Genetics and Human Brain Evolution

quote:

---

I think it will help a lot if we took a good look at the Chimpanzee Genome paper and some of the comparisons they made.

---

And I very much doubt that taking a good look at the chimpanzee genome paper will do any good. Assuming you're Mark Kennedy, and not merely someone copying his arguments and his prose style, then we've already been through the chimpanzee genome paper at great length over on Christian Forums, and you're still making the same mistakes about it.Regardless of whether you're Mark or not, you're making numerous mistakes. Probably the most important one is trying to compare the mutation rate (as measured in modern humans) for single-base substitutions with the total number of bases mutated (from all kinds of mutation) in the comparison of humans and chimpanzees. You can't compare the rate of mutation events with the total number of bases changed in mutations, at least not if you want to do anything sane.

quote:

---

You don't realize that the regulatory genes come in amino acid sequences do you? When 18 nucleotides diverge that means that at least 6 amino acids are different.

---

He doesn't realize it because it isn't true. The regulatory gene in question, HAR1, does not code for any amino acids -- it's an RNA gene that is never translated into protein. (And a sequence of amino acids does not code for a protein; a sequence of (bonded) amino acids is a protein.)

quote:

---

What that counts is 35 million single nucleotide substitutions, those are the only ones measured in nucleotides. The indels and chromosomal rearrangements are measured in base pairs.

---

Base pairs are pairs of nucleotides. What are you talking about here?

quote:

---

Just in case you really are on to something here, tell me about the indels that mark the divergence between humans. In comparing the genomes of chimpanzees and humans the indels out numbered the indels as measured in base pairs. Does that hold true for human divergence?

---

I have no idea what this question is supposed to mean.

quote:

---

Because it would require 20 mutations (counting the rearrangements) per year for 7 million years. The mutation rate observed has a lot of variables but it's not the hundreds of mutations that would have had to be fixed. Much, if not most, of the divergence is fixed between humans and chimpanzees.

---

No, it would not require 20 mutations per year; it would require 20 mutated nucleotides (including indels) per year. Those 20 mutated nucleotides occur in ~5 mutations per year. (And that's including mutations in both chimps and humans.)

quote:

---

If you don't like 2x10^-8 then try another one that adequetly fits the divergence. Let me guess, you think 400 base pairs diveging between the two genomes per generation is no big deal right?

---

I don't know about anyone else, but I certainly think it's no big deal

quote:

---

Like counting all of the base pairs in the indels and applying them to the mutation rate as measured in base pairs.

---

No, like counting all the base pairs in the indels and applying them to the mutation rate as measured in mutation events, which is what you've just done here. The 2x10^-8/bp/generation is the number of mutation events, not the number of base pairs. (It's also just the single-base substitution rate, but that's less important.) It doesn't matter how many times you make that comparison: it will be wrong every time you do.

quote:

---

So it's insane to measure a mutation by the number of base pairs involved? Like I keep trying to tell you, they should be measured in base pairs.

---

No, it's not insane to measure a mutation by the number of base pairs. It would be a fine thing to do, if we had any way of doing it for current human mutations. We don't. That's why we make comparisons using the mutation rates that we actually have measured, like the single-base substitution rate.If you want to compare the total human/chimp divergence in base pairs against the measured rate at which base pairs change by mutation in humans, that's a perfectly sensible thing to do. To do it, however, you're first going to have to go out and measure that second number, because no one else has done it yet. Good luck with that.

quote:

---

The average indel is something like 300 bps,

---

Where did you get that number? The numbers you love to quote from the chimp genome paper give 5 million indels, totaling ~90 million bp. That's 18 bp per indel, not 300.

quote:

---

your trying to tell me that every generation there was at least one fixed along with 5 single nucleotide substitutions.

---

No, I'm trying to tell you that every generation there were ~50 single nucleotide substitutions fixing and 7 indels fixing.

quote:

---

I'm pretty much convinced that the only mistake I'm making is introducing myself as a creationist.

---

You may be convinced of that, but in reality you've made numerous errors in basic biology and genetics.

quote:

---

You mean to tell us that he's been shooting this line for a year or more, and he's still coming out with stuff like this

---

It's been going on for a couple of years on Christian Forums, with hundreds of posts replying to him.

quote:

---

Good grief.

​

This isn't an argument, it's a collection of idées fixes.

---

Well, yes. The sad thing is that he's still more interesting that 99% (at least) of creationists.

quote:

---

Ok, so the triplet codons in regulatory genes don't code for amino acids.

