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Author Topic:   Genetics and Human Brain Evolution
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 16 of 157 (358946)
10-26-2006 7:17 AM
Reply to: Message 12 by eggasai
10-25-2006 9:05 PM


sex and the not so single species
... this one caught my attention. You are quoting from a news article based on a limited study. Why don't you check out the Initial Sequence fo the Chimpanzee Genome (Nature, 2005).
If you read the other links you will see that I have. I will see how you respond to Mick on your cherry=picking of statistics - this is twice now this issue has been brought up.
Meanwhile I can't help but notice you did not say anything with regard to the real issue - the fact that no matter WHAT the number is we are still more closely related to chimpanzees genetically than to any other known living species, and that there is a definite progression from human to neander to chimp to gorilla etc.
I also noticed that you didn't address the issue of sexual selection that can easily cause the kind of rapid evolution you are complaining is not possible.
Please stop dancing around and address these issues when you return, rather than continue to misquote or misrepresent materials and sources.
Enjoy.
Edited by RAZD, : tpoy

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This message is a reply to:
 Message 12 by eggasai, posted 10-25-2006 9:05 PM eggasai has not replied

  
eggasai
Inactive Member


Message 17 of 157 (359164)
10-26-2006 8:40 PM
Reply to: Message 15 by mick
10-26-2006 6:58 AM


Re: Getting the numbers right
quote:
Eggasai, you are completely wrong here. The Nature article cites a total nucleotide divergence of around 4%; 1% caused by 35 million substitution mutations, and 3% caused by a total of 5 million indel mutations.
You are confusing the actual paper with the Nature webpage announcing the paper. Type 'chimpanzee genome' into google and this will be at the top:
"What makes us human? We share more than 98% of our DNA and almost all of our genes with our closest living relative, the chimpanzee. Comparing the genetic code of humans and chimps will allow the study of not only our similarities, but also the minute differences that set us apart."
Chimp genome : Web focus : Nature
mick is completely wrong about what I said. I said that Nature claimed 98% of the DNA in chimpanzees and humans is the same in the announcement of the Chimpanzee Genome paper that said 95%.
Before you go around telling people I'm wrong you should be clear what it is I actually said. Did you even read the paper? If so do you think that a KA/KS > 1 in 600 genes and 40,000 amino acid seqeunces substituted is in keeping with the observed mutation rate in hominds?
Also, the 5 million mutations you are glossing over total 90 Mb and dwarf the single substitutions. You are contradicting me and you have only read the abstract? You have to be putting me on, I've been going over this paper with one of the authors for months.
Edited by eggasai, : Missed a point

This message is a reply to:
 Message 15 by mick, posted 10-26-2006 6:58 AM mick has replied

Replies to this message:
 Message 18 by mick, posted 10-26-2006 10:31 PM eggasai has not replied

  
mick
Member (Idle past 4986 days)
Posts: 913
Joined: 02-17-2005


Message 18 of 157 (359187)
10-26-2006 10:31 PM
Reply to: Message 17 by eggasai
10-26-2006 8:40 PM


