutations in hundreds if not thousands of genes. The chimpanzee chromosome paper was intended to be the gold standard for it but I suppose that was of very little interest.

 

[Manic Depressive Mouse]

All Marks arguments are based on his misunderstanding and misrepresentation of the facts.

The basis of his argument is that all mutations are detrimental and that they all get fixed in the population. Not only are both these statements wrong, but they are also contradictory. If all mutations were detrimental then they wouldn't get fixed in the population, quite the opposite they would all be eliminated by natural selection. Which is exactly what we have observed happening. Couple that with the fact that benificial mutations are propigated throughout the population and that Pete's calculations have proved the rate of them is high enough for evolution and there is no problem whatsoever.

The fact that Mark keeps repeating these things whenever all have been proved to be lies by me, Tom, Gluadys, Pete and others on numerous occasions shows that he does not care about the truth.

Let him ignore all the evidence and think he has a PHD understanding of evolution and has disproved it when he can't even grasp the basics. Let him make all his baseless assertions, like the magical boundary between species.

Don't waste time on him, he's demonstrated it's futile.

 

[mark kennedy]

It keeps on occurring to me that Mark doesn't have a good grip on one central question, namely what the difference is between what a harmful mutation does to the individual and what a harmful mutation does to the population. I've noticed this in earlier threads, and it seems that the same thing comes up here again. He seems to be doing this on a lot of things that have both an effect on the individual and an effect on the population.

It seems to me that evolutionists on here have trouble discerning between a beneficial effect and a harmfull one. What is truely puzzling about the pithy statements about natural selection eliminating harmfull mutations and preserving beneficial ones is that its not supported by the evidence. There are only two ways I know of that a change in the effective genome to effect an entire population. Either the same conditions that cause the mutation are effecting the entire population or some kind of a founder effect occurs and only the carriers survive.

 

[Pete Harcoff]

Now I don't know where you get the idea that deleterious mutations do not become fixed in populations but they do.

See, it's stuff like this that proves you aren't reading what I am writing. I had written in the very post you were quoting from:

"Now, obviously it is possible for deleterious mutations to become fixed or even accumulate in a population."

My point was that not ALL deleterious mutations will become fixed. So even if rates of deleterious mutation are higher than beneficial mutations, the trend will be for deleterious mutations to be eliminated. You've made repeated mistakes like this by simply just not reading things properly, whether it's posts on the forums or scientific papers. I think more careful reading on your part would go a long way to clear up many of the misunderstandings we are having.

 

[Valkhorn]

It seems to me that evolutionists on here have trouble discerning between a beneficial effect and a harmfull one. What is truely puzzling about the pithy statements about natural selection eliminating harmfull mutations and preserving beneficial ones is that its not supported by the evidence. There are only two ways I know of that a change in the effective genome to effect an entire population. Either the same conditions that cause the mutation are effecting the entire population or some kind of a founder effect occurs and only the carriers survive.

Once again the burden of proof falls on you. Please back up these claims:

It seems to me that evolutionists on here have trouble discerning between a beneficial effect and a harmfull one.

Where has this been shown?

What is truely puzzling about the pithy statements about natural selection eliminating harmfull mutations and preserving beneficial ones is that its not supported by the evidence.

Where has this been shown?

There are only two ways I know of that a change in the effective genome to effect an entire population. Either the same conditions that cause the mutation are effecting the entire population or some kind of a founder effect occurs and only the carriers survive.

And can you back this up?

 

[Manic Depressive Mouse]

What is truely puzzling about the pithy statements about natural selection eliminating harmfull mutations and preserving beneficial ones is that its not supported by the evidence

It is supported by the evidence, math and logic Mark. Just because you don't like this fact doesn't make it untrue.

Gluady's in your formal debate even mathematically showed, using chi diagrams and the Hardy-Weinberg equation, that this happens.

We see it happening every day.

Yet all you do is whine that "it doesn't happen because I say so" blah blah Mark you're getting old and most of us are getting sick of this.

So Mark, stop lying. Stop misrepresenting and twisting papers and facts to suit your agenda. Stop ignoring any and all evidence that disproves the rubbish you come out with. And most importantly stop making baseless assertions, because that's all your argument is.

