Pete's Quite Thread post

[mark kennedy]

It was no coincidence that the above picture was on the inside cover of Erasmus Darwin's book, the Temple of Nature.

 

[gluadys]

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.

In most cases, speciation is the direct opposite of hybridization. The principles are quite different.

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

That depends on how you identify "kind" and how you define "altogether different". A cladistic view of evolution agrees that a species will never transform into a different clade. If creationists identified "kind" with "clade" we would have no disagreement on the limits of evolution.

It only makes since that the deleterious mutations were being fixed at that time.

Why? And btw, how do you define "fixed" in this context?

 

[notto]

It was no coincidence that the above picture was on the inside cover of Erasmus Darwin's book, the Temple of Nature.

http://www.stanford.edu/class/engl174b/chain.html

Perhaps this is more to your liking. From the sounds of it, it is a scientific model in your eyes.

 

[mark kennedy]

In most cases, speciation is the direct opposite of hybridization. The principles are quite different.

You do realize that it is called natural selection because it is an analogy from artificial selection right?

That depends on how you identify "kind" and how you define "altogether different". A cladistic view of evolution agrees that a species will never transform into a different clade. If creationists identified "kind" with "clade" we would have no disagreement on the limits of evolution.

Most creationists would not doubt that 'kind' is far more the species level changes. Kind is probably more like what taxonomy refers to as class are conceivably phylum.

Why? And btw, how do you define "fixed" in this context?

That would be the limits of changes in the functional dna to produce an expression in the phenotype. Novel alleles being the most important expression of these changes in the DNA sequences, particularly at an amio acid sequence level.

 

[mark kennedy]

http://www.stanford.edu/class/engl174b/chain.html

Perhaps this is more to your liking. From the sounds of it, it is a scientific model in your eyes.

Cute notto. I don't know what signifigance you think this bizzare print has to do with mutation rates but I doubt seriously it is more then a dig.

 

[maha]

Mark, could you please briefly restate your theory/hypothesis about mutation rates; also if you could, frame it in the context of your overall perception of evolution. A bunch of scientific jargon is not going to do much for me, so if you could just recap the gist of your argument (in layman's terms) I would appreciate it. I'm not sure if you are contesting how mutation effects selection or what. I'd appreciate some clarification.

 

[mark kennedy]

Mark, could you please briefly restate your theory/hypothesis about mutation rates; also if you could, frame it in the context of your overall perception of evolution. A bunch of scientific jargon is not going to do much for me, so if you could just recap the gist of your argument (in layman's terms) I would appreciate it. I'm not sure if you are contesting how mutation effects selection or what. I'd appreciate some clarification.

I'd be glad to maha, basiclly I think that there are natural mechanisms for adaptation, many of which have been identified. A mutation is kind of like a typo in one of your posts and just as you will go back and correct it there are ways that mutations (transcript errors) are edited out of the genetic code. These editors are called enzymes and they are kind of like factory workers that carefully examine the product for defects and mistakes in the manufactured product. Pete is aware of these problems but we are argueing about how many of these changes can happen without serious damage being deadly.

What I am doing in this thread is trying to get Pete to look at the dangers of genetic mutations. Most mutations are caused by the dna not being properly copied and it results in diseases and medical disorders. I think that the way that living systems adapt to new environments can be boiled down to turning certain genes on and off, different combinations of genes and a couple of other things. I don't think that a copy error will result in an adaptation that makes living organisms more able to survive.

There are rare occasions when a copy error can do this but it is the exception, not the rule. When this happens it only gives these groups a small advantage and it only lasts for a while.

I hope that helps to clarify a little.

Grace and peace,
Mark

 

[maha]

Mark Kennedy wrote:
I think that the way that living systems adapt to new environments can be boiled down to turning certain genes on and off, different combinations of genes and a couple of other things

Okay. It sounds like you are talking about adaptive evolution--genetic changes occuring in one individual during its lifetime (before it reproduces) and the altered DNA pattern being passed down to its progeny. I wasn't aware that this was even possible or that there is any new scientific evidence to support it. Although that may be what you are claiming, I'm not sure.

I know that you mentioned deleterious vs. beneficial genetic mutations, and I guess, the frequency of each among species. But I always thought that genetic drift allowed for changes to occur, and that natural selection sorted out the rest. It sounds like you are sort of insinuating an "intelligent design" angle into the process. Are you saying that mutation is not random and that there are other mechanisms that attribute to an individual being better genetically suited to survive?