Re: Getting the numbers right
Hi eggasai,
eggasai writes:
You are confusing the actual paper with the Nature webpage announcing the paper. Type 'chimpanzee genome' into google and this will be at the top
I can assure you that I am doing nothing of the sort. I read the pdf version of the paper yesterday evening, before replying to your post, and I have also read it in the past. I did not type anything into google, I located the article in an abstracting and indexing database and downloaded the pdf directly. The figures given in my reply were drawn directly from the article itself.
eggasai writes:
"What makes us human? We share more than 98% of our DNA and almost all of our genes with our closest living relative, the chimpanzee. Comparing the genetic code of humans and chimps will allow the study of not only our similarities, but also the minute differences that set us apart."
Chimp genome : Web focus : Nature
Amusingly, immediately after telling me that I have confused the actual paper with the website announcing the paper, you go on to give a link to the website announcing the paper, and a quote from the website announcing the paper! WTF?
eggasai writes:
Before you go around telling people I'm wrong you should be clear what it is I actually said. Did you even read the paper? If so do you think that a KA/KS > 1 in 600 genes and 40,000 amino acid seqeunces substituted is in keeping with the observed mutation rate in hominds?
I gave a quite a reasonably detailed albeit "back of the envelope" numerical analysis of the data and showed that the number of mutation events is perfectly consistent with natural mutation rates. If you have a problem with my numbers, you should tell me which ones you disagree with.
In fact, I can provide direct quotations from the pdf to back me up.
Here we go. I will give quotations from my previous post, and follow them with quotations from the pdf. The pdf is available here
mick writes:
The Nature article cites a total nucleotide divergence of around 4%; 1% caused by 35 million substitution mutations, and 3% caused by a total of 5 million indel mutations.
quote:
We calculate the genome-wide nucleotide divergence
between human and chimpanzee to be 1.23confirming
recent results from more limited studies12,33,34. The differences
between one copy of the human genome and one copy of the
chimpanzee genome include both the sites of fixed divergence
between the species and some polymorphic sites within each species.
By correcting for the estimated coalescence times in the human and
chimpanzee populations (see Supplementary Information ”Genome
evolution’), we estimate that polymorphism accounts for 14-22% of
the observed divergence rate and thus that the fixed divergence is
1.06% or less... The analysis of modest-sized insertions reveals,32Mb of humanspecific sequence and ,35Mb of himpanzee-specific sequence, contained in 5million events in each species... On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 40-45Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total ,90Mb. This difference corresponds to 3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions; this confirms and extends several recent studies63-67. Of course, the number of indel events is far fewer than the number of substitution events (,5 million compared with ,35 million, respectively)....
  —nature
So that's 5 million indels accounting for divergence in 3% of the genome, 35 million substitutions accouting for divergence in one percent of the genome, precisely as I stated.
Mick writes:
You appear to have cherry-picked the lowest measure of identity you could find in the article (29%) in order to bolster your case. However that is the percentage of whole proteins (not nucleotide positions) which are identical in terms of their complete amino acid sequence.
Nature writes:
Orthologous proteins in human and chimpanzee are extremely
similar, with ,29% being identical and the typical orthologue
differing by only two amino acids, one per lineage...
Clear enough?
Mick writes:
Anyway, if the fact that 29% of whole proteins are identical in human and chimp seems low to you, you should spend a moment considering the implications. According to the Nature article, the remaining 71% of proteins differed by an average of only two amino acids. The average length of a protein is around 1000 amino acids. This means that the probability that an amino acid from a chimp protein is identical to the corresponding amino acid in the human orthologue is equal to : (0.29 * 1.0) + (0.71 * 998/1000) = 99.858%.
If (as seems likely) the probability that human and chimp orthologous proteins are identical is inversely proportional to protein length, this estimate will be a little high. Let us imagine, conservatively, that the average of 2 amino acids differing per protein was consistent across all proteins, not just the longest 71% of them. This would mean that the probability that two orthologous amino acids are identical is equal to (998/1000) or 99.8%.
So the average probability of identity for single amino acids is close to 100% and over 99.5%, whichever way you look at it. NOT 29%!!!
Finally, there is your assertion that the natural mutation rate cannot account for the number of differences between chimp and human genomes. Let's say that the generation length for humans, chimps and their proto-species is around 15-20 years. Over the six million years since divergence, that gives us 300,000 to 400,000 generations per lineage. Since there are two lineages that can accumulate mutations, we have a total of 600,000 to 800,000 fertilization events separating a modern chimp from a modern human. Given that the nature paper declared 40 million mutation events, that gives us 50-66 mutations fixed per POPULATION per generation.
The number of new mutations arising per individual is around 100. If we were to assume a mean historical effective population size of around 25,000 for each proto-species (consistent with chimpanzee demographic data), the observed divergence between chimps and humans requires something of the order of 2-3 mutations to be fixed for each 100,000 mutations occuring. That doesn't seem unreasonable by any means.
Summary:
Probability that two orthologous amino acids are identical = 99.8%
Probability that two orthologous nucleotides are identical = 96%
Probability that two orthologous proteins are identical = 29%
Anything in there that you specifically disagree with? Was my arithmetic incorrect? The assumption of generation time and population size reasonable?
I think it is important to get the numbers right. I am happy to accept I have made mistakes if you care to show them, but assertions that I have not read the paper will not do.
Mick
Edited by mick, : No reason given.

This message is a reply to:
 Message 17 by eggasai, posted 10-26-2006 8:40 PM eggasai has not replied

  
eggasai
Inactive Member


Message 19 of 157 (359209)
10-27-2006 1:31 AM
Reply to: Message 15 by mick
10-26-2006 6:58 AM


