Design and the Brain

[Pete Harcoff]

They do in fact tend to be very rare, and they do in fact tend to be temporary.

<snip>

I know they are rare. I have never denied that they are rare. In fact, they are so rare that I only know of a single paper that estimates the rate of beneficial mutations based on 66 such mutations in a 1,000 generation experiment with E. coli. That said, I don't believe they are rare enough to necessarily be a problem for evolution.

I still have no idea where this "temporary" idea keeps coming from. I scanned the paper you linked and didn't see it there. Mark has yet to provide any citations to back this up either.

All I want is to see where this claim is coming from. Is that so difficult?

Obviously you never comprehended my earlier statements about nucleotide shielding.

I didn't even see them. And a Google search for "nucleotide shielding" returns 4 results. A Google scholar search for the same term returns 0 results. That leads me to wonder if this is something else that is made up.

 

[plindboe]

There are 22 amino acids of life

http://en.wikipedia.org/wiki/Essential_amino_acid

"An essential amino acid or indispensable amino acid is an amino acid that cannot be synthesized de novo by the organism (usually referring to humans), and therefore must be supplied in the diet." - "Nine amino acids are generally regarded as essential for humans: isoleucine, leucine, lysine, threonine, tryptophan, methionine, histidine, valine and phenylalanine."

Peter

 

[MrBoo]

I know they are rare. I have never denied that they are rare. In fact, they are so rare that I only know of a single paper that estimates the rate of beneficial mutations based on 66 such mutations in a 1,000 generation experiment with E. coli. That said, I don't believe they are rare enough to necessarily be a problem for evolution
I still have no idea where this "temporary" idea keeps coming from. I scanned the paper you linked and didn't see it there. Mark has yet to provide any citations to back this up eitherAll I want is to see where this claim is coming from. Is that so difficult?

I didn't even see them. And a Google search for "nucleotide shielding" returns 4 results. A Google scholar search for the same term returns 0 results. That leads me to wonder if this is something else that is made up.

Pete, you were actually in the thread where I mentioned this sheilding paradox, and fishface actually responded to it, so I assumed that you had at least read the posts which led up to your own posts, but thats what I get for making an assumption about what you may or may not have read.

Secondly just because I invented a term for a very real phenomenon does not mean I made it up or invented it.
Necessity is the mother of invention, and since early population geneticists lied about what a gene pool is, it necessitates new definitions. Since I am familiar with concepts of quantum theory such as 'electron sheilding', and this phenomenon most resembles it, I simply chose the best word for the situation.

Third I did not invent this idea, as much as I simply have coined the term shielding for my own understanding of it. Most of the research in this area that I follow has been from Dr. John Sanford ideas about genomic degeneration.

Now I'll try to explain what I mean by nucleotide shielding again, and instead of trying to find evidence of this very basic idea, I would rather challenge you to find evidence against it.

What Im referring to when I talk about nucleotide shielding is first of all shielding from what? Shielding from natural selection. When a beneficial mutation arises in the gene pool of a population it arises in an individual, but unless that beneficial mutation is effecting the fitness or a fitness component of that individual, then it will die with that individual, it will not exist in that population's gene pool any longer, it will be shielded, and it will thus be temporary. I cannot speak for Mark Kennedy, but this is what I mean when I say that most beneficial mutations are temporary. They are wiped out before they have a chance to be expressed.

I hope I answered your question, there is a lot more to this, and what implications it has for mutations and evolution, but I dont want to derail this thread too far, though in my opinion most of the comments from evolutionists in this thread have been completely aimed at dislodging and derailing the OP of this thread.

So apologies to the OP for taking this side trail.

 

[MrBoo]

http://en.wikipedia.org/wiki/Essential_amino_acid

"An essential amino acid or indispensable amino acid is an amino acid that cannot be synthesized de novo by the organism (usually referring to humans), and therefore must be supplied in the diet." - "Nine amino acids are generally regarded as essential for humans: isoleucine, leucine, lysine, threonine, tryptophan, methionine, histidine, valine and phenylalanine."

