Pete's Quite Thread post

[mikeynov]

I really have bad luck in Mark Kennedy threads. I typed up another big post a few minutes ago and lost it, much as I've lost another one or two in the past.

Oh well.

 

[mark kennedy]

I really have bad luck in Mark Kennedy threads. I typed up another big post a few minutes ago and lost it, much as I've lost another one or two in the past.

Oh well.

Don't worry about it mikeynov, I have a pretty good idea what you wanted to say. The fact is, I would love to say some of it myself, but too much would be lost in the translation.

 

[Tomk80]

We have the cranial capacity but I am not supprised that you failed to realize this.

He did realize that, but you can't do anything with that information. Mutations do not occur only in cranial capacity, but also in various other parts of the body. Some we can find, some we don't. We have, as far as I know, no way to tell which mutations occurred when, and since changes in morphology and genetic mutations are not related on a 1 to 1 basis, we have no way to tell how many changes occurred in what time period. The only thing we 'know' is that between 5 and 10 million years humans and chimps diverged from a common ancestor and now we have a 95% difference in our total genome sequence.

 

[mikeynov]

Also, as a consideration, Mark:

Couple the info on frequency of identical genes cited on page 2 (which you found "interesting") with other areas of study:

* Frequency of shared ERV's and how this matches hypotheses concerning common ancestry
* Frequency of shared pseudogenes, same as above
* Phylogenies of humans and their closest hypothesized relatives using morphological and genetic characters

Now, say for the sake of argument these lines of evidence line up and point to a similar conclusion. Do you feel that an inability to articulate the step-wise process of evolution on a mutation per mutation basis is enough to invalidate this convergence?

Parallel example: within cosmology, there is a fair amount of data on star formation, and the conditions under which this occurs. But we've never observed this happen step-wise, and certainly can't replicate it in the lab.

Would it be fair to reject what we do know and can test because of this inability? Should we conclude that stars are intelligently designed?

 

[mark kennedy]

“The size of human brain tripled over a period of _2 million years (MY) that ended 0.2–0.4 MY ago. This evolutionary expansion is believed to be important to the emergence of human language and other high-order cognitive functions, yet its genetic basis remains unknown.”

Evolution of the Human ASPM Gene, a Major Determinant of Brain Size

* Phylogenies of humans and their closest hypothesized relatives using morphological and genetic characters

This is what I am looking at and the genetic basis is largely a matter of conjecture.

Mutations do not occur only in cranial capacity, but also in various other parts of the body.

Oh, I agee, you can't just have changes in an organ like the brain without it effecting all of the others. We finally agree on something.

 

[mikeynov]

Then just answer this ONE question:

If all these lines of evidence point to a common phylogeny (regardless of whether the mechanism in question is sufficient), then what is the reason for this convergence of errant individual lines of evidence?

In other words, if the reasoning involved in each of these independent lines of evidence (I note you didn't talk about ERV's or shared pseudogenes) is flawed, then how and why are they flawed in such a way as to produce a common phylogeny in terms of the relatedness of humans and their closest hypothesized relatives?

 

[Randall McNally]

“The size of human brain tripled over a period of _2 million years (MY) that ended 0.2–0.4 MY ago. This evolutionary expansion is believed to be important to the emergence of human language and other high-order cognitive functions, yet its genetic basis remains unknown.”

Evolution of the Human ASPM Gene, a Major Determinant of Brain Size



This is what I am looking at and the genetic basis is largely a matter of conjecture.

You need to stop overstating your case.

The precise mutational pathway is unknown =! conjecture

To date, you have provided little (if anything) to support a contention that the evolution of the human brain presents logistical difficulties, much less that it is impossible. Your mumblings about deleterious mutations and fitness have implications for evolution as a whole; or they would if they were actually based on proper understanding.

This is really much ado about nothing until you reinforce the gossamer threads which currently underpin your argument.

Oh, I agee, you can't just have changes in an organ like the brain without it effecting all of the others. We finally agree on something.

