Gene Involved in Brain Development Evolved Rapidly in Humans

[JohnR7]

It is, perhaps unsurprisingly, an RNA regulatory gene.

The researchers compared the genomes of humans, chimpanzees, mice and rats and identified sections of DNA that have remained largely unchanged over the 80 million years or so since we all shared a common ancestor.

They do not have a DNA sample from 80 million years ago.
So they do not know if the DNA has changed any in that amount of time or not.
It is pure speculation on their part, because they otherwise have no evidence.

 

[mark kennedy]

http://www.livescience.com/humanbiology/060816_har1_gene.html

It is, perhaps unsurprisingly, an RNA regulatory gene.

Mark Kennedy, the ball is firmly in your court.

First of all, if you are going to address me in an OP I would appreciate a PM letting me know about it. Secondly, I think something in the way of an actual argument makes more sense then a link and a one line challenge. Let's see what you have:

"Some DNA regions have hardly changed at all over many millions of years in most species," said study team member Katherine Pollard, who is now at the University of California, Davis. "My twist was to look for a subset of these genes that have changed just in humans."​

According to most of the research I have been looking at the genetic basis for human evolution is elusive at best.

"It is logical to tackle the genetic aspects via both genome-wide analyses and candidate gene
studies. Genome-wide surveys could eliminate the majority of genomic sequence differences from consideration, while simultaneously identifying potential targets of opportunity. Meanwhile, candidate gene approaches can be based on such genomic surveys, on genes that may contribute to known differences in phenotypes or disease incidence/severity, or on mutations in the human population that impact unique aspects of the human condition."​

(Comparing the human and chimpanzee genomes: Searching for needles in a haystack http://www.ncbi.nlm.nih.gov/entrez/...ve&db=PubMed&list_uids=16339373&dopt=Abstract)

I'll take a look at the thread and see where the conversation went but that should be as much as the OP merits.

 

[TeddyKGB]

First of all, if you are going to address me in an OP I would appreciate a PM letting me know about it.

Sorry. It was probably an unneccessarily provocative statement now that I think about it.

Secondly, I think something in the way of an actual argument makes more sense then a link and a one line challenge. Let's see what you have:

"Some DNA regions have hardly changed at all over many millions of years in most species," said study team member Katherine Pollard, who is now at the University of California, Davis. "My twist was to look for a subset of these genes that have changed just in humans."
​

And? Do you have a particular objection to the passage?

According to most of the research I have been looking at the genetic basis for human evolution is elusive at best.

"It is logical to tackle the genetic aspects via both genome-wide analyses and candidate gene
studies. Genome-wide surveys could eliminate the majority of genomic sequence differences from consideration, while simultaneously identifying potential targets of opportunity. Meanwhile, candidate gene approaches can be based on such genomic surveys, on genes that may contribute to known differences in phenotypes or disease incidence/severity, or on mutations in the human population that impact unique aspects of the human condition."​

(Comparing the human and chimpanzee genomes: Searching for needles in a haystack http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=16339373&dopt=Abstract)

Doesn't that kind of genetic divergence between humans and chimps, coupled with rapidly-mutating regions as mentioned in the OP, prove difficult for your assertions that there hasn't been enough time for that genetic distance to accumulate?

Actually, I'm not sure I know what your position is anymore.

I'll take a look at the thread and see where the conversation went but that should be as much as the OP merits.

I'm sure you already consider it insufficient before reading a single word.

 

[mark kennedy]

Sorry. It was probably an unneccessarily provocative statement now that I think about it.

Provocative does not bother me a bit but if your going to challenge me let me know at least. I was surfing the net reading articles on this general topic and imagine my suprise to find this thread with my name in the OP.

And? Do you have a particular objection to the passage?

First of all I can't find anything but news stories, have they published their findings yet? I am trying to find the genes mentioned at Entrez Gene, it appears to be an mRNA gene involved in regulation. I'll let you know when I come up with something.

