Design and the Brain

[Blayz]

Mark, the others are correct, you have no real understanding of biology at all.

Like I have told you repeatedly, most mutations are selectively neutral.

yeah, said it repeatedly, shown no evidence for it ever.

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

No, they don't. Indels can cause a frameshift, a substitution never can. It is clear the one that has no understanding of frameshift is you.

 

[mark kennedy]

Mark, the others are correct, you have no real understanding of biology at all.

There it sits, supported by pure affirmation and no better then the ignorance that proceeded it.

yeah, said it repeatedly, shown no evidence for it ever.

Evidence is irrelevant to an a priori assumption.

No, they don't. Indels can cause a frameshift, a substitution never can. It is clear the one that has no understanding of frameshift is you.

I know well enough and a point mutation can. That is completely beside the point. You, like most biologists have in clue what the genetic basis for human evolution from that of the apes would be. That despite the fact that you insist that it be assumed unconditionally.

You'll have to do better then that, I have been worked over by experts.

By the way, I never had the chance to thank you for the adjustments to the mutation rate charts. So thanks, I appreciate it.

 

[Pete Harcoff]

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.

2) What the heck you mean by "Beneficial effects from mutations are very rare and tend to be temporary"? Exactly how, if a beneficial mutation by definition undergos a selective sweep and becomes fixed in a population is that "temporary"?

 

[mark kennedy]

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.

2) What the heck you mean by "Beneficial effects from mutations are very rare and tend to be temporary"? Exactly how, if a beneficial mutation by definition undergos a selective sweep and becomes fixed in a population is that "temporary"?

Just type 'mutations affecting the human brain' into the Pub Med search engine and you tell me.

Let me guess, you have already done that and don't want to talk about it.

 

[Pete Harcoff]

I never said that.

Yes you did:

Substitutions do not produce frameshifts.

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

Maybe there was some misinterpretation along the way, but you pretty much claimed that substitutions cause frameshifts.

Just type 'mutations affecting the human brain' into the Pub Med search engine and you tell me.

Let me guess, you have already done that and don't want to talk about it.

Or, instead of playing stupid games, you could just answer my question. Assuming you have an answer in the first place and this isn't something you've made up.

 

[Blayz]

There it sits, supported by pure affirmation and no better then the ignorance that proceeded it.

T'aint ignorance mate, its 25 years of working in biology. You do not grokk genetics, it is cler from what you post. You have read some stuff, and strung some ideas together badly, but you simply do not understand the basics. I have taught these subjects at University level, I recognise a lack of undestanding when I see it.

Evidence is irrelevant to an a priori assumption.

So "most mutations are deleterious" is an a priori assumption? I don't think so.

I know well enough and a point mutation can.

It really cannot Mark. Really. Have another look at your literature. A frameshift involves shunting the reading frame left or right by 1 or 2. You cannot move the reading frame by simply changing a base, you have to insert some, or delete some.

That is completely beside the point. You, like most biologists have in clue what the genetic basis for human evolution from that of the apes would be. That despite the fact that you insist that it be assumed unconditionally.

Mark, we are more than happy to say "we don't know yet", what we are not willing to say is goddidit. We do not assume anything unconditionally.

By the way, I never had the chance to thank you for the adjustments to the mutation rate charts. So thanks, I appreciate it.

You are welcome Mark, Even though it was a meaningless exercise because you have no understanding of what you were asking for.

 

[mark kennedy]

It really cannot Mark. Really. Have another look at your literature. A frameshift involves shunting the reading frame left or right by 1 or 2. You cannot move the reading frame by simply changing a base, you have to insert some, or delete some.

The effect is deleterious and you know it, that is of course if you are being honest.

Mark, we are more than happy to say "we don't know yet", what we are not willing to say is goddidit. We do not assume anything unconditionally.

You assume that God didn't do it, that's no problem. That's unconditional...right or wrong?

You are welcome Mark, Even though it was a meaningless exercise because you have no understanding of what you were asking for.

An honest admission is never meaningless. Thanks man, you did more then you realize.

 

[Chalnoth]

The effect is deleterious and you know it, that is of course if you are being honest.

While this does not appear to be a response to the post you quoted, it's also false. Yes, often mutations to active areas are deleterious. But then if one such mutation happens there, it's quickly selected out (often immediately), and won't propagate. Those few that are beneficial are amplified by natural selection and become fixed in the population.

Clearly other genes in the human ancestral lineage changed which allowed some substitution mutations in HAR1 to be beneficial.

As for your whole frame shift argument, that's so off topic it's not even funny.