All of the other what?

 

[Split Rock]

Nope, can you explain how 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level?

Its called evolution Mark. Both the apes that lead to Man and those that led to Chimps have been diverging in different directions for millions of years.

The authors of the paper you cited indicated that they did not know how many of these differences are ones that caused actual phenotypic changes. The majority are most likely neutral and due to Genetic Drift. These would not be weeded out by selective pressure. This leaves us with an unknown number of genes with an unknown number of phenotypically important mutations. If your point is that we still have a lot to learn, then I agree.

 

[Pete Harcoff]

We have the cranial capacity but I am not supprised that you failed to realize this.

That's morphology. Rates of morphological change and rates of genetic change are not always analogous.

"As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population." - source

I read your post, did you read your source material?

"The central role of beneficial mutations for adaptive processes in natural populations is well established. Thus, there has been a long-standing interest to study the nature of beneficial mutations. Their low frequency, however, has made this class of mutations almost inaccessible for systematic studies. In the absence of experimental data, the distribution of the fitness effects of beneficial mutations was assumed to resemble that of deleterious mutations."

Assumed to resemble? Give me a break, there is no basis for comparison.

Did you read my source material? If you'd just read one more sentence:

"For an experimental proof of this assumption, we used a novel marker system to trace adaptive events in an evolving Escherichia coli culture and to determine the selective advantage of those beneficial mutations."

And slightly further:

"Consistent with an exponential distribution of the fitness effects, we observed a large fraction of advantageous mutations with a small effect and only few with large effect."

Examples of beneficial mutations that effect the human brain, neural systems or other vital organs. Get with the program, we are talking about the differences you alluded to in your Quite Thread post, you even cited and linked the Chimpanzee Chromosome Consortiums paper so you should at least address the findings of their research.

Again, you didn't like the examples you were given (and you were given more than two), you have selectively ignored them, then you repeat your demands. You are becoming a broken record.

 

[yossarian]

mark, you just keep repeating the same thing over and over
this stuff has been explained to you numerous different times

you're like a brick wall

 

[Edx]

I really have bad luck in Mark Kennedy threads. I typed up another big post a few minutes ago and lost it, much as I've lost another one or two in the past.

Oh well.

Try writing them in another word type program first.

Ed

 

[mark kennedy]

It is disappointing that no one is interested in a 'Maltusian parameter' but that would require admitting that there are limits beyond which one species can change into an altogether different kind. *shudders*

I don't know where you get the idea that I am arguing against evolution. I'll probably never post any of it on here but I have a number of evolutionary mechanism that are viable canidates for major mophological change. You need to understand that there is a difference between a transcript error and an adaptation. Random mutations result in disease and disorder if they do anything at all. The very few beneficial mutations observed are dwarfed the things like cancer, tumors, Huntings disease...etc.

The change, from old world monkeys to new world monkeys, the split between chimpanzee and bonobo, eastern and western gorilla, orangutan to gorilla are all changes I accept. Bear in mind all of this has to happen within, say, 20 to 50 generations. The thing is, spontaneous mutations have nothing to do with it and neither does natural selection (preservation). Speciation is not going to happen as a result of a lack of resources. Something they don't tell you in these papers, the mutations that they observe are actually reversable and cyclical. There are variations to the left and right of the mean and these changes aren't permenant and by the way, the bacteria no matter how many mutations will never have a nucleous.

"Mutations have a very limited 'constructive capacity'; this is why the formation of hair by mutation of reptilian scales seems to be a phenomenon of infinitesimal probability; the formation of mammae by mutation of reptilian integumentary glands is hardly more likely .... Mutations, in time, occur incoherently. They are not complementary to one another, nor are they cumulative in successive generations toward a given direction. They modify what preexists, but they do so in disorder, no matter how. ... As soon as some disorder, even slight, appears in an organized being, sickness, then death follow. There is no possible compromise between the phenomenon of life and anarchy" (Grasse, Pierre-Paul, 1977, Evolution of Living Organisms)."