Doesn't that kind of genetic divergence between humans and chimps, coupled with rapidly-mutating regions as mentioned in the OP, prove difficult for your assertions that there hasn't been enough time for that genetic distance to accumulate?

Your kidding I hope, these genes have experienced rapid evolution. Let's take a closer look:

"Topping off the list was HAR1, a section of DNA made up of 118 bases, or "letters." A computational analysis of HAR1 showed that is essentially the same in all mammals except humans."

Did you miss this, the human condition especially the human brain is unique. It is a promising article but I would really like to get some more specifics and I wanted to respond to this thread as soon as I found it.

Actually, I'm not sure I know what your position is anymore.

Allow me to clarify, the human brain is three times the size of our closest relative. The genetic basis for this evolutionary leap remains elusive while the line of ancestory remains an unquestioned a priori fact in the minds of scientists. Do you think random mutations are some kind of an explanation because the researchers don't seem to think so.

"In the time since humans and chimps split about 6 million years ago, HAR1 has racked up 18 base substitutions when only one or none would be expected by chance.

For comparison, the HAR1 region of chickens and chimps only differ by two substitutions, even though more than 310 million years have passed since they shared a common ancestor."​

Simple answers for how these genes underwent such a dramatic transformation do not exist. Chance mutations will result in dangerous deleterious effects as I am sure we will find to be the case.

I'm sure you already consider it insufficient before reading a single word.

I read the article and your OP before scanning the thread for something substantive. Most of these discussions drift onto tangents and I am still trying to track down these genes. I'll get back to you on that one.

By the way, it's a fascinating article I just wish you had given me a heads up before posting the challenge.

 

[mark kennedy]

Ok, I found an article with more information:

We devised a ranking of regions in the human genome that show significant evolutionary acceleration. Here we report that the most dramatic of these 'human accelerated regions', HAR1, is part of a novel RNA gene (HAR1F) that is expressed specifically in Cajal-Retzius neurons in the developing human neocortex from 7 to 19 gestational weeks, a crucial period for cortical neuron specification and migration. HAR1F is co-expressed with reelin, a product of Cajal-Retzius neurons that is of fundamental importance in specifying the six-layer structure of the human cortex. HAR1 and the other human accelerated regions provide new candidates in the search for uniquely human biology.

http://johnhawks.net/weblog/2006/08/16

This thread looks like a hoot, balls in your court now Teddy.

 

[mark kennedy]

They do not have a DNA sample from 80 million years ago.
So they do not know if the DNA has changed any in that amount of time or not.
It is pure speculation on their part, because they otherwise have no evidence.

On the contray John, they have found excellent evidence that the human genome is unique. However, there is no evidence supporting that this gene could be altered so dramatically by mutational forces that are thought to have shaped it.

As far as it being speculation...I would say supposition and metaphysics that have no place in a scientific discussion as Teddy has pointed out.

 

[Chalnoth]

On the contray John, they have found excellent evidence that the human genome is unique. However, there is no evidence supporting that this gene could be altered so dramatically by mutational forces that are thought to have shaped it.

I'm sorry, but who has ever claimed that?

 

[TeddyKGB]

Your kidding I hope, these genes have experienced rapid evolution. Let's take a closer look:

"Topping off the list was HAR1, a section of DNA made up of 118 bases, or "letters." A computational analysis of HAR1 showed that is essentially the same in all mammals except humans."

Did you miss this, the human condition especially the human brain is unique. It is a promising article but I would really like to get some more specifics and I wanted to respond to this thread as soon as I found it.

No one has ever argued that the human brain is anything other than a remarkable advantage.

The wholly unsupported undercurrent of your position seems to be that whatever makes humans unique must be special, unevolvable, and therefore designed.

Allow me to clarify, the human brain is three times the size of our closest relative. The genetic basis for this evolutionary leap remains elusive while the line of ancestory remains an unquestioned a priori fact in the minds of scientists. Do you think random mutations are some kind of an explanation because the researchers don't seem to think so.

"In the time since humans and chimps split about 6 million years ago, HAR1 has racked up 18 base substitutions when only one or none would be expected by chance.

