Design and the Brain

[Naraoia]

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

So what? Then perhaps mutation rates are bigger, or divergence time longer than we thought. Don't see a point here.

 

[FishFace]

You have that backwards, I have focused almost exclusively on the evidence while you have talked in short pedantic quips.

You provide no evidence for why the gene in question could not have changed randomly.

A statement supported exclusively upon the credibility of the poster which remains to be established.

Sure. But you didn't understand, regardless of his credibility. I trust you do now, and are not still under the misconception that he was saying that ingesting protein could effect genetic changes?

You don't even define the problem and I have ample source material.

That is an obvious distortion, I said that mutations are no explanation at all. Eating protein has absolutely nothing to do with it. At best eating meat could be an effect of an adaptive trait being expressed but can in no way be considered a cause of adaptive evolution. The amino acid sequence of the protein coding genes determines the protein product, not the other way around.

No, it's not an obvious distortion - you still seem to think that I/we think that eating protein affects your genes. That isn't true. Eating just (apparently) can cause an increase in brain-size without any genetic change.

The absurdity of your statements are not only evident, they are obvious.

No - the absurdity of your strawman is obvious.

 

[Pete Harcoff]

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

It's been quite awhile since I've looked at this stuff, so I'd have to re-read up on it (which I don't have time for now) to give you an answer.

The only thing I can venture from memory is that the rate the increase in divergence has largely been the result of identification of large indels which account for 1/10 the rate of single substitutions in terms of actual mutation events.

Therefore, I would assume the rate (in terms of events) of mutations wouldn't need increase all that much.

 

[MoonLancer]

When I look at the human brain, I see workmanship and intelligent design. How did Evolution design male and female brains? How could Evolution differeniate between lots of testosterone in one brain and estrogen in another?

I do not see how Evolution could design a human brain. Especially when you examine the difference between male and female brain chemicals.

This one is for you

http://www.youtube.com/watch?v=5SHc67Hep48


and this one is for the rest of us

http://www.youtube.com/watch?v=VuJ3Tjj40P8

 

[mark kennedy]

It's been quite awhile since I've looked at this stuff, so I'd have to re-read up on it (which I don't have time for now) to give you an answer.

The question is actually pretty straight forward, when the divergence changed did the mutation rate?

The only thing I can venture from memory is that the rate the increase in divergence has largely been the result of identification of large indels which account for 1/10 the rate of single substitutions in terms of actual mutation events.

That's fine but the divergence should line up with the mutation rate.

Therefore, I would assume the rate (in terms of events) of mutations wouldn't need increase all that much.

Divergence goes from 1.33% to 6% and you don't think the mutation events increased?

Think about that one Pete and I'll get back to you.

 

[mark kennedy]

You provide no evidence for why the gene in question could not have changed randomly.

The fact that it only allowed 2 substitutions in 400 million years doesn't mean anything to you?

Sure. But you didn't understand, regardless of his credibility. I trust you do now, and are not still under the misconception that he was saying that ingesting protein could effect genetic changes?

I don't know what he thinks for sure but I know for a fact that ingesting protein has nothing to do with this.

You don't even define the problem and I have ample source material.

That was a quote from me and it remains true.

No, it's not an obvious distortion - you still seem to think that I/we think that eating protein affects your genes. That isn't true. Eating just (apparently) can cause an increase in brain-size without any genetic change.

It cannot and does not have anything to do with brain size.

No - the absurdity of your strawman is obvious.

You keep talking in circles and have no interest in the detailed scientific research introduced into the discussion. The facts speak for themself and you have not bothered to address a single one.

 

[Naraoia]

The fact that it only allowed 2 substitutions in 400 million years doesn't mean anything to you?

It means no less and no more than that purifying selection was pretty hard on it for 400 million years. So what?

 

[mark kennedy]

It means no less and no more than that purifying selection was pretty hard on it for 400 million years. So what?

So something had to make the change? What?

 

[Pete Harcoff]

Divergence goes from 1.33% to 6% and you don't think the mutation events increased?

Depends on what you are actually measuring. From what I remember of the chimp genome paper, the number of indels accounted for significantly more divergence in terms of nucleotides, but on a mutation event basis, they were one tenth as common as point mutations.

Which raises a point, what are those rates quoted actually measuring? I know, it's a mutation rate, but what are the units of expression? Without knowing more details, I can't really comment further (I suppose I could look up the paper when I have time).