The biggest problem I have with Pete's post in the Quiet Thread is that he never factored in the deleterious and neutral effects of mutations. He also overestimated the rate at which they become fixed in populations over time. Can mutations result in a novel gene, a permenant mophological change or an adaptation? Sure they can, but when you compare the ones that have been directly observed and demonstrated they don't result in the presumed morphologies like the cambrian explosion or human evolution from apes.

They are in the process of figuring out which genes would have to have been involved in human evolution. Were these changes the result of random mutations there would have had to be so many that that it defies logic.

"Although many genetic changes that have occurred in the human lineage have been found, including chromosomal fusion, gene duplication, gene deletion/inactivation, nucleotide substitution, and change in gene expression, very few, if any, of these changes have been linked to specific phenotypes important to the origin and well being of our species "

http://www.genetics.org/cgi/content/full/162/4/1825

Genetic mutations has never offered anything but cyclical change and a slight selective advantage for a short time. When you weigh that against the deleterious and neutral effects mutations create an enormous problem for evolution. That is, of course, if that is what you are using as a demonstrated mechanism for adaptive evolution.

 

[Pete Harcoff]

Random mutations result in disease and disorder if they do anything at all. The very few beneficial mutations observed are dwarfed the things like cancer, tumors, Huntings disease...etc.

This is what's so frustrating. You are so completely fixated on deleterious mutations that you think that that's all that happens. Really, mark, was are the consequences in your mind? That we're are going to go extinct? Do you understand the concept of differential reproductive success? Do you understand that not every single person winds up with a deleterious mutation that prevents them from reproducing?

The biggest problem I have with Pete's post in the Quiet Thread is that he never factored in the deleterious and neutral effects of mutations. He also overestimated the rate at which they become fixed in populations over time.

I never overestimated anything because I have no idea how many mutations, especially beneficial mutations, it would take. Does it take a thousand, ten thousand, hundred thousand beneficial mutations to go from that common ancestor to a modern human? I have no idea. All I have is rough estimates. You have suggested that there should be a beneficial mutation fixed in every single generation, but I have no idea where you pulled that from (I never suggested it).

In fact, I even stated very clearly, "This doesn't take into account fixation of neutral or even possibly deleterious mutations which could account for many more differences between humans and chimps." This is still a point of contention among biologists anyway (i.e. selection versus genetic drift).

All I did was calculate a rough figure (64000 mutations) and tried to compare it to the amount of genetic divergence between the two species. Had the beneficial mutation rate been so low that there would have been few mutations (say, in the hundreds) then I would figure there was a problem.

What you are doing is blowing what I calculated completely out of proportion. The point of my thread was simply an answer to the various charges that beneficial mutation rates were too low for evolution to work. All I did was look at the available data to see if this was true or not.

Can mutations result in a novel gene, a permenant mophological change or an adaptation? Sure they can, but when you compare the ones that have been directly observed and demonstrated they don't result in the presumed morphologies like the cambrian explosion or human evolution from apes.

But this is an entirely different argument. You want to know the specifics. I'm just looking at rough generalities.

They are in the process of figuring out which genes would have to have been involved in human evolution. Were these changes the result of random mutations there would have had to be so many that that it defies logic.

Except it doesn't deny logic, because that's the whole point of mutation rates. The mutation rates aren't a problem. What you are arguing is that the specific mutations are the problem.

 

[Manic Depressive Mouse]

It is disappointing that no one is interested in a 'Maltusian parameter' but that would require admitting that there are limits beyond which one species can change into an altogether different kind

Funnily enough that's because there is no evidence, in fact no reason at all to believe that one exists. Unless of course you're so desperate to validate your interpretation of a passage in the Bible that you're willing to make things up and ignore anything that disagrees with your belief... Oh, right.