 

[plindboe]

There are actually 22:

He said essential amino acids, of which there are 9.

mark, you seem like an intelligent guy who have learned alot of facts. That said, you often say stuff that is simply blatantly wrong, and refuse to acknowledge it when people correct you. I advice some humility.

To understand why substitutions doesn't cause frameshifts perhaps you need to read some actual university books. I get the feeling that your research have primarily been online, and you've gotten bits and pieces of information without really understanding how it all fits together.

Peter

 

[FishFace]

Who said I was trying to falsify evolution? You jump to yet another conclusion without a clue.

Then what is your point?

No, you are grasping at straws.

If it were straw-grasping you'd be able to tell us all why positive feedback is implausible.

Like I have told you repeatedly, most mutations are selectively neutral. That vast majority of the one strong enough to trigger selection are deleterious. Only in very remote circumstances do mutations have a selective advantage and the rarest of mutations are the one that are fixed.

Yes, you've told us that repeatedly, but you've not provided evidence ever.

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

Before:

123123123123123123
ACGTACTTACAAGCGTAC

After:

123123123123123123
ACGTACT[B]G[/B]ACAAGCGTAC

The reading frame remains the same. Because it's a substitution. Deletions and insertions cause frameshifts, mark. But then, you of course know this, since you're lecturing me about my knowledge of biology!

<staff edit>

What you should be looking for is a molecular mechanism, not a rhetorical device.

So - you don't have a molecular mechanism? Then you "don't know." There, was that so hard? No. Now let those of us interested in changing that to "I do know" get on with it.

A triplet codon determines the amino acid.

But, as I said, a triplet codon is not identical with the amino acid it codes for.

Keep it up, your making this easy.

Says mark, who doesn't know what causes a frameshift.

It also depends on an amino acid sequence that will produce a useful protein.

Of course, that was implicit in my answer - amino acid sequence determines the location of functional groups.

That is not what would have had to happen, you would need highly conserved genes involved in neural functions to undergo a major overhaul.

You say that without evidence. As it happens, there were changes in genetics, but it turns out that they were allowed by a change in diet.

Your chasing the wind here but be my guest.

Did you do the search? Because someone's already done the research, and it's there for you to find. A change in diet accounts for the change in mutation rate, because it allowed those mutations to be beneficial.

Your assuming that they occurred, had a beneficial affect on the brain and then were fixed.

Of course they occurred - we can see them right there in the genome. What mechanism do you propose got them there?

Type 'mutations affecting the human brain' in Pub Med and educate yourself.

Why would I want to search for something that is clearly going to turn up results related to genetic diseases affecting the brain?

Then you should know that diet does not change the genetic code affecting the human brain.

I'm sick and tired of telling you, so here it is for the last time: I never suggested that. <staff edit>

I notice you didn't bother to quote cite or link anything remotely related. By the way, of course I read it. <staff edit>

That should do it, you made no real points and beat this diet thing to death. Get some new material. Hey! I have an idea, why don't you try reading the scientific literature before you start pontificating about it.

You want me to read some literature? How about these chaps?

 

[FishFace]

There are actually 22:

OH NO! Mark just flaunted his lack of knowledge for ALL TO SEE! An essential amino acid is one that we cannot synthesize - not just one that we use!

OOPS!

Do you notice what it says at the top of that diagram, mark? It says "insertion" and "deletion." NOT substitution. That's because substitution doesn't cause a change in the reading frame!

OOPS!

Beneficial effects from mutations are very rare and tend to be temporary.

You provide zero evidence. Computer simulations contradict your assertion.

Make me!

No evidence? Then you retract implicitly.

Basic biology is often too much to ask from evolutionists, they rely too much on their rhetoric.

That BOOM was the sound of every irony meter in the world exploding simultaneously. Basic biology indeed! You're more than twice my age, and seem to know less than half the biology! What have we learnt today?

1. Substitutions don't cause frameshifts
2. There are 9 essential amino acids
3. Triplet codons are not the same as the amino acid they code for
4. Change in diet allowed for mutations which gave us a bigger brain
5. Unevidenced assertions are no match for actual knowledge and research.

 

[mark kennedy]

OH NO! Mark just flaunted his lack of knowledge for ALL TO SEE! An essential amino acid is one that we cannot synthesize - not just one that we use!

OOPS!

Pedantic sarcasm, I always know I have you guys when you resort to this.

Do you notice what it says at the top of that diagram, mark? It says "insertion" and "deletion." NOT substitution. That's because substitution doesn't cause a change in the reading frame!

OOPS!