 

[mark kennedy]

Depends on what you are actually measuring. From what I remember of the chimp genome paper, the number of indels accounted for significantly more divergence in terms of nucleotides, but on a mutation event basis, they were one tenth as common as point mutations.

Nucleotides, that is what they are measuring. Here is the deal, when the nucleotide divergence increases from 1.33% to 6% how does the mutation rate change? It's as simple as that.

Which raises a point, what are those rates quoted actually measuring? I know, it's a mutation rate, but what are the units of expression? Without knowing more details, I can't really comment further (I suppose I could look up the paper when I have time).

One more time:

Many previous estimates of the mutation rate in humans have relied on screens of visible mutants. We investigated the rate and pattern of mutations at the nucleotide level by comparing pseudogenes in humans and chimpanzees to (i) provide an estimate of the average mutation rate per nucleotide, (ii) assess heterogeneity of mutation rate at different sites and for different types of mutations, (iii) test the hypothesis that the X chromosome has a lower mutation rate than autosomes, and (iv) estimate the deleterious mutation rate. Eighteen processed pseudogenes were sequenced, including 12 on autosomes and 6 on the X chromosome. The average mutation rate was estimated to be 2.5 x 10-8 mutations per nucleotide site or 175 mutations per diploid genome per generation.​

(Estimate of the Mutation Rate per Nucleotide in Humans, Genetics, Vol. 156, 297-304, September 2000)

I could post the charts again but you get the idea. Notice the title of the paper is 'per nucleotide' and I'll keep tracking the thread.

 

[tanzanos]

So basically if you give a species enough time, they are bound to become superior. If I leave my car in the snow for years, I do not think it will look like a better car in the spring.

Comparing a car to humans? Whatever you are taking has to be unique in the field of pharmacology!

You haven't the foggiest what evolution is all about!

What you are missing is the fact that change is a mandatory prerequisite for life to exist. Since the physical conditions on earth change, life has to adapt to these changes by changing itself into a form suitable for survival in those new conditions. No mutations = no life possible. Now if you bother to read the TOE you will realise that complexity is not necessarily beneficial to a life-form. Complexity is just a result of adaptation to ones environmental conditions.
A very good example is the moth in the industrial revolution.

You do a great disservice to your God by not using the brain he gave you.

USE IT!

 

[FishFace]

The fact that it only allowed 2 substitutions in 400 million years doesn't mean anything to you?

Of course it means something, but it doesn't necessitate that it then had only 2 substitutions in the next 400 million years. As you no doubt know, mutations are random, and selection pressure can change.
It also seems likely that there could have been some positive feedback going on - once one mutation becomes fixed, we move toward an ecological niche wherein more brain mutations are more advantageous.

I don't know what he thinks for sure but I know for a fact that ingesting protein has nothing to do with this.

If extra protein gives us a bigger brain without affecting our genes, it has everything to do with this.

That was a quote from me and it remains true.

All your sources seem to contradict you.

It cannot and does not have anything to do with brain size.

Why not? The size of our muscles and the rest of our body depends on more than just our genes.

You keep talking in circles and have no interest in the detailed scientific research introduced into the discussion. The facts speak for themself and you have not bothered to address a single one.

What facts have you raised? Mutation rates? You have not established that they must be fixed, so there's nothing to address.

 

[mark kennedy]

Of course it means something, but it doesn't necessitate that it then had only 2 substitutions in the next 400 million years. As you no doubt know, mutations are random, and selection pressure can change.

2 substitutions in in 400 million years and the 2 million years ago random chance produced 18. One thing is obvious, this could not happen by random but I don't expect you to see it since you don't look.

It also seems likely that there could have been some positive feedback going on - once one mutation becomes fixed, we move toward an ecological niche wherein more brain mutations are more advantageous.

You are assuming positive feedback, fixation and nucleotide substitutions that produce a functional amino acid sequence without causing a frameshift. This happens no where in nature and yet you assume it unconditionally simply because the alternative is unappealing to you.

If extra protein gives us a bigger brain without affecting our genes, it has everything to do with this.

Again you are making a fundamental mistake due to a lack of knowledge. Nucleotide sequences join together in triplet codons, these codons are the amino acid sequence. In the protein coding genes the way they fold together determines the three dimensional structure of the parts of the cell. Protein ingested through meat has nothing to do with the size and complexity of the brain. You haven't gotten anything right yet so the fact that you made another fundamental error does not surprise me in the slightest.