Mark you've demonstrated time and time again that you're unwilling to even acknowledge any evidence shown to you, and also fail to show any evidence to support your myriad of baseless assertions. So why should anyone bother?

Your entire argument is garbage Mark. You seem to think that gaps in knowledge in some areas is somehow proof against evolution, and not only that but that this non-evidence somehow disproves all the other actual evidence for evolution and common descent.

As someone earlier said; You, and Creationists, have nothing. All you are are a bunch of naysayers with nothing to back you up.

 

[mark kennedy]

This is what's so frustrating. You are so completely fixated on deleterious mutations that you think that that's all that happens.

That is not all I think happens, remember the nylon bug? What happened was an open reading frame was switched out. There are also ways that bacteria can turn genes on and off, single base substitutions can change the expression in the proteins by altering the amino acids. The thing is, I don't like the term mutation just like I don't like the term natural selection, they are both misnomers. Some times adaptive evolution is the result of special molecular mechanisms that can relax functional constraints but in order for this to happen the enzymes must be altered first.

Really, mark, was are the consequences in your mind?

What are the consequences of random mutations becoming fixed in protein coding or regulatory genes? What are the chances that a typo in one of these posts will produce a more effective argument?

That we're are going to go extinct? Do you understand the concept of differential reproductive success? Do you understand that not every single person winds up with a deleterious mutation that prevents them from reproducing?

Of course I do. Do you understand that there are limits to how many mutations can be introduced. Hybrids are known for having limited reproductive success and when reintroduced to the wild they will revert back to their original wild type. I was reading a rather disurbing article about bananas some time ago, apparently the hybrids that they are using cannot reproduce. This is what Darwin called the bane of horticulture and he makes other inferances from artifical selection in breeding animals.

This is also a problem in the wild when you stop to consider the consequences of, say, a mutant allele being introduced into a population. However, we do know that speciation happens along these lines since there is very little question that eastern/western gorillas, chimps and bonobos, new world and old world monkeys have a common lineage. The genetic divergance is measurable and as strange as it might seem the differences within the chimpanzees collective genomes will be greater then the ones between chimps and bonobos.

I never overestimated anything because I have no idea how many mutations, especially beneficial mutations, it would take. Does it take a thousand, ten thousand, hundred thousand beneficial mutations to go from that common ancestor to a modern human? I have no idea. All I have is rough estimates. You have suggested that there should be a beneficial mutation fixed in every single generation, but I have no idea where you pulled that from (I never suggested it).

No matter how many generations there are you will need a ratio of synonomous/nonsynonomous genes. Here is where I got the idea of 1 mutation being fixed per generation and notice, its 1.6.

"It has been suggested that humans may suffer a high genomic deleterious mutation rate. Here we test this hypothesis by applying a variant of a molecular approach to estimate the deleterious mutation rate in hominids from the level of selective constraint in DNA sequences. Under conservative assumptions, we estimate that an average of 4.2 amino-acid-altering mutations per diploid per generation have occurred in the human lineage since humans separated from chimpanzees. Of these mutations, we estimate that at least 38% have been eliminated by natural selection, indicating that there have been more than 1.6 new deleterious mutations per diploid genome per generation. Thus, the deleterious mutation rate specific to protein-coding sequences alone is close to the upper limit tolerable by a species such as humans that has a low reproductive rate, indicating that the effects of deleterious mutations may have combined synergistically. Furthermore, the level of selective constraint in hominid protein-coding sequences is atypically low. A large number of slightly deleterious mutations may therefore have become fixed in hominid lineages."(High genomic deleterious mutation rates in hominids, available online)

In fact, I even stated very clearly, "This doesn't take into account fixation of neutral or even possibly deleterious mutations which could account for many more differences between humans and chimps." This is still a point of contention among biologists anyway (i.e. selection versus genetic drift).