Peter

This is an example of the sorts of unsophisticated arguments that litter this forum. I am sure he knows that there are nine (I accept this number only for argumentation's sake) essential amino acids which we cannot self-manufacture, the amino acids he was talking about were essential to creating the proteins we need. If you dont think that the proteins created by the 22 amino acids are essential and indispensible to life I suggest you attempt to live without the other 13. Not only was this argument trifling, but it was also irrelevant and it only proves that there seems to be no direct response to his points.

Regardless, the number nine is only correct for humans, and that number for humans is not necessarily correct, I would say that there are only eight unambiguous essential amino acids.

Also, Have you bothered to show how many essential amino acids chimps have, bonobos? Therefore the entire point is not only irrelevant, but wrong.

Now, will FishFace admit he is wrong? I highly doubt it. SO he would be hypocritical for expecting it out of MK, and he would be slanderous for accusing MK for not admitting it, and DEAD wrong.

 

[UncleHermit]

When a beneficial mutation arises in the gene pool of a population it arises in an individual, but unless that beneficial mutation is effecting the fitness or a fitness component of that individual, then it will die with that individual, it will not exist in that population's gene pool any longer, it will be shielded, and it will thus be temporary. I cannot speak for Mark Kennedy, but this is what I mean when I say that most beneficial mutations are temporary. They are wiped out before they have a chance to be expressed.

I don't understand. If the mutation doesn't affect the fitness of the individual, how can it be considered a beneficial or even a detrimental mutation?

 

[Pete Harcoff]

Pete, you were actually in the thread where I mentioned this sheilding paradox, and fishface actually responded to it, so I assumed that you had at least read the posts which led up to your own posts, but thats what I get for making an assumption about what you may or may not have read.

I might have skimmed past them, but I didn't read those posts.

What Im referring to when I talk about nucleotide shielding is first of all shielding from what? Shielding from natural selection. When a beneficial mutation arises in the gene pool of a population it arises in an individual, but unless that beneficial mutation is effecting the fitness or a fitness component of that individual, then it will die with that individual, it will not exist in that population's gene pool any longer, it will be shielded, and it will thus be temporary. I cannot speak for Mark Kennedy, but this is what I mean when I say that most beneficial mutations are temporary. They are wiped out before they have a chance to be expressed.

But they aren't always wiped out. I don't disagree that it's possible for a beneficial mutation to not survive until fixation in a gene pool. It could be eliminated for any number of reasons (genetic drift, subsequention deleterious mutations, change in selection pressure whereby the mutation is no longer beneficial, etc).

However, generally the definition of a beneficial mutation involves a mutation that is favored by selection due to a positive effect on the fitness of the carrier relative to the population, thus they are favored to sweep through the population and become fixed in the gene pool.

For instance, this paper deals with the E.coli experiment I mentioned and the identification of beneficial mutations in evolving populations.

I also think that people tend to fixate too much on "beneficial" mutations. After everything I've read in the literature, most evolutionary change seems to be relatively neutral. So the necessity of beneficial mutations is overstated.

 

[FishFace]

Frameshift
Since protein-coding DNA is divided into codons three bases long, insertions and deletions can alter a gene so that its message is no longer correctly parsed. These changes are called frameshifts.
For example, consider the sentence, “The fat cat sat.” Each word represents a codon. If we delete the first letter and parse the sentence in the same way, it doesn’t make sense.
In frameshifts, a similar error occurs at the DNA level, causing the codons to be parsed incorrectly. This usually generates proteins that are as useless as “hef atc ats at” is uninformative.

There are other types of mutations as well, but this short list should give you an idea of the possibilities.​

Types of Mutations

http://evolution.berkeley.edu/evosite/evo101/IIIC3aTypes.shtml

That type of mutation - the substitution - is not included in the list that cause frameshifts.