All your sources seem to contradict you.

As if you actually read them.

Why not? The size of our muscles and the rest of our body depends on more than just our genes.

Diet can be a factor in certain traits but what happens is genes are expressed differently, sometimes turned on and off by prions but not altered on an amino acid sequence level. When you are talking about random mutations you are talking about an error in the DNA replication process that most often does nothing at all. In those rare instances that they have a strong enough effect to be acted upon by selection it's deleterious the vast majority of the time. Beneficial effects from mutations are very rare and tend to be temporary. They certainly are not producing adaptive traits on an evolutionary scale in vital organs.

What facts have you raised? Mutation rates? You have not established that they must be fixed, so there's nothing to address.

I have spoken in passing about one regulatory gene that would require 18 substitutions in a gene 118 nucleotides long. They must have been fixed because they are fixed. The only reason there is nothing to address is because you did not bother to learn basic biology before you jump on the bandwagon.

 

[h2whoa]

Mark, you accuse people in quite an arrogant and conceited manner of having no knowledge but you demonstrate a tremendous lack as you talk. To give you credit, you obviously have at least read things, but I get the distinct impression you haven't understood what you have read.

Normally this wouldn't bother me, but a) you're being hypocritical and b) you throw around words and phrases that you have picked up from various places and fundamentally misuse them. As somebody who has dedicated their career path to genetics it troubles me to see somebody setting themselves up as an authority when they clearly have vast misunderstandings.

You throw around phrases like codons and prions, and harp on about your knowledge of dietary feedback mechanisms in transcriptional pathways and yet you don't understand them.

The most frustrating part of it is that you have convinced yourself that you have a firm grasp on what you're talking about. People who think they are experts when in fact they display glaring errors that would embarass a first year undergrad on their first day generally refuse to be told any different.

Stop thinking you actually know what you're talking about in this context. You don't. And it is frustrating to see legitimate scientific terminology used in order to further butcher science.

 

[TeddyKGB]

2 substitutions in in 400 million years and the 2 million years ago random chance produced 18. One thing is obvious, this could not happen by random but I don't expect you to see it since you don't look.

Haven't you been shown the calculations demonstrating that it could have happened?

You are assuming positive feedback, fixation and nucleotide substitutions that produce a functional amino acid sequence without causing a frameshift. This happens no where in nature and yet you assume it unconditionally simply because the alternative is unappealing to you.

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

Again you are making a fundamental mistake due to a lack of knowledge. Nucleotide sequences join together in triplet codons, these codons are the amino acid sequence. In the protein coding genes the way they fold together determines the three dimensional structure of the parts of the cell. Protein ingested through meat has nothing to do with the size and complexity of the brain. You haven't gotten anything right yet so the fact that you made another fundamental error does not surprise me in the slightest.

Where do you think the amino acids used to synthesize proteins come from? Can you even name the nine essential amino acids?

Beneficial effects from mutations are very rare and tend to be temporary. They certainly are not producing adaptive traits on an evolutionary scale in vital organs.

Evidence or retract. Immediately.

I have spoken in passing about one regulatory gene that would require 18 substitutions in a gene 118 nucleotides long. They must have been fixed because they are fixed. The only reason there is nothing to address is because you did not bother to learn basic biology before you jump on the bandwagon.

"Basic biology" like essential amino acids?

 

[FishFace]

2 substitutions in in 400 million years and the 2 million years ago random chance produced 18. One thing is obvious, this could not happen by random but I don't expect you to see it since you don't look.

No, that's not obvious at all. Nor does a non-random cause falsify evolution in any way.

You are assuming positive feedback

No, I am positing positive feedback as a possible cause.

fixation

As you know, fixation happens rapidly to advantageous mutations. If that fixation allows further advantageous mutations, or opens up an ecological niche with strong selective pressure for a big brain, then we have positive feedback.

and nucleotide substitutions that produce a functional amino acid sequence without causing a frameshift.

Substitutions do not produce frameshifts.

This happens no where in nature and yet you assume it unconditionally simply because the alternative is unappealing to you.

Which do I assume? None of them. I posit the first as a possible explanation. It is a fairly plausible explanation, in fact. I accept the second because of observed facts, as with the third.
I don't know what the alternative you're suggesting actually is. The only true alternatives are "I don't know" or "it happened randomly." I don't mind either of those, but it's nonetheless useful to think about explanations.