That is because all of life is about balance and there are limits to how much functional constraint can be relaxed. The numbers I have seen are about 80% neutral and the remainder having a fraction that are harmfull and a smaller fraction that are lethal. Mutations that have a beneficial effect are rare but they have been known to give a small minority a slight selective advantage and can even achieve equilibrium. That is why the 'Maltusian parameter' is so important and if you had focused on this and used a viable formula for it I would have reped your post rather then criticizing it. You have to factor in neutral and harmfull effects Pete, that's all I am saying. You can't just say that there are as many beneficial effects as there are harmfull ones. You can't just say (I realize you didn't so don't take this wrong) that natural selection keeps the beneficial ones and eliminates the harmfull ones because it doesn't. The 'fittest' will be the population with the stongest ability to adapt to environmental challanges and most of the time is random assortments of existing genes, not spontaneous mutations that bring it about.

All I did was calculate a rough figure (64000 mutations) and tried to compare it to the amount of genetic divergence between the two species. Had the beneficial mutation rate been so low that there would have been few mutations (say, in the hundreds) then I would figure there was a problem.

You don't need to account for all of them, the ones you should have focused on were the ones in the genes that are resposible for unique human features. Two of the most important ones are ASPM and the FOX2 genes. All you would have had to do is find the Ka/Ks ratios and go from there. I would have had some problems with it but had you focused on something that tangible and allowed for the delerious effects all I could have used against it would have been arguments from incredulity. What you have isn't that bad really, it's just incomplete.

What you are doing is blowing what I calculated completely out of proportion. The point of my thread was simply an answer to the various charges that beneficial mutation rates were too low for evolution to work. All I did was look at the available data to see if this was true or not.

It all depends on what you think the mutation is supposed to do and saying that mutation rates is not a problem is an oversimplification. It is a problem that researchers have been struggling with and there is a lot of research out there that have done exactly what you were trying to do. The problem is that beneficial mutations are vitually nonexistant in human genetics so measuring them is next to impossible. It is puzzling at best equivate bacterial mutation rates with eukaryotes. Mutation rates are very different for different groups:

Rates of spontaneous mutation per genome as measured in the laboratory are remarkably similar within broad groups of organisms but differ strikingly among groups...Among the mutations that affect a typical gene, different kinds produce different impacts. A very few are at least momentarily adaptive on an evolutionary scale. Many are deleterious. Some are neutral, that is, they produce no effect strong enough to permit selection for or against; a mutation that is deleterious or advantageous in a large population may be neutral in a small population, where random drift outweighs selection coefficients.

Homo sapiens:...With 6.4 x 109 base pairs in the diploid genome, a mutation rate of 10-8 means that a zygote has 64 new mutations. It is hard to image that so many new deleterious mutations each generation is compatible with life, even with an efficient mechanism for mutation removal. Thus, the great majority of mutations in the noncoding DNA must be neutral."

(Rate of Spontaneous mutation)

But this is an entirely different argument. You want to know the specifics. I'm just looking at rough generalities.

I just don't see bacteria mutation rates as being a base line for homo sapien mutation rate. What is more, saying the beneficial mutation rate are roughly equal to deleterious ones is simply not a valid assumption. There is good reason why we know so much about delerious mutations that effect humans and have such a hard time finding beneficial ones, because the one that produce an effect are almost allways deleterious.

Except it doesn't deny logic, because that's the whole point of mutation rates. The mutation rates aren't a problem. What you are arguing is that the specific mutations are the problem.

They are a problem when you take into consideration the effect of mutations on populations when they are expressed in the phenotype. I have never seen or heard of an indel creating an improved vital organ in humans. I have literally seen dozens of diseases and disorders that are the direct result of mutations. It is a problem Pete, what you are looking for is a positive adaptive trait that results from something other then a random transcript error.

 

[mikeynov]

mark, you just keep repeating the same thing over and over
this stuff has been explained to you numerous different times

you're like a brick wall

^^^

 

[Pete Harcoff]

What are the consequences of random mutations becoming fixed in protein coding or regulatory genes? What are the chances that a typo in one of these posts will produce a more effective argument?