Re: Getting the numbers right
quote:
Eggasai, you are completely wrong here. The Nature article cites a total nucleotide divergence of around 4%; 1% caused by 35 million substitution mutations, and 3% caused by a total of 5 million indel mutations.
What I said was that the Nature webpage announcing the Chimpanzee Genome paper claimed 98% of the DNA was the same, when the paper said 95% counting indels.
quote:
You appear to have cherry-picked the lowest measure of identity you could find in the article (29%) in order to bolster your case. However that is the percentage of whole proteins (not nucleotide positions) which are identical in terms of their complete amino acid sequence.
Oh for goodness sakes, I don't know what got you so turned around but here are a couple of choice quotes:
"Orthologous proteins in human and chimpanzee are extremely similar, with 29% being identical and the typical orthologue differing by only two amino acids, one per lineage."
They are different at an amino acid seqeunce level which means that the proteins are coded differently. A single nucleotide seqeunce can shut a reading frame down, which is why a codon out of place is not just a minor variation it's most likely going to be deleterious. You do know that groups of three nucleotides are triplet codons designating the amino acid right? Then the amino acid seqeunces are translated into proteins, they are talking about amino acid sequences. They are saying that taken together 29% of the protein coding genes differ by two amino acids.
I have no idea where you got the whole protein thing but it's wrong.
quote:
Just to repeat what the Nature article actually says: Around 96% of the total genome is identical (not 29% as you imply). These differences were caused by a total of 40 million mutation events (not 145 million, as you claim)
Wrong again! They said that there 35 Mb of single nucleotide substitutions and 5 million indels and 'verious chromosomal rearrangements'. In the paper they discuss the indels that are 90 Mb taken together and more or less evenly split between the chimpanzee and human genome. There is an additional 9 chromosomal rearrangements 2 Mb to 4 Mb long totally around 20 Mb. Taken together this comes to 145 Mb.
quote:
Anyway, if the fact that 29% of whole proteins are identical in human and chimp seems low to you, you should spend a moment considering the implications. According to the Nature article, the remaining 71% of proteins differed by an average of only two amino acids. The average length of a protein is around 1000 amino acids. This means that the probability that an amino acid from a chimp protein is identical to the corresponding amino acid in the human orthologue is equal to : (0.29 * 1.0) + (0.71 * 998/1000) = 99.858%.
What about the probablity of a single amino acid substitution being anything other then delerious? When you add up all the amino acid seqeunces that diverge we are talking about 40,000 aminio acid sequences. That comes to at least 120,000 nucleotides and like I told you earlier a single nucleotide substitution can shut down the reading frame. The chances of an amino acid seqeunce turning into one of the amino acids of life is less then one in three. There are 20 amino acids in all living things, there are 4 nucleotides that are used to make them. 4^4 is 64 and there are 20 amino acids so that's about a 1/3 ratio. I'll give you the rest of your biology primer when you digest that much.
quote:
If (as seems likely) the probability that human and chimp orthologous proteins are identical is inversely proportional to protein length, this estimate will be a little high. Let us imagine, conservatively, that the average of 2 amino acids differing per protein was consistent across all proteins, not just the longest 71% of them. This would mean that the probability that two orthologous amino acids are identical is equal to (998/1000) or 99.8%.
You guys and your probability arguments...ok...you were saying...
quote:
So the average probability of identity for single amino acids is close to 100% and over 99.5%, whichever way you look at it. NOT 29%!!!
Look at the quote and we can take this up when you realize what I am talking about.
quote:
Finally, there is your assertion that the natural mutation rate cannot account for the number of differences between chimp and human genomes. Let's say that the generation length for humans, chimps and their proto-species is around 15-20 years. Over the six million years since divergence, that gives us 300,000 to 400,000 generations per lineage. Since there are two lineages that can accumulate mutations, we have a total of 600,000 to 800,000 fertilization events separating a modern chimp from a modern human. Given that the nature paper declared 40 million mutation events, that gives us 50-66 mutations fixed per POPULATION per generation.
Finally something at least reasonably cognizant. The high end would be 7 million years but most molecular clocks would put it under 5 mya. Prior to 2 1/2 million years ago your imaginary human ancestors stood three foot tall, had the cranial capacity of a chimpanzee and wre for all intents and purposes knuckle dragging apes. The first truely human looking hominid was Turkana Boy who stood 6 foot tall with a cranial capacity of 900 cc at adulthood which puts him well within the human range.
Nevertheless, the outer limit for the chimpanzee/human split is 7 million years. That is 350,000 generations with the mutation rate at...let's see...2 x 10^-8 per diploid generation. That's 2 per 1oo,ooo,ooo nucleotides copied. The human genome is 2.85 billion nucleotides long but lets round it off to 3 billion. That is 60 per duplication and there are two geneomes, one from each of the parents. That comes to 120 per generation and believe me that is a rough estimate.
This is the point, that is not the 200 nucleotides that would have had to be fixed in 350,000 generations. Mind you these mutations our ape cousins are experiencing are germline mutations which makes them inheritable, not nessacarily fixed.
quote:
The number of new mutations arising per individual is around 100. If we were to assume a mean historical effective population size of around 25,000 for each proto-species (consistent with chimpanzee demographic data), the observed divergence between chimps and humans requires something of the order of 2-3 mutations to be fixed for each 100,000 mutations occuring. That doesn't seem unreasonable by any means.
The protein coding genes account for roughly 1% of the human genome. That would make it 300 Mb and you are wanting 1 or 2 mutations fixed. You are obviously talking about amino acid substitutions so you should take into consideration the deleterious effects. Don't worry about calculating this the paper has allready done that for you:
"Under the assumption that synonymous mutations are selectively neutral, the results imply that 77% of amino acid alterations in hominid genes are sufficiently deleterious as to be eliminated by natural selection. Because synonymous mutations are not entirely neutral (see below), the actual proportion of amino acid alterations with deleterious consequences may be higher. Consistent with previous studies8, we find that KA/KS of human polymorphisms with frequencies up to 15% is significantly higher than that of human-chimpanzee differences and more common polymorphisms (Table 3), implying that at least 25% of the deleterious amino acid alterations may often attain readily detectable frequencies and thus contribute significantly to the human genetic load."
Well over 80% of mutations do nothing at all and the vast majority of the balance are deleterious. There is a rare beneficial effect, especially in highly conserved regions like the brain. So you have 100-120 bp worth of mutations. Of those 1-2 are in the actual genes, of those 3 out of 4 are going to be delerious enough to be acted upon by natural selection. That means you will need at least 4 per per diploid generation.
This is the thing, the Human Genome Project has found millions of these little buggers and do you want to know what the effects are? You allready know, in the event that you don't I can provide you with an extensive list from the Human Genome Project I can even tell you how to get a free poster with them listed.
Interested in a free poster from HGP?
quote:
Summary:
Probability that two orthologous amino acids are identical = 99.8%
Probability that two orthologous nucleotides are identical = 96%
Probability that two orthologous proteins are identical = 29%
I'm just curious at this point since there is not a snowballs chance in Bagdad that this is an accurate statement. Do you usually get by with this kind of a jacked up misrepresentation of scientific literature?
Have a nice day.
eggasai
Edited by eggasai, : transcript errors
Edited by eggasai, : No reason given.