You have yet to support anything Mark, even on the logical level your arguments are garbage.

 

[Pete Harcoff]

The basis of his argument is that all mutations are detrimental and that they all get fixed in the population. Not only are both these statements wrong, but they are also contradictory. If all mutations were detrimental then they wouldn't get fixed in the population, quite the opposite they would all be eliminated by natural selection. Which is exactly what we have observed happening.

Technically, there are ways for deleterious mutations to become fixed in a population. I've read papers on that subject. But what mark seems to be arguing is that therefore all deleterious mutations would become fixed. I stated this isn't true, then he asserts I don't think deleterious mutations can become fixed period, even after I say they can. It's like all-or-nothing with him. I just can't fathom how he conceptualizes evolution.

 

[Manic Depressive Mouse]

Technically, there are ways for deleterious mutations to become fixed in a population. I've read papers on that subject. But what mark seems to be arguing is that therefore all deleterious mutations would become fixed. I stated this isn't true, then he asserts I don't think deleterious mutations can become fixed period, even after I say they can. It's like all-or-nothing with him. I just can't fathom how he conceptualizes evolution.

I spent months debating with Mark and it's all such a waste. He just refuses to accept anything, and just asserts that things aren't true. No matter how much you show him his points are not true he just refuses to accept it.

I remember he once said that the difference between a cold blooded and warm blooded animal is huge and would require so many genetic alterations as to be impossible. I then showed him a few closely related species of shark that were warm blooded, cold blooded and something in-between. This destroys his assertion, yet he refused to admit it and had the cheek to start criticising me for posting irrelevant material.

He's doing the same thing about your genetics calculations.

It's pretty saddening when people are so blinded by belief that they result to any means to justify it.

 

[gluadys]

It seems to me that evolutionists on here have trouble discerning between a beneficial effect and a harmfull one. What is truely puzzling about the pithy statements about natural selection eliminating harmfull mutations and preserving beneficial ones is that its not supported by the evidence. There are only two ways I know of that a change in the effective genome to effect an entire population. Either the same conditions that cause the mutation are effecting the entire population or some kind of a founder effect occurs and only the carriers survive.

What happens if a larger and larger proportion of the population inherits a mutation in each generation?

 

[mikeynov]

The answer is honestly simple:

Mark has very little understanding of population genetics.

Mark, I can't recommend taking such a course at your local university enough. You'll be forced into using natural selection, even demonstrating it mathematically, and just about every concern of yours will disappear.

 

[Tomk80]

It seems to me that evolutionists on here have trouble discerning between a beneficial effect and a harmfull one. What is truely puzzling about the pithy statements about natural selection eliminating harmfull mutations and preserving beneficial ones is that its not supported by the evidence. There are only two ways I know of that a change in the effective genome to effect an entire population. Either the same conditions that cause the mutation are effecting the entire population or some kind of a founder effect occurs and only the carriers survive.

How many offspring does an individual with a neutral mutations get in comparison to one with a detrimental mutation. Do the math for once Mark. There's plenty of literature out there which can help you with that.

 

[mark kennedy]

The answer is honestly simple:

Mark has very little understanding of population genetics.

Mark, I can't recommend taking such a course at your local university enough. You'll be forced into using natural selection, even demonstrating it mathematically, and just about every concern of yours will disappear.

If I'm going to take a course it will be in either molecular biology or genetics. You don't need natural selection for that, in fact, I don't think you need it at all. I insist that random mutations don't drive evolution, recombinations do and so I don't know what I'm talking about. I insist that the differences in comparative genomes of chimpanzees and humans are too great to be the result of random mutations, so I'm just being willfully ignorant. I carefully read and research evolutionary literature both as a philosophy of science and a model for empirical research but somehow but I couldn't understand TOE and still be a creationist. Mind you, most of my reading is by evolutionists and I am especially fond of neodarwinism but I still don't accept the core assumptions of evolutionary biology, so I just don't understand. I don't buy it.

 

[mikeynov]

I insist that random mutations don't drive evolution,

Neither do people who accept evolution.

Selection drives evolution. Within the context of nature, nature itself is doing that selecting. So natural selection has been the driving force behind evolution throughout history, by and large.