More mutations are harmful than helpful. I have NEVER claimed otherwise.

Of course I do. Do you understand that there are limits to how many mutations can be introduced. Hybrids are known for having limited reproductive success and when reintroduced to the wild they will revert back to their original wild type.

We're not talking about hybrids, though.

This is also a problem in the wild when you stop to consider the consequences of, say, a mutant allele being introduced into a population. However, we do know that speciation happens along these lines since there is very little question that eastern/western gorillas, chimps and bonobos, new world and old world monkeys have a common lineage. The genetic divergance is measurable and as strange as it might seem the differences within the chimpanzees collective genomes will be greater then the ones between chimps and bonobos.

I still find it utterly bizarre that you accept common ancestry for primates, but reject it for humans. Is it fair to say that your religious beliefs might have something to do with that?

No matter how many generations there are you will need a ratio of synonomous/nonsynonomous genes. Here is where I got the idea of 1 mutation being fixed per generation and notice, its 1.6.

"Under conservative assumptions, we estimate that an average of 4.2 amino-acid-altering mutations per diploid per generation have occurred in the human lineage since humans separated from chimpanzees. Of these mutations, we estimate that at least 38% have been eliminated by natural selection, indicating that there have been more than 1.6 new deleterious mutations per diploid genome per generation."

I'm still not sure why you think those mutations are necessarily being fixed in the population. In fact, I think you're reading that whole abstract wrong. It's saying that there's 4.2 mutations per diploid per generation. IOW, each individual will have 4.2 mutations unique to their own protein-coding DNA. And of those, 1.6 will be deleterious. But that doesn't mean that those 1.6 deleterious mutations will be fixed in the population.

That is because all of life is about balance and there are limits to how much functional constraint can be relaxed. The numbers I have seen are about 80% neutral and the remainder having a fraction that are harmfull and a smaller fraction that are lethal. Mutations that have a beneficial effect are rare but they have been known to give a small minority a slight selective advantage and can even achieve equilibrium. That is why the 'Maltusian parameter' is so important and if you had focused on this and used a viable formula for it I would have reped your post rather then criticizing it. You have to factor in neutral and harmfull effects Pete, that's all I am saying. You can't just say that there are as many beneficial effects as there are harmfull ones. You can't just say (I realize you didn't so don't take this wrong) that natural selection keeps the beneficial ones and eliminates the harmfull ones because it doesn't. The 'fittest' will be the population with the stongest ability to adapt to environmental challanges and most of the time is random assortments of existing genes, not spontaneous mutations that bring it about.

And yet you have previously stated that you accept new alleles appearing a population. Those new alleles are fair game to be fixed in population.

You don't need to account for all of them, the ones you should have focused on were the ones in the genes that are resposible for unique human features. Two of the most important ones are ASPM and the FOX2 genes. All you would have had to do is find the Ka/Ks ratios and go from there. I would have had some problems with it but had you focused on something that tangible and allowed for the delerious effects all I could have used against it would have been arguments from incredulity. What you have isn't that bad really, it's just incomplete.

I was never trying to argue the specifics of human evolution, however. Just theoretical mutation rates. Remember, people kept saying there aren't enough beneficial mutations for evolution and were basing this data on... nothing.

It all depends on what you think the mutation is supposed to do and saying that mutation rates is not a problem is an oversimplification. It is a problem that researchers have been struggling with and there is a lot of research out there that have done exactly what you were trying to do. The problem is that beneficial mutations are vitually nonexistant in human genetics so measuring them is next to impossible. It is puzzling at best equivate bacterial mutation rates with eukaryotes. Mutation rates are very different for different groups:

<snippage>

Yet, the rate per cell generation is about 1/300 across the board. Which is why I extrapolated the way I did. I certainly didn't assume that the number of mutations per organism were the same between bacteria and humans!

I just don't see bacteria mutation rates as being a base line for homo sapien mutation rate.