This message is a reply to:
 Message 15 by mick, posted 10-26-2006 6:58 AM mick has replied

Replies to this message:
 Message 20 by mick, posted 10-27-2006 4:23 AM eggasai has replied
 Message 21 by Wounded King, posted 10-27-2006 4:26 AM eggasai has replied

  
mick
Member (Idle past 4986 days)
Posts: 913
Joined: 02-17-2005


Message 20 of 157 (359221)
10-27-2006 4:23 AM
Reply to: Message 19 by eggasai
10-27-2006 1:31 AM


Re: Getting the numbers right
Hi eggasai,
Your post was a little confused and I'm not really sure where to start. I don't really want to go through the whole thing so here are some of the more glaring errors:
egassai writes:
A single nucleotide seqeunce can shut a reading frame down
No. A single coding nucleotide sequence always has at least one reading frame.
egassai writes:
which is why a codon out of place is not just a minor variation it's most likely going to be deleterious.
Whether fixed mutations are deleterious or not makes no difference to the proportion of observed differences between the two genomes. We don't even need to know the function of the genes that differ, just the number of nucleotides. I must say that your entire discussion of selection against deleterious mutation seems irrelevant when we are discussing fixed mutations.
egassai writes:
You do know that groups of three nucleotides are triplet codons designating the amino acid right? Then the amino acid seqeunces are translated into proteins, they are talking about amino acid sequences. They are saying that taken together 29% of the protein coding genes differ by two amino acids.
No. First, amino acids are not translated into proteins. More substantively, you have to read more carefully:
nature writes:
Orthologous proteins in human and chimpanzee are extremely similar, with 29% being identical and the typical orthologue differing by only two amino acids, one per lineage.
They are saying that 29% of the proteins do NOT differ at any amino acid positions. The remaining proteins, which DO differ, differ by an average of only two amino acids. This is a surprisingly high level of similarity, not a low level.
(in edit - I also need to read more carefully - the sentence is properly understood as saying that the median number of amino acid differences is two, including 29% of proteins with zero differences. An overall mean of 2 was used in my previous posts)
egassai writes:
Wrong again! They said that there 35 Mb of single nucleotide substitutions and 5 million indels and 'verious chromosomal rearrangements'. In the paper they discuss the indels that are 90 Mb taken together and more or less evenly split between the chimpanzee and human genome. There is an additional 9 chromosomal rearrangements 2 Mb to 4 Mb long totally around 20 Mb. Taken together this comes to 145 Mb.
Sure, I ignored chromosomal rearrangements since there are only nine of them. Compared to the 40 million substitution or indel mutations they are negligible in terms of the mutation rate calculations. Repeat my analysis with "forty-million and nine" mutations instead of "forty million mutations" and there should be little consequence.
egassai writes:
When you add up all the amino acid seqeunces that diverge we are talking about 40,000 aminio acid sequences. That comes to at least 120,000 nucleotides
You think three nucleotides have to mutate in order to change a single amino acid? You are wrong.
egassai writes:
The chances of an amino acid seqeunce turning into one of the amino acids of life is less then one in three. There are 20 amino acids in all living things, there are 4 nucleotides that are used to make them. 4^4 is 64 and there are 20 amino acids so that's about a 1/3 ratio. I'll give you the rest of your biology primer when you digest that much.
Hmmmn.... Hard to grasp what you are getting at, but you seem to think that only 20 possible codons are valid? This might explain why you think random mutation is such a non-starter. But if that's what you think, you are wrong. In the standard genetic code there are sixty-four possible codons (that is 4^3, not 4^4 as you claim) and arond 61 of them code for valid amino acids, the remainder for stop codons.
eggasai writes:
Nevertheless, the outer limit for the chimpanzee/human split is 7 million years. That is 350,000 generations with the mutation rate at...let's see...2 x 10^-8 per diploid generation. That's 2 per 1oo,ooo,ooo nucleotides copied. The human genome is 2.85 billion nucleotides long but lets round it off to 3 billion. That is 60 per duplication and there are two geneomes, one from each of the parents. That comes to 120 per generation and believe me that is a rough estimate.
This is the point, that is not the 200 nucleotides that would have had to be fixed in 350,000 generations.
all very nice, except that your "200 nucleotides" figure comes from a misunderstanding that the number of nucleotides that differ is equal to the number of necessary mutations that must be fixed. You can't seriously believe that as you have already given examples of single mutations resulting in numerous nucleotide differences (hint - a single deletion throwing off the reading frame).
etc. etc.
Edited by mick, : No reason given.
Edited by mick, : No reason given.