For comparison, the HAR1 region of chickens and chimps only differ by two substitutions, even though more than 310 million years have passed since they shared a common ancestor."​

Simple answers for how these genes underwent such a dramatic transformation do not exist. Chance mutations will result in dangerous deleterious effects as I am sure we will find to be the case.

One of the "simple answers" is selection pressure - natural, sexual, and otherwise. And frankly, I'm absolutely fed up with having to remind you every single time you enter a discussion that mutations themselves are only half the picture.

By the way, it's a fascinating article I just wish you had given me a heads up before posting the challenge.

It's okay. You won't lose any imaginary points for being a late-comer.

 

[mark kennedy]

I'm afraid your response doesn't make a lot of sense to me. Why do you call this "new, more complex information"? The changes are simple substitutions of one nucleotide for another. What's more complex about replacing an A by a T, or a G by an A, something that happens randomly all the time? In your version of genetics, does DNA become even more complex if the T is later replaced by an A again, and you end up with the identical sequence you started with?

I also don't see why this would be difficult to accomplish with random mutations. Over the last seven million years, every nucleotide in the region (as with any region in the genome) has mutated a couple of hundred times in one of our ancestors. The raw material for selection, the "ERRORS" must have happened, so why shouldn't they have been selected for?

"The region is highly conserved: only two bases are different between chimpanzees and chickens. In contrast, there have been 18 substitutions on the human lineage! It's like every other species is driving the same Plymouth Reliant, and humans are driving a Ferrari!"

You don't see why it would be difficult with random SNPs accumulated for a grand total of 18 nucleotides or 6 amino acids? Only two bases diverge between chimpanzees and chickens as compared to 18 in humans. Random mutations does not seem like much of an explanation, perhaps you would care to suggest some other mutational force capable of this?

Your well versed in Genetic statistics, what do you think of this statement?

Like the other scientists, Rogers was impressed by the scale of the evolution of the HAR1 gene when the odds were so seemingly stacked against it.

"A change like what they found?" Rogers said. "It's way, way out there on the probability curve."

http://www.chron.com/disp/story.mpl/headline/metro/4122722.html

 

[TeddyKGB]

On the contray John, they have found excellent evidence that the human genome is unique.

Yeah, it's called 'every species' genome is unique.'

However, there is no evidence supporting that this gene could be altered so dramatically by mutational forces that are thought to have shaped it.

What a priori limitation prevents "mutational forces" from doing so?

 

[mark kennedy]

No one has ever argued that the human brain is anything other than a remarkable advantage.

The human brain is only part of the puzzle, the most important part, but there are others:

"A genus of the Hominidae with the following characters; the structure of the pelvic girdle and the hind-limb skeleton is adapted to habitual erect posture and bipedal gail; the fore-limb is shorter than the hind-limb skeleton is adapted to habitual erect posture and bipedal gait; the well developed precision grip; the cranial capacity unusually well developed and fully opposable and the hand is capable not only of a power grip but a precision grip."

(A New Species of the Genus Homo from Olduvai Gorge, L. Leaky, P. Tobias, J. Napier. Nature April 4, 1964)

The wholly unsupported undercurrent of your position seems to be that whatever makes humans unique must be special, unevolvable, and therefore designed.

Whatever makes us unique has to have a genetic basis for a mutational force capable of changing highly conserved genes like the HAR1 gene. Are you going to go into the particulars are talk in circles with generalities?

One of the "simple answers" is selection pressure - natural, sexual, and otherwise. And frankly, I'm absolutely fed up with having to remind you every single time you enter a discussion that mutations themselves are only half the picture.

Natural selection can only act once there is an effect, you have failed to identify any viable cause. That tells us less then nothing of how 18 nucleotides were changed resulting in 6 amino acids involved in the development of the neocortex. Relaxed functional constraints is out the window since this is such a vital area. The only alternative is a selective advantage based on a statistical likelyhood that is off the charts. How many random mutations does it take to pull this off Teddy?