Fair enough, it may not be. BUT, we don't know the beneficial mutation rate for homo sapiens. Despite this, people were claiming there weren't enough beneficial mutations. So, I took what data was available and crunched some numbers. That's it.

What is more, saying the beneficial mutation rate are roughly equal to deleterious ones is simply not a valid assumption.

I never said they were. Where the heck are you getting this from? You seem to be reading something that I never wrote.

There is good reason why we know so much about delerious mutations that effect humans and have such a hard time finding beneficial ones, because the one that produce an effect are almost allways deleterious.

Not so much that, but healthy people don't usually subject themselves to medical testing. Obviously there is going to be far more research into harmful mutations because (aside from them being more frequent) that is what affects people's quality of life. When have you ever heard of a person undergoing medical treatment for being too intelligent or running too fast?

They are a problem when you take into consideration the effect of mutations on populations when they are expressed in the phenotype. I have never seen or heard of an indel creating an improved vital organ in humans. I have literally seen dozens of diseases and disorders that are the direct result of mutations. It is a problem Pete, what you are looking for is a positive adaptive trait that results from something other then a random transcript error.

Once again, that's nothing to do with mutation rates. Specific effects of mutations and estimated rates of mutations are two entirely different things. You keep conflating the two.

Besides, I gave you an example of beneficial indel: AIDS resistance. But you first didn't understand it very well (since you ignored the homozygous genotype), then you reject it because it's not affecting a vital organ or something.

I honestly don't think you know what you want and I don't think you'd recognize it if you saw it.

 

[Split Rock]

It is disappointing that no one is interested in a 'Maltusian parameter' but that would require admitting that there are limits beyond which one species can change into an altogether different kind. *shudders*

I have yet to hear from any creationist (including yourself) just what constitutes a "Kind." Creationists talk about the mysterious limit that prevents one Kind from changing into another Kind, but I have never seen a good definition of what a Kind is, or how many Kinds there are.

As far as fear is concerned, it is Creationists that fear Common Descent, not evolutionists that fear Special Creation. Evolution for us is not a faith that can be threatened. The only "shudders" that I can see are from Creationists.

 

[mark kennedy]

More mutations are harmful than helpful. I have NEVER claimed otherwise.

I wouldn't be having this conversation that was deluded enough to conclude otherwise.

We're not talking about hybrids, though.

Why do you think Darwin called the process by which species evolve into another species natural selection? Speciation may well be far more involved then a simple hybrid but the principles are virtually identical, the only difference is the scale. In other words you can have a single hybrid but speciation effects entire populations.

I still find it utterly bizarre that you accept common ancestry for primates, but reject it for humans. Is it fair to say that your religious beliefs might have something to do with that?

Of course my religious beliefs have something to do with it. I was close to a TE or reformed creationist postion when I started looking into genetics. I was expecting to find elaborate molecular mechanisms that facilated adaptive evolutionary events. Instead reliance on random mutations did not square with the directly observed and demonstrated effects of these changes. I am still frustrated with creationism at large and would really love it if they would develop their concepts with more detailed genetic analysis.

There are limits beyond which species can transform into an altogether different kind, I am convinced of that.

I'm still not sure why you think those mutations are necessarily being fixed in the population. In fact, I think you're reading that whole abstract wrong. It's saying that there's 4.2 mutations per diploid per generation. IOW, each individual will have 4.2 mutations unique to their own protein-coding DNA. And of those, 1.6 will be deleterious. But that doesn't mean that those 1.6 deleterious mutations will be fixed in the population.

The reason the 4.2 figure was reduced to 1.3 is because 38% have been purged. Among those deleterious mutations there will be a certain percentage that are harmfull and a smaller fraction that will be lethal. You bring in the Chimpanzee Chromosome paper that identifies some 15 gross structural differences in the context of mutation rates. It is obvious from even a superficial reading of the genetic research that beneficial effects from mutations are both rare and only offer a small selective advantage for a small minority. How this does not create a problem for the theory of evolution is a complete mystery.