---

It would be nice if you could accurately paraphrase even one thing you're responding to. I said that the this regulatory gene does not code for any amino acids. I didn't say anything about regulatory genes in general.

quote:

---

Just tell me something, does it give you pause when you see a regulatory gene with 18 nucleotides that divergen between chimpanzees and humans? I mean especially when chickens and chimps only diverge by two and their LCA lived 310 mya.

​

Let me guess, it doesn't supprise you one bit.

---

My reaction was, "Wow, that's a lot of substitutions." Then I thought about it for a minute and realized that this was the most extreme case in the genome, and the most extreme case of anything in the genome is likely to be rather, well, extreme. And then I remembered that the extreme case among protein-coding genes had (if I remember correctly) fourteen amino-acid differences between humans and chimpanzees, and I didn't find it all that surprising. Impressive, yes, but not really surprising.

quote:

---

If you were to take all of the mutations in your personal genome and that measured them in single nucleotide/base pair increments, would the single nucleotides substitutions be greater or lessor in your genome?

---

You need to clarify your clarification, because that isn't even English. Do you mean do I have more base pairs that have changed within the last generation because of indels than because of single-base substitutions? If that's your question, then I don't know the answer, since it depends on the individual. On average, the number of base pairs changed by indels is larger than the number changed by substitutions, but for most individuals the number is probably smaller. That's because the rarer large deletions skew the average.

quote:

---

So you have one indel 300+ bps plus 5 single nucleotide substitutions in your genome that you will, of did, pass onto your offspring in as a permenant fixture in their genomes?

---

No, I have about 100 substitutions and about 14 indels. That works out to about 5 or 6 per year. (Generations are longer than years.) And indels still aren't 300+ bp long (on average).

quote:

---

I think it is a very big deal since the mutation rates I am looking at measure mutations by the base pair, not by mutational events.

---

And what mutation rates might these be that you're looking at? Where did you get them from? The only mutation rates based on modern human populations that include indels that I've seen are hopelessly biased against observing long indels.

quote:

---

I am also suspect that the accumulated single nucleotide substitutions outweigh indels in length as measured in base pairs.

---

Your suspicions don't count for anything.

quote:

---

Finally, I think most, if not virtually all the transcript errors in the germline cells are repairable in successive generations.

---

Transcript errors aren't mutations. This is one of the basic biology mistakes you keep making.

quote:

---

What is really important here is that even if you are totally convinced that the divergance in the two genomes are accounted for by the observed mutation rate, it does not account for the human brain.

---

Great. Combine your assertion with some evidence, and you'll have . . . some evidence.

quote:

---

It's the number of mutations (2) per 100,000,000 base pairs (10^-8), per diploid generation (a generation of 20-25 yrs). I am very familar with the formula, I have been taking to this guy for some time now.

---

That's reasonably close to correct. (I don't know what "diploid" is doing in there -- a generation is the interval between parent and offspring, whether they're diploid or not.)So now look at what you go on to say:

quote:

---

Let me see if I have your logic down here, bp is mutation events not base pairs and generation is plural not singlular (whatever that is supposed to mean).

---

Look back at what you wrote above. The mutation rate is the number of mutations. The "per" parts then tell you how often the mutations occur -- the number for each generation that passes, and the number for each base pair you have in your genome. That's what "per" means. You measure rotation rates in revolutions per minute -- how many revolutions happen in each minute. RPM is not measured in minutes, is it? If you put an old 45 on a record player, does "45 RPM" mean it lasts 45 minutes? If you plant one seed per foot, are seeds measured in feet? Your argument here is just ridiculous.

quote:

---

Naughty sfs!!
Barging in here, without as much as a 'by your leave', and scaring off our creationists.

​

You're hardly ever in, you don't call to let us know where you are but you turn up like the proverbial bad penny to frighten the latest squeaky rubber creationist bit substitute, for our champing horse like teeth, back into the undergrowth.

---

That's me, the scourge of creationists, the terror of CvE boards everywhere. I ride into town: IDists cower, and creationsts head gibbering and howling for the hills, never(*) to be seen again. In my wake I leave famine and desolation.Oh, and I almost forgot . . . Bwa ha ha.(*) "Never" in the sense of "not for at least twenty minutes".

quote:

---

I am most cross with you.

---

Then my work here is done.

---

Barmaid! Bring me stronger ale, and some plump, succulent babies to eat.
-- Olaf the troll

quote:

---

Let me guess...NO NO NO YOU DONT UNDERSTAND!!!...the trouble is I understand fine.

---

No, Mark, you don't understand fine. I see no point to further discussion with you, since no communication is taking place here. You've invented the idea that mutation rates are measured in base pairs out of whole cloth, invented me saying that "bp" doesn't mean base pairs, and ignored all attempts to point out your mistakes. What's the point? You're talking about your own fantasies, not science.