You were wrong - why do you refuse to admit it?

There are 22 amino acids of life

Yes, mark, we know. But you were asked to name the 9 essential amino acids and said there were 22. Remember? You were wrong - why do you refuse to admit it?

You keep going deeper and deeper into irrelevant nonsense, I have no idea why.

Because, mark, you tried to claim you had superior knowledge of genetics than I. If you want to argue from your own authority you have to establish your authority. These three elementary errors - and your inability to even admit that you made them - show just what kind of a person we're dealing with here.
If you were presenting actual arguments and evidence, this wouldn't matter. Since you just want us to take your word for it, and since you cast erroneous aspersions about my lack of knowledge, it became relevant.

Admit it - you made these three basic mistakes, and shouldn't have been making comments about people's knowledge. Then we can move on.

Like I said, you have the cart before the horse which is the whole problem with the a priori assumptions of universal common ancestry.

The papers I linked to contain a priori assumptions? Where? Or did you not read the papers, and are you still ignoring the evidence?

You still struggle with basic concepts and fundamental truth. There are 22 amino acids of life

And only 9 of those are termed essential amino acids. Did you not know that? Was it a gap in your knowledge?

and a frameshift mutation would be the only known result of 18 substitutions in the HAR1f regulatory gene.

Were they substitutions? Or insertions? If they were substitutions, there is no way they could cause a frameshift. If they were insertions, then it is quite possible they caused frameshifts along the way, but not certain. The insertion could have been a single, wholesale insertion event, and 18 is divisible by three.
Also, I remember that diagram of yours showing how the mRNA of the gene folds up. Interesting, that, so I decided to check the relevant article you lifted the picture from. (I love University Information Services) Here's an interesting quotation:

"Here we report that the most dramatic of these 'human accelerated regions', HAR1, is part of a novel RNA gene (HAR1F)"

Now, mark, with that vast knowledge you're always telling us about, should know what this means for frameshifts: they're UTTERLY IRRELEVANT. RNA genes don't produce proteins, they produce non-coding RNA. So there is no reading frame.

This shoots to the dust any argument you thought you had about hAR1f, mark. Your lack of knowledge of the subject at hand, coupled with your bias, has produced this embarrassment of an argument. Time to admit you were wrong (about 4 things, now) and forget about it.

I'm not admitting that you made a single point. You are off topic in the extreme and if I make a mistake I will certainly own up to it, unlike you.

Can you even name the nine essential amino acids?

There are actually 22

That's a mistake.

Substitutions do not produce frameshifts.

Yes they do

So's that.

Amino acids are combinations of three nucleotides

As is that.

That's three mistakes. Now you're just lying to us - you can't face up to your errors.

I read scientific literature on a regular basis and I know when I'm talking to someone else who does. You are not one of those people and the only reason you are not being called on it is because you are proevolution.

If you read and understood the literature you use you'd realise it usually contains nearly all the material necessary to knock down your arguments. Read that nature article - if you understand what a reading frame is (as you accused me of not knowing) you will know that your frameshift argument is completely wrong.

It's been fun poking holes in you ridiculas rationalizations but your starting to bore me.

It's been fun using your own sources to destroy your "arguments."

 

[Split Rock]

This is why I don't bother arguing with Mark anymore:

Substitutions do not produce frameshifts.

Yes they do but I don't expect you to know what a reading frame is anyhow.

This reads like gibberish. Are you saying that "positive feedback, fixation, and nucleotide substitutions" cause a frameshift mutation in every case?

Not every one, just the vast majority.

mark,

Could you please explain:

1) How a substitution causes a frameshift? I've taken genetics at the university level and must've missed that particular lecture.

I never said that. What I was talking about was the 18 substitutions required for the HARf regulatory gene. What happened is my original position was twisted, not the first time and it won't be the last.

Weeeeeeeeeeeeeeeeeeeeeeeeee!!!