This message is a reply to:
 Message 19 by eggasai, posted 10-27-2006 1:31 AM eggasai has replied

Replies to this message:
 Message 22 by eggasai, posted 10-27-2006 5:41 PM mick has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 21 of 157 (359222)
10-27-2006 4:26 AM
Reply to: Message 19 by eggasai
10-27-2006 1:31 AM


Getting anything right
The chances of an amino acid seqeunce turning into one of the amino acids of life is less then one in three.
This is just complete nonsense. Where did you come up with such a ludicrous 'fact'. Take a look at the genetic code, this figure uses the RNA codons so for the DNA counterparts substitute Ts for Us.
Looking at this it should be clear that of the 64 possible codons only 3 do not code for 'one of the amino acids of life'.
This is such an incredible failure to grasp one of the most basic principles of molecular biology that I don't see how you can possibly hope to give anyone a 'biology primer'.
The chances are only very roughly something like 1/3 that any particular nucleotide substitution will lead to a change to a different 'one of the amino acids of life'.
I see that Mick has already addressed this, but I think the figure is still useful.
TTFN,
WK
Edited by Wounded King, : No reason given.

This message is a reply to:
 Message 19 by eggasai, posted 10-27-2006 1:31 AM eggasai has replied

Replies to this message:
 Message 23 by eggasai, posted 10-27-2006 6:17 PM Wounded King has not replied

  
eggasai
Inactive Member


Message 22 of 157 (359365)
10-27-2006 5:41 PM
Reply to: Message 20 by mick
10-27-2006 4:23 AM