It's okay. You won't lose any imaginary points for being a late-comer.

I'll get caught up, don't worry about that.

 

[mark kennedy]

Yeah, it's called 'every species' genome is unique.'

Let me put this in perspective for you, the human brain is 6 times the size of mammals in general and 3 times that as the closest ape.

What a priori limitation prevents "mutational forces" from doing so?

The very real deleterious affects of mutations on genes involved in the development of the human brain.

 

[TeddyKGB]

Whatever makes us unique has to have a genetic basis for a mutational force capable of changing highly conserved genes like the HAR1 gene. Are you going to go into the particulars are talk in circles with generalities?

I consider it out of my hands at this point. And I will continue to do so until you come up with an objection more specific than "It didn't happen via evolution."

Natural selection can only act once there is an effect, you have failed to identify any viable cause.

What? It's pretty underhanded to proclaim ignorance in the matter of selective advantages of a giant cerebral cortex.

That tells us less then nothing of how 18 nucleotides were changed resulting in 6 amino acids involved in the development of the neocortex. Relaxed functional constraints is out the window since this is such a vital area. The only alternative is a selective advantage based on a statistical likelyhood that is off the charts. How many random mutations does it take to pull this off Teddy?

Who said it was "off the charts"? A low probability series of mutations is hardly impossible, especially given the massive advantages in planning inherent to a well-developed frontal cortex.

I sure hope you aren't trying to play like the quotes you have posted so far support your impossibility case.

 

[TeddyKGB]

Let me put this in perspective for you, the human brain is 6 times the size of mammals in general and 3 times that as the closest ape.

I refuse to take lessons in perspective from someone whose idea of a logical argument against human brain evolution is "Look how big it is!"

The very real deleterious affects of mutations on genes involved in the development of the human brain.

Do you have any idea how many conception events end in spontaneous abortion? Do you have any idea what causes the bulk of those?

 

[mark kennedy]

I consider it out of my hands at this point. And I will continue to do so until you come up with an objection more specific than "It didn't happen via evolution."

You mean you simply don't have an answer for how the gene was altered. Now after challenging me with a news article you refuse to even discuss the abstract of the paper the article was based on.

What? It's pretty underhanded to proclaim ignorance in the matter of selective advantages of a giant cerebral cortex.

Sure it is, once you actually have a better developed cerebral cortex. The problem is that there is no known genetic mechanism for altering the HAR1 gene on this level. You are starting with the effect which is the selective advantage you assumed a priori to have resulted. When I press you for the actual cause of the 18 nucleotide change you simply don't have an answer. Typical.

Who said it was "off the charts"? A low probability series of mutations is hardly impossible, especially given the massive advantages in planning inherent to a well-developed frontal cortex.

You didn't read anything about this did you.

"Now, this is the fastest of the regions of rapid evolution in the non-protein-coding genome, according to the paper. But if there are any substantial number of these, the number of selected substitutions they involve could easily exceed the number of amino acid substitutions between the human and chimpanzee genomes (already more than 40,000). "

http://johnhawks.net/weblog/2006/08/16

I sure hope you aren't trying to play like the quotes you have posted so far support your impossibility case.

I sure hope you don't intend to ignore the fact that you challenged me personally and all the quotes and links are directly related to the discussion you proposed?

Do you want to discuss this research or just talk in circles around it?

 

[mark kennedy]

I refuse to take lessons in perspective from someone whose idea of a logical argument against human brain evolution is "Look how big it is!"

You refuse to look at the actual facts and instead rely on an a priori assumption of a common ancestor. At this point I am simply saying look at the actual evidence and then propose a cause for the effect.

Do you have any idea how many conception events end in spontaneous abortion? Do you have any idea what causes the bulk of those?

Let's see...how about lethal mutations for one? Particularly the ones that alter a gene involved in the development of the; "Cajal-Retzius neurons in the developing human neocortex from 7 to 19 gestational weeks, a crucial period for cortical neuron specification and migration. HAR1F is co-expressed with reelin, a product of Cajal-Retzius neurons that is of fundamental importance in specifying the six-layer structure of the human cortex."