Again you are making a fundamental mistake due to a lack of knowledge. Nucleotide sequences join together in triplet codons, these codons are the amino acid sequence.

Actually, it appears you have the lack of knowledge. The codons are not the amino acid sequence; the codons (having been transcribed and translated) code for the amino acid sequence. I know all of this and, apparently, you don't.
Whose lack of knowledge?

In the protein coding genes the way they fold together determines the three dimensional structure of the parts of the cell.

The protein folding (determined by the location of functional groups available for hydrogen bonding, disulphide bridges and so on) determines the shape of the protein.

Protein ingested through meat has nothing to do with the size and complexity of the brain.

How do you know? Have you done the study, or looked for them? No. This is the null hypothesis, sure, but you don't have evidence to discount it.
You have ignored everything I've said on this topic so far, it seems. I KNOW HOW PROTEIN SYNTHESIS WORKS. But you don't seem to understand that diet can affect the body without affecting the genome! According to your line of thought, the only way our muscles will shrink is if our genome changes! Not so - if we don't eat, our body removes protein from the muscles to metabolise.

A quick google for "protein diet brain" will reveal a few studies on the topic. It turns out that we can't evolve a bigger brain if we don't have adequate food supplies because having a big brain requires a lot of energy and a lot of protein.
So it is not that ingesting protein changes our genome as you are still falsely accusing me of saying but that having more food allows these 18 new mutations to be beneficial because they don't just waste energy we don't have.

You haven't gotten anything right yet so the fact that you made another fundamental error does not surprise me in the slightest.

Please - get over yourself. I know what I'm talking about; I'm not exactly uneducated in biology - certainly I know the ins and outs of transcription and translation. In fact, the enzyme reverse transcriptase does exactly what you claim is impossible - affects the genome. Of course it's not relevant, but it doesn't surprise me in the least that you don't know about it.
So please stop misrepresenting my(our) arguments and start addressing them: Improved diet causes increased brain size. Not by directly affecting the genome.

As if you actually read them.

Hah! You clearly didn't read the one from which you stole that image comparing human and chimpanzee brains, which discussed the evolution of the former from something resembling the latter!

Diet can be a factor in certain traits but what happens is genes are expressed differently, sometimes turned on and off by prions but not altered on an amino acid sequence level.

Lack of food causes muscle wastage without affecting your genes. Please note that you imply that the amino acid sequence is identical with the genetic sequence which is incorrect.

When you are talking about random mutations you are talking about an error in the DNA replication process that most often does nothing at all. In those rare instances that they have a strong enough effect to be acted upon by selection it's deleterious the vast majority of the time.

Source? Not that it matters - deleterious mutations are eliminated from the gene pool rapidly.

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

Looks like you ignored the evidence raised by the other people here in the topic. Computer simulations show that traits with a >1% advantage over the rest of the population become fixed rapidly.

I have spoken in passing about one regulatory gene that would require 18 substitutions in a gene 118 nucleotides long. They must have been fixed because they are fixed. The only reason there is nothing to address is because you did not bother to learn basic biology before you jump on the bandwagon.

On the contrary it is YOU who seems not to know basic biology, and it is YOU who KEEPS ON MISREPRESENTING THE ARGUMENT. Do you really need to rely on a lie to make your point?

 

[Naraoia]

Nucleotides, that is what they are measuring. Here is the deal, when the nucleotide divergence increases from 1.33% to 6% how does the mutation rate change? It's as simple as that.

No, it's not as simple. A big indel may be one mutation but many nucleotides. Mutation rates ought to measure the rate at which events occur, because identifying a rare large insertion as a hundred much more frequent single base insertions makes no sense whatsoever. Of course, it's kinda hard to be sure if that large indel is one event or not... but there's still not much point in breaking it up into many smaller ones.

But now I'm off, I have to catch a plane to Cardiff.

See you guys on... probably Monday.

 

[Split Rock]

The most frustrating part of it is that you have convinced yourself that you have a firm grasp on what you're talking about. People who think they are experts when in fact they display glaring errors that would embarass a first year undergrad on their first day generally refuse to be told any different.

Stop thinking you actually know what you're talking about in this context. You don't. And it is frustrating to see legitimate scientific terminology used in order to further butcher science.