Getting fundamental biology right
quote:
No. A single coding nucleotide sequence always has at least one reading frame.
Don't you get tired of being wrong? Nonesense, there is no such thing as a coding nucleotide. There are aminio acid seqeunces in protein coding gene have to translate into meaningfull proteins. If the chain is broken a stop codon will be inserted shutting down the reading frame. There is no actual frame, it's just an expression and if you are going to be making this kind of a fundamental mistake I'm going to have some fun with this.
quote:
Whether fixed mutations are deleterious or not makes no difference to the proportion of observed differences between the two genomes. We don't even need to know the function of the genes that differ, just the number of nucleotides. I must say that your entire discussion of selection against deleterious mutation seems irrelevant when we are discussing fixed mutations.
Whether they are deleterious or not is the key factor in whether or not they are fixed. Three out of four will be deleterious enough for there to be negative selection. That means that most of the mutations that pop up on the NS radar get zapped. Deleterious mutations do get fixed and the result is disease, disorder and death.
Fundamental error #2, you don't realize the roles of deleterious effects on fixation.
quote:
No. First, amino acids are not translated into proteins. More substantively, you have to read more carefully:
No, first of all you need to learn basic biology before you start pontificating about how things work:
quote:
They are saying that 29% of the proteins do NOT differ at any amino acid positions. The remaining proteins, which DO differ, differ by an average of only two amino acids. This is a surprisingly high level of similarity, not a low level.
That's the first thing you got right and you didn't correct what I said, you finally understood something fundamental. Most of the protein coding gene differ by one amino acid sequence in each of the two genomes. That's a mean average with some diverging by a more.
quote:
(in edit - I also need to read more carefully - the sentence is properly understood as saying that the median number of amino acid differences is two, including 29% of proteins with zero differences. An overall mean of 2 was used in my previous posts)
Those mutations that you are putting in the protein coding genes are probably deleterious and could shut the reading frame down. You don't seem to have a grasp of this fact so I will continue to repeat it until you do.
quote:
Sure, I ignored chromosomal rearrangements since there are only nine of them. Compared to the 40 million substitution or indel mutations they are negligible in terms of the mutation rate calculations. Repeat my analysis with "forty-million and nine" mutations instead of "forty million mutations" and there should be little consequence.
The ones described in the paper are only the major ones, there are a lot of others. These are 2 Mb to 4 Mb in length for 20 Mb and they don't interest you even though we are talking about half as many base pairs involved as the single nucleotide substitutions.
quote:
You think three nucleotides have to mutate in order to change a single amino acid? You are wrong.
No, I don't think that nor have I said anything of the sort. It could be a single nucleotide in each of the amino acid seqeunces but if it's just one nucleotide you are limited to what kind of an amino acid sequence it involved. Like I keep telling you a single nucleotide can shut the reading frame down making the gene inoperative. Your not getting that but it's not my fault you didn't learn basic biology before you started preaching it.
quote:
Hmmmn.... Hard to grasp what you are getting at, but you seem to think that only 20 possible codons are valid? This might explain why you think random mutation is such a non-starter. But if that's what you think, you are wrong. In the standard genetic code there are sixty-four possible codons (that is 4^3, not 4^4 as you claim) and arond 61 of them code for valid amino acids, the remainder for stop codons.
You are right about the sixty-four possible codons, it is 4^3=64, I was all set to compliment you on getting something right. There are 20 amino acids of life not 61, notice the three stop codons you were trying to factor in on the chart:
Codons don't code for anything, triplet codons are formed together in amino acid seqeucnes, the amino acid seqeunces are translated into proteins. You are defending your sacred evolution from creationist infidels and you don't know the central dogma of biology!?
I'll give you a hint, DNA-transcription-RNA-translation. Artemis will not be pleased with you if you don't learn the central dogma.
Edited by eggasai, : transcription errors

This message is a reply to:
 Message 20 by mick, posted 10-27-2006 4:23 AM mick has replied

Replies to this message:
 Message 24 by mick, posted 10-27-2006 9:24 PM eggasai has replied

  
eggasai
Inactive Member


Message 23 of 157 (359368)
10-27-2006 6:17 PM
Reply to: Message 21 by Wounded King
10-27-2006 4:26 AM


Getting the topic right!
quote:
This is just complete nonsense. Where did you come up with such a ludicrous 'fact'. Take a look at the genetic code, this figure uses the RNA codons so for the DNA counterparts substitute Ts for Us.
You guys like to exaggerate pedantic points don't you? Your buddy had one fundamental error after another but that's ok, he's an evolutionist. Anyway, when we have trudged through the pedantic biology sermons maybe you guys would like to get back on topic. You might want to clue your buddy in on the terminiology and actually read some of the literature before we start.
The thread is about the genetic basis for this giant leap of evolution:
I'm glad you are so well versed in basic biology, your going to need it.
Edited by eggasai, : transcript errors
Edited by AdminJar, : No reason given.
Edited by eggasai, : Checking out what the Mod did.

This message is a reply to:
 Message 21 by Wounded King, posted 10-27-2006 4:26 AM Wounded King has not replied

Replies to this message:
 Message 25 by RAZD, posted 10-27-2006 10:25 PM eggasai has replied

  
mick
Member (Idle past 4986 days)
Posts: 913
Joined: 02-17-2005


Message 24 of 157 (359400)
10-27-2006 9:24 PM
Reply to: Message 22 by eggasai
10-27-2006 5:41 PM