Irrelevant

You provide zero evidence. Computer simulations contradict your assertion.

Computer simulations are not molecular mechanisms

No evidence? Then you retract implicitly.

You buried the evidence beneath an avalanche of nonsense.

That BOOM was the sound of every irony meter in the world exploding simultaneously. Basic biology indeed! You're more than twice my age, and seem to know less than half the biology! What have we learnt today?

First you propose that diet will change the amino acid sequence of the genes involved in neural functions. Then you refuse to address the real issue of how the genes were altered. Then you resort to the pedantic satire, let's look at this off the wall list.

1. Substitutions don't cause frameshifts
2. There are 9 essential amino acids
3. Triplet codons are not the same as the amino acid they code for
4. Change in diet allowed for mutations which gave us a bigger brain
5. Unevidenced assertions are no match for actual knowledge and research.

1. Irrelevant
2. There are 22 amino acids of life
3. Amino acids are combinations of three nucleotides, chart provided and ignored.
4. Still no genetic basis for the alterations of highly conserved genes involved in neural functions.
5. No evidence of any kind for superficial pretense of knowledge.

All you have to do on here to be considered scientific is to contradict a creationist.

I'm through with your pointless rationalizations and obvious disdain for the genuine article of science.

Have a nice day
Mark

 

[mark kennedy]

If you guys have the courage of your convictions you will answer this challenge. It is rare in the extreme that an evolutionist will so I expect nothing from you.

How does this change when the divergence goes from 1.33% to 6%?

"Rates and patterns of molecular evolution:
We observed a total of 199 differences between the human and chimpanzee sequences: 131 transitions (66%), 52 transversions (26%), and 16 insertion-deletion variants (8%). Insertion-deletion variants were less than one-tenth as common as nucleotide substitutions and consisted of changes of 1 bp (8 mutations), 2 bp (5 mutations), 3 bp (1 mutation), and 4 bp (2 mutations). Thus, 15/16 of these insertion-deletion variants would have resulted in frameshift mutations in coding regions. Approximately one-fifth of all single nucleotide mutations were transitions at CpG dinucleotides...

Table 3. Estimates of mutation rate assuming different divergence times and different ancestral population sizes

4.5 mya, pop.= 10,000 mutation rate is 2.7 x 10^-8
4.5 mya, pop.= 100,000 mutation rate is 1.6 x 10^-8
5.0 mya, pop.= 10,000 mutation rate is 2.5 x 10^-8
5.0 mya, pop.= 10,0000 mutation rate is 1.5 x 10^-8
5.5 mya, pop.= 10,000 mutation rate is 2.3 x 10^-8
5.5 mya, pop.= 10,000 mutation rate is 1.4 x 10^-8
6.0 mya, pop.= 10,000 mutation rate is 2.1 x 10^-8
6.0 mya, pop.= 100,000 mutation rate is 1.3 x 10^-8

Table 4. Estimates of mutation rate for different sites and different classes of mutation

Transition at CpG mutation rate 1.6 x 10^-7
Transversion at CpG mutation rate 4.4 x 10^-8
Transition at non-CpG mutation rate 4.4 x 10^-8
Transversion at non-CpG mutation rate 5.5 x 10^-9
All nucleotide subs mutation rate 2.3 x 10^-8
Length mutations mutation rate 2.3 x 10^-9
All mutations mutation rate 2.5 x 10^-8

Rates calculated on the basis of a divergence time of 5 mya, ancestral population size of 10,000, generation length of 20 yr, and rates of molecular evolution given in Table 1.


Calculations are based on a generation length of 20 years and average autosomal sequence divergence of 1.33%
-----------------------------------------------------

Estimate of the Mutation Rate per Nucleotide in Humans (Michael W. Nachmana and Susan L. Crowella
Genetics, 297-304, September 2000) "​

Since this was published the known divergence has grown by 5X:

 

[FishFace]

1. Irrelevant
2. There are 22 amino acids of life
3. Amino acids are combinations of three nucleotides, chart provided and ignored.
4. Still no genetic basis for the alterations of highly conserved genes involved in neural functions.
5. No evidence of any kind for superficial pretense of knowledge.

1. You claimed that substitutions caused frameshifts. You were wrong.
2. You claimed there were 22 essential amino acids. You were wrong.
3. No, amino acids are a type of molecule possessing an amine group and a carboxylic acid group. A codon is a combination of three nucleotides. These are two different things which you need to separate in your mind.
4. The reason they could change is because our diet changed (as evidenced by the two papers I linked to.) allowing us more energy to use for the brain. Before this, mutations which increased brain-size would be deleterious.
5. I've provided evidence - the two papers I linked to. You have provided nothing but arguments from incredulity and ignorance.