And yet you have previously stated that you accept new alleles appearing a population. Those new alleles are fair game to be fixed in population.

These new alleles, if they are the result of mutant genes are going to be deleterious if not utterly lethal. If you know of a novel allele that resulted in a unique trait being fixed in a human population I have yet to see it. All I am finding are disease and disorders and there are more of these then you can shake a stick at.

I was never trying to argue the specifics of human evolution, however. Just theoretical mutation rates. Remember, people kept saying there aren't enough beneficial mutations for evolution and were basing this data on... nothing.

They are basing in on directly observed and demonstrated effects.

Yet, the rate per cell generation is about 1/300 across the board. Which is why I extrapolated the way I did. I certainly didn't assume that the number of mutations per organism were the same between bacteria and humans!

I don't have a clue what the ration 1/300 is supposed to be but this is what you said. "Based on these rates, 1 in every 625000 mutations is beneficial."

Fair enough, it may not be. BUT, we don't know the beneficial mutation rate for homo sapiens. Despite this, people were claiming there weren't enough beneficial mutations. So, I took what data was available and crunched some numbers. That's it.

You overestimated the amount of time in which the major mophological changes (supposedly resulting from random mutations). Most of the changes occured in roughly a 2 million year period. It only makes since that the deleterious mutations were being fixed at that time. You also estimated the divergance between humans and chimps to be about 2% which is absolutly false, its more like 5%. There is also a 20% difference in the protein coding genes with 83% in the comparitive chromsomes showing differences on an amino acid sequence level.

I never said they were. Where the heck are you getting this from? You seem to be reading something that I never wrote.

"This is due to the fact that many more mutations occur in humans (typical estimates are over 100), but most are in non-protein coding DNA. But in the E.Coli genome, almost the entire genome is considered the "effective genome". Therefore, for the purposes of this comparison I'm going to compare rates in effective genome only. I should also point out that 1.6 mutations is one of the lower estimates I've seen (some estimates are over 4 per human per generation)."

That is where you equivacated bacteria mutation rate with human. Since the focus was on effective genome we are talking about dna that actually does something. You take a deleterious mutation rate and then from a ratio of 1 in every 625000 mutations from that number. So there are 1.6 deleterious mutations per generation for 100,000 generations which would give us 6 or 7 beneficial mutations. Now unless you consider the number of beneficial effects equal with the deleterious ones you have created a formula that would be suitable for a creationist essay on the subject.

Not so much that, but healthy people don't usually subject themselves to medical testing. Obviously there is going to be far more research into harmful mutations because (aside from them being more frequent) that is what affects people's quality of life. When have you ever heard of a person undergoing medical treatment for being too intelligent or running too fast?

When they are taking dna samples they are not going to be able to identify the deleterious mutations unless they know what a normal genome looks like. They have taken samples across broad demographic lines and there is very little variance in the effective genome of homo sapiens.

Once again, that's nothing to do with mutation rates. Specific effects of mutations and estimated rates of mutations are two entirely different things. You keep conflating the two.

Besides, I gave you an example of beneficial indel: AIDS resistance.

Right, and it resulted in a slight advantage and resistance to one strain of HIV that afforded a 1 year reprive from full blown AIDs. This is due to a defective T cell receptor, not an improved resistance.

But you first didn't understand it very well (since you ignored the homozygous genotype), then you reject it because it's not affecting a vital organ or something.

I honestly don't think you know what you want and I don't think you'd recognize it if you saw it.

I know exactly what I am looking for and I can only find it in evolutionary literature. I am looking for molecular mechanisms that lead to dramatic morpholgical change. It makes as much sense to assume multiple common ancestors as it does to assume a single one. In fact, it makes a lot more sense then relying on random mutations to grow the effective genome.

 

[gluadys]

I don't think mark believes in natural selection.

Mark thinks natural selection is metaphysics and paganistic goddess-worship. "Artemise" (sic) did it!"