Re: Getting fundamental biology right
Hi eggasai,
eggasai writes:
Codons don't code for anything, triplet codons are formed together in amino acid seqeucnes, the amino acid seqeunces are translated into proteins. You are defending your sacred evolution from creationist infidels and you don't know the central dogma of biology!?
It would be nice to go on to discuss the evolution of brain-related genes, as you suggest, but I don't see how it can be constructive if you misunderstand the most basic elements of molecular biology (notwithstanding your hubristic attacks on the understanding of others).
eggasai writes:
Codons don't code for anything
How can you write that, directly after providing a figure showing precisely the opposite?
Codons "code for" amino acids. A triplet of nucleotides (i.e. a codon) within the DNA sequence or within the transcribed RNA sequence directly corresponds to a single amino acid within the protein. That correspondence is called "coding".
eggasai writes:
triplet codons are formed together in amino acid seqeucnes
Amino acid sequences are not made out of codons, nor are codons "formed" in amino acid sequence. An amino acid sequence is just that - a series of amino acids. There are no nucleotides or codons within an amino acid sequence.
eggasai writes:
the amino acid seqeunces are translated into proteins
No, the amino acid sequence IS the protein.
I'm sorry to keep pressing on these basic matters but I don't see how it will be possible to discuss mutation rates in protein-coding genes involved in the brain without agreement on these matters.
For example your belief:
eggasai writes:
The chances of an amino acid seqeunce turning into one of the amino acids of life is less then one in three. There are 20 amino acids in all living things, there are 4 nucleotides that are used to make them. 4^4 is 64 and there are 20 amino acids so that's about a 1/3 ratio.
This is really just the result of your not understanding transcription and tranlsation. But your view that two out of three nonsynonymous mutations result in an inviable protein (presuming that a protein "not containing the amino acids of life" is inviable) is going to seriously cloud your judgement of the likelihood of mutations being fixed in brain-related genes.
Cheers
Mick
Edited by mick, : No reason given.

This message is a reply to:
 Message 22 by eggasai, posted 10-27-2006 5:41 PM eggasai has replied

Replies to this message:
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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 25 of 157 (359410)
10-27-2006 10:25 PM
Reply to: Message 23 by eggasai
10-27-2006 6:17 PM


Re: Getting the topic right!
The thread is about the genetic basis for this giant leap of evolution:
Not really, because human did not "leap" from chimpanzees. A better picture of what this thread is about is:

(Source of picture is 29 Evidences for Macroevolution: Part 1)
Of course actually showing the intermediate stages - transitionals - kind of takes the impression of a "giant leap" out of the picture doesn't it?
Enjoy.
Edited by RAZD, : added picture source information

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This message is a reply to:
 Message 23 by eggasai, posted 10-27-2006 6:17 PM eggasai has replied

Replies to this message:
 Message 28 by eggasai, posted 10-28-2006 1:29 AM RAZD has replied

  
eggasai
Inactive Member


Message 26 of 157 (359430)
10-28-2006 1:12 AM
Reply to: Message 24 by mick
10-27-2006 9:24 PM


Re: Getting fundamental biology right
quote:
It would be nice to go on to discuss the evolution of brain-related genes, as you suggest, but I don't see how it can be constructive if you misunderstand the most basic elements of molecular biology (notwithstanding your hubristic attacks on the understanding of others).
I noticed that you are not as hypercritical about mistakes when it's one of your own. I just wonder how many creationists you have poisoned the well for, but no matter. Rest assured that the deleterious affects of mutations on neural genes is going to be discussed.
quote:
How can you write that, directly after providing a figure showing precisely the opposite?
Because they don't unless they come in triplet codons. Your boy Mick said that each nucleotide had at least one reading frame. I didn't see you go into spasms over that, I expect this is just a diversionary tactic while you try to get a handle on the Chimpanzee Genome paper.
quote:
Codons "code for" amino acids. A triplet of nucleotides (i.e. a codon) within the DNA sequence or within the transcribed RNA sequence directly corresponds to a single amino acid within the protein. That correspondence is called "coding".
No they don't, amino acids code for proteins, nucleotides are just the basic element of precise amino acid sequences. I'm neither baffled nor dazzled by how you conflate that basic biology and try to magnify percieved errors. I've done this before and I know what happens when you guys are confronted with the evidence.
quote:
Amino acid sequences are not made out of codons, nor are codons "formed" in amino acid sequence. An amino acid sequence is just that - a series of amino acids. There are no nucleotides or codons within an amino acid sequence.
You preach fundamentalist biology to me and make an assinine remark like that? Amino acids are composed of triplet codons which are three nucleotides called triplet codons, it just an expression really. Watson and Crick determined that codons were triplet by removing 1 or two of the nucleotides. This became the 'central dogma' of biology (DNA-trascription-RNA-translation) in their famous paper on the subject.
quote:
No, the amino acid sequence IS the protein.
No it's not, the amino acid sequence is translated into proteins in the ribosome...jezzz...talk about a fundamental error.
quote:
I'm sorry to keep pressing on these basic matters but I don't see how it will be possible to discuss mutation rates in protein-coding genes involved in the brain without agreement on these matters.
I don't either, you guys need basic biology. At this point diving into the scientific literature would be worse then useless. If you learned something about comparitive genomics now you would probably learn it wrong. We can spend some time on the Biology primer, it's better then trying to explain everything about the papers we are going to be looking at.
quote:
This is really just the result of your not understanding transcription and tranlsation. But your view that two out of three nonsynonymous mutations result in an inviable protein (presuming that a protein "not containing the amino acids of life" is inviable) is going to seriously cloud your judgement of the likelihood of mutations being fixed in brain-related genes.
I'm glad you brought that up, you guys have no clue what a deleterious effect from a mutation is either. Why don't you forget about the synonomous/nonsynonomous ratio right now, you aren't even congnizant of it's relevance or signifigance. You need to learn what happens when a mutation happens in the amino acid seqeunce:
So why don't you elaborate on the 'central dogma' of biology?
You can't continue into comparitive genomics untill you get some basic terminology down and at least a rudimentary understanding of the principles.