Mark is still doing his impression of a self-taught "Creation Geneticist." The simple fact that he has never actually done any genetic research does not prevent him from criticizing those who have.

 

[mark kennedy]

No, that's not obvious at all. Nor does a non-random cause falsify evolution in any way.

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

No, I am positing positive feedback as a possible cause.

No, you are grasping at straws.

As you know, fixation happens rapidly to advantageous mutations. If that fixation allows further advantageous mutations, or opens up an ecological niche with strong selective pressure for a big brain, then we have positive feedback.

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.

Substitutions do not produce frameshifts.

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

Which do I assume? None of them. I posit the first as a possible explanation. It is a fairly plausible explanation, in fact. I accept the second because of observed facts, as with the third.

No you didn't, you assumed natural selection was a magic pixie fairy. Your not the first, Charles Darwin's grandfather believed the same thing.

I don't know what the alternative you're suggesting actually is. The only true alternatives are "I don't know" or "it happened randomly." I don't mind either of those, but it's nonetheless useful to think about explanations.

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

Actually, it appears you have the lack of knowledge. The codons are not the amino acid sequence; the codons (having been transcribed and translated) code for the amino acid sequence. I know all of this and, apparently, you don't.

A triplet codon determines the amino acid.

That hard part is for the protein to fold into a useful protein structure:

Whose lack of knowledge?

Keep it up, your making this easy.

The protein folding (determined by the location of functional groups available for hydrogen bonding, disulphide bridges and so on) determines the shape of the protein.

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

How do you know? Have you done the study, or looked for them? No. This is the null hypothesis, sure, but you don't have evidence to discount it.

I don't need it, they unanimously admit they are clueless about the genetic basis for the evolution of the human brain from that of apes.

You have ignored everything I've said on this topic so far, it seems. I KNOW HOW PROTEIN SYNTHESIS WORKS. But you don't seem to understand that diet can affect the body without affecting the genome! According to your line of thought, the only way our muscles will shrink is if our genome changes! Not so - if we don't eat, our body removes protein from the muscles to metabolise.

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

A quick google for "protein diet brain" will reveal a few studies on the topic. It turns out that we can't evolve a bigger brain if we don't have adequate food supplies because having a big brain requires a lot of energy and a lot of protein.

Your chasing the wind here but be my guest.

So it is not that ingesting protein changes our genome as you are still falsely accusing me of saying but that having more food allows these 18 new mutations to be beneficial because they don't just waste energy we don't have.

Your assuming that they occurred, had a beneficial affect on the brain and then were fixed. Type 'mutations affecting the human brain' in Pub Med and educate yourself.

Please - get over yourself. I know what I'm talking about; I'm not exactly uneducated in biology - certainly I know the ins and outs of transcription and translation. In fact, the enzyme reverse transcriptase does exactly what you claim is impossible - affects the genome. Of course it's not relevant, but it doesn't surprise me in the least that you don't know about it.
So please stop misrepresenting my(our) arguments and start addressing them: Improved diet causes increased brain size. Not by directly affecting the genome.

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

Hah! You clearly didn't read the one from which you stole that image comparing human and chimpanzee brains, which discussed the evolution of the former from something resembling the latter!

I notice you didn't bother to quote cite or link anything remotely related. By the way, of course I read it but an indepth exposition would be wasted on you.

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.

 

[mark kennedy]

Haven't you been shown the calculations demonstrating that it could have happened?

No, primarily because they don't exist when compared to what happens in real living systems.

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.

Where do you think the amino acids used to synthesize proteins come from? Can you even name the nine essential amino acids?

What's next the Zone Pilate explanation for the evolution of the human brain from that of apes?

There are actually 22:

A frameshift mutation is one in which the change in DNA base sequence results in a change in the mRNA that translates into a major difference in the amino acid added to the growing polypeptide chain. In the example, the addition of a base to the DNA sequence changes every amino acid added to the polypeptide that is encoded by a gene that comes after the added base, a consequence of a completely shifted reading frame. This change will profoundly affect protein function because all amino acid downstream from the altered gene will be different from the original protein. Consequences of Point Mutations: FRAMESHIFT MUTATION​

Beneficial effects from mutations are very rare and tend to be temporary. They certainly are not producing adaptive traits on an evolutionary scale in vital organs.

Evidence or retract. Immediately.

Make me!

"Basic biology" like essential amino acids?

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