There are other factors which account for the diversity we see, of course, including genetic drift and sexual selection.

But in terms of adaptive change over time, it's largely seen as a product of natural selection doing the driving, and acting upon the raw variation provided (primarily) by mutation.

 

[mark kennedy]

Neither do people who accept evolution.

Selection drives evolution. Within the context of nature, nature itself is doing that selecting. So natural selection has been the driving force behind evolution throughout history, by and large.

There are other factors which account for the diversity we see, of course, including genetic drift and sexual selection.

But in terms of adaptive change over time, it's largely seen as a product of natural selection doing the driving, and acting upon the raw variation provided (primarily) by mutation.

"The most serious objection to the modern theory of evolution is that since mutations occur by `chance' and are undirected, it is difficult to see how mutation and selection can add up to the formation of such beautifully balanced organs as, for example, the human eye." Dobzhansky as quoted in 'A Biochemical Mechanism for Nonrandom Mutations and Evolution'

Natural selection and variation from recombination does not account for all of the changes that would have to occur down through natural history as it is described in TOE. I am looking around for nonrandom mechanisms of change and I have been pleasantly supprise by just how many of them are out there. Obviously, being a creationist I am pretty skeptical of modern evolutionary thinking but creationism needs evolutionary mechanisms to account for diversity.

I am serious about learning as much as I can about evolutionary theory for one reason, that is the only way to qualify and quantify creation science. Creationists and atheistic materialists alike consider this to be self-defeating and contradictory. I am not convinced of that, in fact, I think creationists would do well to learn what these evolutionary mechanisms are.

 

[maha]

Mark, I'd be interested in hearing what those nonrandom mechanisms of change are, but I fear they don't exist. Also, if they do exist, then how do you reconcile natural selection as the driving force behind evolution? You're kind of throwing the baby out with the bath water when you make such a claim.

Another point which I don't understand is how these nonrandom mechanisms would alter the genome...without reproduction. Because you're saying that some sort of molecular change is happening among individuals which makes them more suitable for survival. That is definitely ID thinking, but it also supports the adaptive evolutionary theories which have been falsified in recent years. Organisms can't willfuly alter their own genetic make up in order to be better suited to survive in their environment...as far as I know.

I'm also now aware that you are a professed creationist which concerns me that you may just be drawing for straws...especially since the evidence that is required to prove your theories has not been produced (but I'm not saying it doesn't exist).

 

[gluadys]

"The most serious objection to the modern theory of evolution is that since mutations occur by `chance' and are undirected, it is difficult to see how mutation and selection can add up to the formation of such beautifully balanced organs as, for example, the human eye." Dobzhansky as quoted in 'A Biochemical Mechanism for Nonrandom Mutations and Evolution'

If you haven't done so yet, I would strongly recommend reading Dobzhanksy directly. He is credited with providing the evidence for the genetic basis of evolution. Since that is a principal concern of yours, it would seem to be pertinent reading.

For my part I am very curious what he said just after the quote above. Typically a scientific paper introduces an objection in order to explain how the objection is overcome by the thesis of the paper.

I think creationists would do well to learn what these evolutionary mechanisms are.

But stop leaving out the mechanism of natural selection.

 

[mikeynov]

"The most serious objection to the modern theory of evolution is that since mutations occur by `chance' and are undirected, it is difficult to see how mutation and selection can add up to the formation of such beautifully balanced organs as, for example, the human eye." Dobzhansky as quoted in 'A Biochemical Mechanism for Nonrandom Mutations and Evolution'

Natural selection and variation from recombination does not account for all of the changes that would have to occur down through natural history as it is described in TOE. I am looking around for nonrandom mechanisms of change and I have been pleasantly supprise by just how many of them are out there. Obviously, being a creationist I am pretty skeptical of modern evolutionary thinking but creationism needs evolutionary mechanisms to account for diversity.

I am serious about learning as much as I can about evolutionary theory for one reason, that is the only way to qualify and quantify creation science. Creationists and atheistic materialists alike consider this to be self-defeating and contradictory. I am not convinced of that, in fact, I think creationists would do well to learn what these evolutionary mechanisms are.

You seriously don't get that natural selection is non-random?