This message is a reply to:
 Message 24 by mick, posted 10-27-2006 9:24 PM mick has not replied

Replies to this message:
 Message 27 by Dr Adequate, posted 10-28-2006 1:28 AM eggasai has not replied
 Message 30 by iceage, posted 10-28-2006 1:48 AM eggasai has replied
 Message 31 by AdminNosy, posted 10-28-2006 3:42 AM eggasai has replied
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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 27 of 157 (359431)
10-28-2006 1:28 AM
Reply to: Message 26 by eggasai
10-28-2006 1:12 AM


Re: Getting fundamental biology right
I noticed that you are not as hypercritical about mistakes when it's one of your own. I just wonder how many creationists you have poisoned the well for, but no matter. Rest assured that the deleterious affects of mutations on neural genes is going to be discussed.
"One day"?
No they don't, amino acids code for proteins, nucleotides are just the basic element of precise amino acid sequences. I'm neither baffled nor dazzled by how you conflate that basic biology and try to magnify percieved errors. I've done this before and I know what happens when you guys are confronted with the evidence.
Okay, now I'm just going to laugh and laugh and laugh and laugh.
And then I'm going to ask you: why didn't you learn the first darn thing about genetics before you tried to lecture us on that subject?
Why?
You titled your post "getting fundamental biology right" and yet you yourself were too lazy to do so.
Why?
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 26 by eggasai, posted 10-28-2006 1:12 AM eggasai has not replied

  
eggasai
Inactive Member


Message 28 of 157 (359432)
10-28-2006 1:29 AM
Reply to: Message 25 by RAZD
10-27-2006 10:25 PM


Demystifying fossil evidence.
This is almost cliche, evolutionists love to cut and paste those skulls and let the illusion of gradual transition sink in. This is what the thread will be about, this is Homo habilis who stood 3 foot tall with the cranial capacity of an ape:
In 2 1/2 million years the cranial capacity had not signifigantly diverged from that of apes. The above skull is not much bigger then an apes,Then in less roughly 300 ka Turkana Boy appears suddenly along with the Homo erectus fossils.
Edited by eggasai, : Had to cut the lesson short

This message is a reply to:
 Message 25 by RAZD, posted 10-27-2006 10:25 PM RAZD has replied

Replies to this message:
 Message 29 by Dr Adequate, posted 10-28-2006 1:32 AM eggasai has not replied
 Message 32 by mick, posted 10-28-2006 4:38 AM eggasai has replied
 Message 33 by RAZD, posted 10-28-2006 8:45 AM eggasai has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 29 of 157 (359433)
10-28-2006 1:32 AM
Reply to: Message 28 by eggasai
10-28-2006 1:29 AM


Re: Demystifying fossil evidence.
This is what the thread will be about...
So it won't be about "Genetics and Human Brain Evolution"?
Well, I guess you have lost that debate.
But if you want to start a new debate, you should really start a new thread.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 28 by eggasai, posted 10-28-2006 1:29 AM eggasai has not replied

  
iceage 
Suspended Member (Idle past 5914 days)
Posts: 1024
From: Pacific Northwest
Joined: 09-08-2003


Message 30 of 157 (359434)
10-28-2006 1:48 AM
Reply to: Message 26 by eggasai
10-28-2006 1:12 AM


Fundamental Biology Question
No they don't, amino acids code for proteins
Is this correct? Admittedly I am out of element on this topic but this quote caught my attention.
I though amino acids make up the basic components of proteins and not code for them. In much the same way nucleotides make up the basic components of the DNA molecule.
Edited by iceage, : No reason given.

This message is a reply to:
 Message 26 by eggasai, posted 10-28-2006 1:12 AM eggasai has replied

Replies to this message:
 Message 34 by crashfrog, posted 10-28-2006 10:07 AM iceage has not replied
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