 

[plindboe]

This is an example of the sorts of unsophisticated arguments that litter this forum. I am sure he knows that these are the essential amino acids, the amino acids he was talking about were essential to creating the proteins we need. If you dont think that the proteins created by the 22 amino acids are essential and indispensible to life I suggest you attempt to live without the other 13. Not only was this argument trifling, but it was also irrelevant and it only proves that there seems to be no direct response to his points.

I do not have to ingest the 13 others to survive just fine, hence they are not essential amino acids. The term has a very specific meaning in biology, and you and mark apparently didn't know it. I advice that you learn from the mistake instead of resisting correction, due to your personal pride.

Peter

 

[FishFace]

Pete, you were actually in the thread where I mentioned this sheilding paradox, and fishface actually responded to it, so I assumed that you had at least read the posts which led up to your own posts, but thats what I get for making an assumption about what you may or may not have read.

As far as I can remember, my response was much the same as Pete's.

Now I'll try to explain what I mean by nucleotide shielding again, and instead of trying to find evidence of this very basic idea, I would rather challenge you to find evidence against it.

I challenge you to find evidence against the invisible pink unicorn!

What Im referring to when I talk about nucleotide shielding is first of all shielding from what? Shielding from natural selection. When a beneficial mutation arises in the gene pool of a population it arises in an individual

OK.

but unless that beneficial mutation is effecting the fitness or a fitness component of that individual, then it will die with that individual,

If it is beneficial, then it affects the fitness of the individual, by definition.

it will not exist in that population's gene pool any longer, it will be shielded, and it will thus be temporary. I cannot speak for Mark Kennedy, but this is what I mean when I say that most beneficial mutations are temporary. They are wiped out before they have a chance to be expressed.

If they are not expressed, then they are not beneficial; they are neutral.

 

[Pete Harcoff]

Most of the research in this area that I follow has been from Dr. John Sanford ideas about genomic degeneration.

Looking up this guy, it says this in Wikipedia:

Formerly an atheist, in the mid-1980s Sanford and his present wife Helen went through a marital crisis, which led him to become a born again Christian and a young earth creationist. More recently, he has written a book entitled Genetic Entropy & the Mystery of the Genome (2005)[3] in which he claims that the genome is deteriorating and therefore could not have evolved. Sanford's claims have received little attention from the scientific community, and have not been published in peer-reviewed scientific journals.

The fact that his work has not been published via peer-review, leaves me more than a little skeptical. While I'm trying not to automatically discount his work, I tend to be suspicious of born-again creationists circumventing scientific scrutiny in favor of publishing books for the lay public.

 

[MrBoo]

If they are not expressed, then they are not beneficial; they are neutral.

Obviously evo and company are misunderstanding again. Who has time to explain it?
So many errors, so little time.

 

[UncleHermit]

Obviously evo and company are misunderstanding again. Who has time to explain it?
So many errors, so little time.

I would like to know.

 

[Split Rock]

Secondly just because I invented a term for a very real phenomenon does not mean I made it up or invented it.

You certainly made up the term, anyway.

Necessity is the mother of invention, and since early population geneticists lied about what a gene pool is, it necessitates new definitions.

Show us that early geneticists lied about what a gene pool is, or retract this statement. Do creationists know what a "lie" is? I believe the KJV bible calls it "bearing false witness." Does that help?

Now I'll try to explain what I mean by nucleotide shielding again, and instead of trying to find evidence of this very basic idea, I would rather challenge you to find evidence against it.

No, if you are proposing this idea, you have to provide evidence for it.

What Im referring to when I talk about nucleotide shielding is first of all shielding from what? Shielding from natural selection. When a beneficial mutation arises in the gene pool of a population it arises in an individual, but unless that beneficial mutation is effecting the fitness or a fitness component of that individual, then it will die with that individual, it will not exist in that population's gene pool any longer, it will be shielded, and it will thus be temporary. I cannot speak for Mark Kennedy, but this is what I mean when I say that most beneficial mutations are temporary. They are wiped out before they have a chance to be expressed.