 

[gluadys]

You do realize that it is called natural selection because it is an analogy from artificial selection right?

Yes, and that hybridization is often used in conjunction with artificial selection to get new varieties. Note, however, that most artificial selection does not lead to speciation.

Hybridization is rare in nature, at least among animals. Most speciation involves no hybridization at all. Have you never checked out cladistic speciation and noticed the difference between cladism and hybridization?

Most creationists would not doubt that 'kind' is far more the species level changes. Kind is probably more like what taxonomy refers to as class are conceivably phylum.

Interestingly, Darwin never promoted the idea of a single common ancestor. In Origin of Species, he, too, considered it likely that each class had a common ancestor.

It may be asked how far I extend the doctrine of the modification of species. The question is difficult to answer, because the more distinct the forms are which we consider, by so much the arguments in favour of community of descent become fewer in number and less in force. But some arguments of the greatest weight extend very far. All the members of whole classes are connected together by a chain of affinities, and all can be classed on the same principle, in groups subordinate to groups. Fossil remains sometimes tend to fill up very wide intervals between existing orders.

Organs in a rudimentary condition plainly show that an early progenitor had the organ in a fully developed condition, and this in some cases implies an enormous amount of modification in the descendants. Throughout whole classes various structures are formed on the same pattern, and at a very early age the embryos closely resemble each other. Therefore I cannot doubt that the theory of descent with modification embraces all the members of the same great class or kingdom. I believe that animals are descended from at most only four or five progenitors, and plants from an equal or lesser number.​

emphasis added
He does continue in the next paragraph that by analogy the concept could be extended to a single common ancestor and gives some arguments for that, but plainly he was not committed to just one common ancestor as his conclusion also shows.

However, why not consider "kind" as analagous to "clade" rather than to a Linnean rank?

That would be the limits of changes in the functional dna to produce an expression in the phenotype. Novel alleles being the most important expression of these changes in the DNA sequences, particularly at an amio acid sequence level.

It appears you have never looked up the biological definition of "fixed". This rambling has nothing to do with fixation of genes/alleles.

Here is Mark Ridley's definition:

A gene has achieved fixation when its frequency has reached 100% in the population. At that stage, all individuals are homozygous for that allele until a new mutation arises.

A gene may be taken to fixation by selection or genetic drift. Populations often maintain polymorphism at a locus.

http://www.blackwellpublishing.com/ridley/a-z/Fixation.asp​

Some biologists don't insist on a 100% level of occurrence, but recognize a gene or allele as fixed when it occurs in over 95% of the population.

Now have you ever checked out the rate of occurrence of alleles which are deleterious? How often does a mutated ASPM gene producing microcephaly occur in humans? Is it anywhere near the fixation level?

 

[mark kennedy]

Okay. It sounds like you are talking about adaptive evolution--genetic changes occuring in one individual during its lifetime (before it reproduces) and the altered DNA pattern being passed down to its progeny. I wasn't aware that this was even possible or that there is any new scientific evidence to support it. Although that may be what you are claiming, I'm not sure.

It sounds like you know more then you are telling, but at any rate, adaptive evolution is the highlighted issue. Evolution cannot be limited to one individule and at best it can be limited to a small population. There are rare instances when an altered DNA pattern can effect the phenotype (offspring, progeny or outward expression) but it is limited to the available genes. There is actually a lot of evidence out there to support a change in DNA producing an advantage for the offspring, they are hard to find but they do exist. I am saying that they have real and measurable limits and transforming creatures into alltogether different kinds is the stuff of science fiction. Most of the beneficial effects of mutations are very limited.

I know that you mentioned deleterious vs. beneficial genetic mutations, and I guess, the frequency of each among species. But I always thought that genetic drift allowed for changes to occur, and that natural selection sorted out the rest. It sounds like you are sort of insinuating an "intelligent design" angle into the process. Are you saying that mutation is not random and that there are other mechanisms that attribute to an individual being better genetically suited to survive?

You are right on both counts, I am talking about deleterious vs. benefical effects of mutaitons and I do approach to topic from an ID perspective. Now as far as the role of genetic mutations I think there are far better explanations for adaptation. Random combinations being the most important but there are ways of switching genes on and off as well. I would advise caution when attributing adaptive changes to an individule, evoltution is population thinking and the focus is on how whole populations are effected.

You are keeping up pretty well, you suprise me maha.