What can I say? You accused me of ignorance when you don't know what an amino acid is, what can cause a frameshift, or what an essential amino acid is.

I'm through with your pointless rationalizations and obvious disdain for the genuine article of science.

Your refusal to accept your mistakes is noted. People would be a lot more willing to play ball if you just admitted you were wrong.

Read those articles.

 

[FishFace]

How does this change when the divergence goes from 1.33% to 6%?

How does what change?

 

[mark kennedy]

How does what change?

The charts FishFace, the charts!

 

[Pete Harcoff]

If you guys have the courage of your convictions you will answer this challenge. It is rare in the extreme that an evolutionist will so I expect nothing from you.

How does this change when the divergence goes from 1.33% to 6%?

I'll bite (I still haven't re-read all of the paper, but just so you don't keep complaining about people ignoring this).

If you change the level of divergence from 1.33% to 6% and keep other variables constant, the mutation rate increases by the same factor as the increase in divergence. Happy now?

That said, I want to include a handful of caveats. First of all, the output is still highly contingent on all the variables involved (generation time, divergence time, and population size). Changing any of those variables will have an impact on the resultant mutation rate. For example, I was able to use a divergence time of 7Ma, generation time of 18 years (down from 20), and ancestral population size of 400k, as well as a 6% rate of divergence and get roughly the same rate as they concluded. So it really hinges on all your input variables.

The other point I want to raise is again the subject of indels versus substitutions. Their rate of divergence is based almost strictly on substitutions. As a result, the final rate is biased towards those types of mutations.

To illustrate, if you have 10 substitutions versus a single 10 bp indel, the rate of mutation on a per nucleotide basis is the same. However, the actual effect on the genome is different. An indel is bound by the fact that whichever bases it deletes or inserts are clustered together. Whereas point mutations are not bound by each other. Therefore, while you can conclude a per nucleotide rate based on the level of change, the resultant effect of change and actual number of mutation events is different.

Can a more learned geneticist expand on this? I could be off base here, so I would appreciate corrections.

Oh and mark, can you answer your claim that beneficial effects of mutations are "temporary"? Since I humored you, can you humor me?

 

[mark kennedy]

1. You claimed that substitutions caused frameshifts. You were wrong.

1. 
   
   
   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
   
   

   You claimed there were 22 essential amino acids. You were wrong.

   
   There are 22 amino acids of life
   
   

   No, amino acids are a type of molecule possessing an amine group and a carboxylic acid group. A codon is a combination of three nucleotides. These are two different things which you need to separate in your mind.

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

   ]The reason they could change is because our diet changed (as evidenced by the two papers I linked to.) allowing us more energy to use for the brain. Before this, mutations which increased brain-size would be deleterious.

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

   ]I've provided evidence - the two papers I linked to. You have provided nothing but arguments from incredulity and ignorance.What can I say? You accused me of ignorance when you don't know what an amino acid is, what can cause a frameshift, or what an essential amino acid is.

   
   You still struggle with basic concepts and fundamental truth. There are 22 amino acids of life and a frameshift mutation would be the only known result of 18 substitutions in the HAR1f regulatory gene. You think you can bury it but you are conceding the point by ignoring it.
   
   

   Your refusal to accept your mistakes is noted. People would be a lot more willing to play ball if you just admitted you were wrong.

   
   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.
   
   

   Read those articles.

   
   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.
   
   It's been fun poking holes in you ridiculas rationalizations but your starting to bore me.
   
   Have a nice day
   Mark

 

[Pete Harcoff]

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.

Whaaaa? Mark, you claimed that substitutions cause frameshifts, then you turned around and claimed you didn't claim that. You don't seem to willing to admit mistakes at all, even relatively trivial ones.

 

[MrBoo]

@Fishface and Pete Harcoff

Beneficial effects from mutations are very rare and tend to be temporary.

They do in fact tend to be very rare, and they do in fact tend to be temporary. Obviously you never comprehended my earlier statements about nucleotide shielding. There is plenty of evidence of both phenomenon, and your misunderstanding of what happens to mutation is the direct result of a misrepresentation by early population geneticists who were zealot evolutionists like yourselves. It is no wonder that misinformation was propagated, and it is no wonder that you would have accepted it. I feel bad for you.

heredity, 84:497-501

Estimation of spontaneous genome-wide mutation rate​

parameters: whither beneficial mutations?, Bataillon, 2000