First of all, the definition of a beneficial mutation is one that increases the fitness of an individual, thus it makes no sense to talk about a beneficial mutation which doesn't improve fitness. Secondly, it is possible for an individual that possesses such a gene to die off anyway. However, we are talking about probabilities here. Possessing a beneficial mutation will increase the probability that an individual will bear offspring. Thus, the frequency of this gene in a population will tend to increase. You also seem to be assuming that a particular beneficial mutation will only occur once in a population, or that there is only one specific mutation that will be beneficial given a particular selective pressure. Neither is necessarily the case.

 

[Split Rock]

I challenge you to find evidence against the invisible pink unicorn!

HA! I have been touched by Her Horn and thus I know She exists!! so there!

 

[MrBoo]

First of all, the definition of a beneficial mutation is one that increases the fitness of an individual, thus it makes no sense to talk about a beneficial mutation which doesn't improve fitness.

So that is your definition of a beneficial mutation? One that increases the fitness of an individual? Surely you don't think that such mutations are responsible for the evolution of new species? You actually think that a series of point mutations and frame shift mutations are what caused all the diversity of life on earth?

 

[UncleHermit]

So that is your definition of a beneficial mutation? One that increases the fitness of an individual?

That's my definition of a beneficial mutation, although I am a mere layman. What's your definition of a beneficial mutation?

 

[Pete Harcoff]

So that is your definition of a beneficial mutation? One that increases the fitness of an individual? Surely you don't think that such mutations are responsible for the evolution of new species? You actually think that a series of point mutations and frame shift mutations are what caused all the diversity of life on earth?

This series of questions reads like a bunch of non-sequiturs. Why don't you just give us your definition of a beneficial mutation, since you appear to be working with a definition that is different from everyone else's.

 

[MrBoo]

This series of questions reads like a bunch of non-sequiturs. Why don't you just give us your definition of a beneficial mutation, since you appear to be working with a definition that is different from everyone else's.

You seem to be fearful of the implications of my question. But my definition doesn't veer from everyone else's. Where do you think you got your definition? How do you know it is not your definitions which are different? I have no desire to play around with word definitions, clearly your trying to avoid my questions by appealing to semantics.

Clearly the beneficial mutations you need to promote your molecules-to-man nonsense are much more creative than simple point mutations and frame-shifts, why would you think these simple mutations were the only ones beneficial?

And what could possibly make you think that these were all that were necessary? layman or not, its a gross oversimplification.

 

[Pete Harcoff]

I have no desire to play around with word definitions, clearly your trying to avoid my questions by appealing to semantics.

You said:

"When a beneficial mutation arises in the gene pool of a population it arises in an individual, but unless that beneficial mutation is effecting the fitness or a fitness component of that individual, then it will die with that individual"

People have called you on this on the grounds that a beneficial mutation is one which by definition affects the fitness of an individual. Therefore, claiming that beneficial mutations will "die with that individual" if they don't have an affect on an individual's fitness makes absolutely no sense.

Clearly the beneficial mutations you need to promote your molecules-to-man nonsense are much more creative than simple point mutations and frame-shifts, why would you think these simple mutations were the only ones beneficial?

You seem to be confusing types of mutations with effects of mutations.

Mutations fall into various types. You have single base sustitutions, inserts/deletions (which may or may not result in a frame shift), translocations, etc.

On the other hand, you can also have different effects depending on what part of the genome the mutation occurs in and the effect it results in. As a result, mutations can be beneficial, deleterious, or neutral. And the effects of deleterious or beneficial mutations can be relatively large or small, with the majority having a lesser effect.

Adding to that, you also have all sorts of other evolutionary forces at work (sexual recombination, lateral gene transfers, genetic drift, selection, etc). So no, mere mutations by themselves are not enough to account for the diversity of life on Earth. But there is more at work than that. The "creativity" of evolution is the result of these various mechanisms acting on populations.