 

[Pete Harcoff]

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.

Eh? Genetic isolation of a population that results in speciation is different than crossing two species. Yes, speciation can result of hybridization, but it's not limited to it.

The reason the 4.2 figure was reduced to 1.3 is because 38% have been purged.

Er, you're reading that completely wrong. 1.6 of the mutations were deleterious. 2.6 were not.

Among those deleterious mutations there will be a certain percentage that are harmfull and a smaller fraction that will be lethal.

So? Say it with me now: differential reproductive success.

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.

It doesn't create a problem. But you keep closing your eyes and plugging your ears anytime anyone tries to demonstrate otherwise.

These new alleles, if they are the result of mutant genes are going to be deleterious if not utterly lethal.

No, mark. Not all alleles are deleterious or 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'd love to see how you define "unique trait". I have this sneaking suspicion you'll play fast and loose with the definition no matter what I give you.

They are basing in on directly observed and demonstrated effects.

That's simply not true.

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."

It's right there in the abstract, mark. Didn't you read the whole thing?

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.

I'm going to repeat this for the umpteenth time: rates of morphological change and genetic change are not necessarily synonymous. Now repeat that over and over until you understand it.

And I'm also going to repeat for the umpteenth time: we don't have a genetic baseline for comparison from 2 million years ago.

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%.

Sure, if you take into account the differences in the entire genome. But I don't care about those differences, just the ones that are likely to affect functional genes. In which case, the differences are smaller.

And yeah, there might have been deleterious mutations fixed in populations as a result of drift or hitchhiking. I even suggested this.

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.

Wrong. I derived that from the total mutation rate, not from the deleterious mutation rate. Go back and read what I wrote.

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.

You've got it all wrong, mark. You're taking what I wrote and twisting it around completely. Go back and re-read everything until you understand it.

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.

Again, you ignore the homozygous genotype for that gene. You must have blinders on.

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.

It sounds to me like you're looking for hopeful monsters.

And it doesn't make sense to consider multiple common ancestors, because then you'd have complete discordance among the nested trees of life. But we don't. All the evidence points to a human/ape divergence. But since it doesn't jive with your religious beliefs, you reject it.

 

[Pete Harcoff]

Most creationists would not doubt that 'kind' is far more the species level changes. Kind is probably more like what taxonomy refers to as class are conceivably phylum.

The reality is that creationists have no clue, considering they've never bothered to define it in any meaningful manner as applicable to biology.

 

[Pete Harcoff]

Mark, how can you say:

I don't think that a copy error will result in an adaptation that makes living organisms more able to survive.

Followed immediately by:

There are rare occasions when a copy error can do this but it is the exception, not the rule.

Either you believe beneficial mutations exist or you don't. There's no middle ground here.

 

[maha]

Mark wrote: It sounds like you know more then you are telling,

I wasn't trying to be coy, I just didn't want to be bogged down with a bunch of specific facts and terms which would've been irrelevant considering what I was trying to find out--your take on the issue. It sounds like this is a debate between you and Pete mostly, however.

You are keeping up pretty well, you suprise me maha.

I do have a pretty good working knowledge of evolutionary theory, but in a very broad sense. I also think that Pete has brought up some good points which suggest a contradiction in your reasoning. Plus, I still don't understand the exact mechanism which you are referencing which would allow for adaptations to occur among populations or individuals for that matter. I guess I'm talking about your "ways of switching genes on and off" in particular.

 

[mikeynov]

The reality is that creationists have no clue, considering they've never bothered to define it in any meaningful manner as applicable to biology.

So mark believes humans DO share non-human ancestry?

 

[mark kennedy]

Eh? Genetic isolation of a population that results in speciation is different than crossing two species. Yes, speciation can result of hybridization, but it's not limited to it.

I don't care if hybrids lead to speciation or not to be honest. That was a side issue.

Er, you're reading that completely wrong. 1.6 of the mutations were deleterious. 2.6 were not.

Right, they were neutral.

So? Say it with me now: differential reproductive success.

What's you point Pete?

It doesn't create a problem. But you keep closing your eyes and plugging your ears anytime anyone tries to demonstrate otherwise.

None so blind as those who will not see, ditto.

No, mark. Not all alleles are deleterious or lethal.

I didn't say that all, I said a smaller fraction were deleterious and an even a smaller fraction was lethal. The fact is that benefical effects are smaller still.