 

[Chalnoth]

TWhatever makes us unique has to have a genetic basis for a mutational force capable of changing highly conserved genes like the HAR1 gene. Are you going to go into the particulars are talk in circles with generalities?

Mutations can happen in any gene. They are highly random. The question is that once a mutation happens, does that mutation lead to a reproductive advantage for the resultant organism?

One possible selection mechanism, for example, would have been social: members of a group demonstrating greater intelligence might have obtained leadership status within the group, which often allows greater mating possibilities among social animals.

Natural selection can only act once there is an effect, you have failed to identify any viable cause. That tells us less then nothing of how 18 nucleotides were changed resulting in 6 amino acids involved in the development of the neocortex.

They changed randomly, and each was separately selected for. Random mutations happen all the time, but the changes which decreased intelligence were selected out of the population, while the changes that increased intelligence were selected for, eventually spreading throughout the population.

 

[mark kennedy]

They changed randomly, and each was separately selected for. Random mutations happen all the time, but the changes which decreased intelligence were selected out of the population, while the changes that increased intelligence were selected for, eventually spreading throughout the population.

Do you mean single nucleotides, small insertions and deletions, interspersed repeats or chromosomal rearrangements? Mind you we are talking about a gene that was highly conserved from 60 million years with only two nucleotides diverging between chickens and chimpanzees. When chimpanzees and humans are compared the HAR1 gene diverges by 18 nucleotides with 1 or 0 expected by chance. How do you explain this?

 

[Chalnoth]

Do you mean single nucleotides, small insertions and deletions, interspersed repeats or chromosomal rearrangements? Mind you we are talking about a gene that was highly conserved from 60 million years with only two nucleotides diverging between chickens and chimpanzees. When chimpanzees and humans are compared the HAR1 gene diverges by 18 nucleotides with 1 or 0 expected by chance. How do you explain this?

Quite simple: the evolutionary pressures were different. Obviously the selection pressures that the chimpanzees were under didn't favor the growing of larger brains. Thus any change to that chromosome that increased brain size wouldn't have been selected for, and wouldn't ever reach a significant portion of the population.

 

[TeddyKGB]

You mean you simply don't have an answer for how the gene was altered. Now after challenging me with a news article you refuse to even discuss the abstract of the paper the article was based on.

My answer is the same as it would be for any other trait: random mutation + differential reproductive success.

If you don't think the interaction of those elements can produce the human brain, you are welcome to explain why. Finding different ways to say "because they can't" isn't an argument.

Sure it is, once you actually have a better developed cerebral cortex. The problem is that there is no known genetic mechanism for altering the HAR1 gene on this level.

This is just insulting. Show me where it has been published that the HAR1 gene changes can't be accounted for by existing mechanisms.

You are starting with the effect which is the selective advantage you assumed a priori to have resulted. When I press you for the actual cause of the 18 nucleotide change you simply don't have an answer. Typical.

Is this some Behe-esque "the evolutionary explanation must explicitly account for the precise location and behavior of every molecule before I consider it valid" rhetoric? Because I'm tired of wasting my time on nonsense.

You didn't read anything about this did you.

"Now, this is the fastest of the regions of rapid evolution in the non-protein-coding genome, according to the paper. But if there are any substantial number of these, the number of selected substitutions they involve could easily exceed the number of amino acid substitutions between the human and chimpanzee genomes (already more than 40,000). "

http://johnhawks.net/weblog/2006/08/16

Show me where it says that the changes can't have happened via evolutionary mechanisms.

It's utterly mind-boggling that you think you can mine support for your position by quoting evolution-supporters out of context. Stop doing it.

I sure hope you don't intend to ignore the fact that you challenged me personally and all the quotes and links are directly related to the discussion you proposed?

Do you want to discuss this research or just talk in circles around it?

I want you to say something other than a variation of "big brain = impossible to evolve."