I'd love to see how you define "unique trait". I have this sneaking suspicion you'll play fast and loose with the definition no matter what I give you.

That would depend on the original genotype would it not?

That's simply not true.

Ok, show me a directly observed or demostrated benefical mutation and I will show you a dozen deleterious effects from the same type of mutation.

It's right there in the abstract, mark. Didn't you read the whole thing?

Fill me in Pete, what did I miss?

I'm going to repeat this for the umpteenth time: rates of morphological change and genetic change are not necessarily synonymous. Now repeat that over and over until you understand it.

But they are mutually dependant or are you going to abandon the dogma of darwinian evolution that mutations drive evolution.

And I'm also going to repeat for the umpteenth time: we don't have a genetic baseline for comparison from 2 million years ago.

For the umpteenth time we don't have a genetic basis for the transition either.

Sure, if you take into account the differences in the entire genome. But I don't care about those differences, just the ones that are likely to affect functional genes. In which case, the differences are smaller.

Last time I check the protein coding genes were functional genes and there are fifteen gross structural changes and a whole lot of other differences that you have failed to account for.

And yeah, there might have been deleterious mutations fixed in populations as a result of drift or hitchhiking. I even suggested this.

Funny, you never bother to give the particulars.

Wrong. I derived that from the total mutation rate, not from the deleterious mutation rate. Go back and read what I wrote.

Go back and learn the differences in the two genomes in your source material.

You've got it all wrong, mark. You're taking what I wrote and twisting it around completely. Go back and re-read everything until you understand it.

I've read all I need to, the mutation rate you offered was far too slight to produce an evolutionary change. Even given the time you generously allowed yourself the amount of benefical mutations do not account for major morphological change.

Again, you ignore the homozygous genotype for that gene. You must have blinders on.

You missed the deleterious effects of mutations and how they dwarf the benefical effects.

It sounds to me like you're looking for hopeful monsters.

I am not into Punk eek, just don't need thousands of mutations for an adaptation.

And it doesn't make sense to consider multiple common ancestors, because then you'd have complete discordance among the nested trees of life. But we don't. All the evidence points to a human/ape divergence. But since it doesn't jive with your religious beliefs, you reject it.

My religious beliefs have nothing to do with the effects of mutations as they are directly observed and demonstrated in modern genetics. The evidence points to independant lineage, whether you like it or not, whether you want to admitt it or not.

 

[mark kennedy]

I wasn't trying to be coy, I just didn't want to be bogged down with a bunch of specific facts and terms which would've been irrelevant considering what I was trying to find out--your take on the issue. It sounds like this is a debate between you and Pete mostly, however.

Yes, this is primarily between Pete and I, I didn't really like the fact that he thought mutations were no problem for evolution.

I do have a pretty good working knowledge of evolutionary theory, but in a very broad sense. I also think that Pete has brought up some good points which suggest a contradiction in your reasoning. Plus, I still don't understand the exact mechanism which you are referencing which would allow for adaptations to occur among populations or individuals for that matter. I guess I'm talking about your "ways of switching genes on and off" in particular.

That is a real problem sometimes, since I accept evolution as it is properly defined and demonstrated in natural science. I do draw the line at speciation being the result of a random mutation and most changes in alleles (recombinations of genes) are nothing like spontaneous mutations. The genes being switched on and off are actually something that they realized about bacteria and I don't really want to get into it right now. What I am looking for are well defined limits to evolutionary change and I am convinced that researchers are finding them as we speak.

 

[gluadys]

What's you point Pete?

That you even have to ask says volumes about your wilful ignorance of natural selection.

I didn't say that all, I said a smaller fraction were deleterious and an even a smaller fraction was lethal. The fact is that benefical effects are smaller still.

So what? Given differentional reproductive success, what do you expect the consequences will be for the population 100 generations down the line? How many of the population will be descendants of those individuals who acquired a lethal mutation, for example?

You missed the deleterious effects of mutations and how they dwarf the benefical effects.

Just how does this happen, mark? How do deleterious effects dwarf beneficial effects?

 

[mark kennedy]

That you even have to ask says volumes about your wilful ignorance of natural selection.

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.

So what? Given differentional reproductive success, what do you expect the consequences will be for the population 100 generations down the line? How many of the population will be descendants of those individuals who acquired a lethal mutation, for example?

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.

Just how does this happen, mark? How do deleterious effects dwarf beneficial effects?

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.

 

[mark kennedy]