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How Much Is .1% Difference In Our Dna?


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#1 ikester7579

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Posted 05 January 2008 - 11:00 PM

Evolutionist claim we are around 99.8% the same as Chimps in our DNA. That's a .2% difference. Does anyone know what that .2% actually means?

If you need help, you can read this article here: http://evolution.ber...ws/060301_crime

#2 jamesf

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Posted 06 January 2008 - 12:03 PM

Evolutionist claim we are around 99.8% the same as Chimps in our DNA. That's a .2% difference. Does anyone know what that .2% actually means?

If you need help, you can read this article here: http://evolution.ber...ws/060301_crime

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Not quite sure where you are getting those numbers (your linked article actually says a 4% difference). However, you will find different numbers in the literature because they can be referring to different aspects of the genome.

Here are two links that give good summaries and background.
http://www.broad.mit...ckgrounder.html
http://en.wikipedia....ionary_genetics

Let's start with 3 billion base pairs in the human genome. About 3 million or 1 in a 1000 of these is different between different humans. That is 0.1% difference on average. It is these that are used to do DNA fingerprinting in crime scenes.

If we include ONLY base pair substitutions, the differences between human and chimp is 10 times larger or 35 million base pairs or about 1%. These substitutions are an important kind of mutation since they are useful in dating how far back the chimp and the human line separated.

This is why you sometimes hear of 99% similarity.

However, this measure does not include all forms of mutational differences. For example, there are 80 genes in the human that are completely missing from the human line that are present in the chimp line. As you can read in the second link...

"80 genes that were specifically lost in the human lineage after separation from the last common ancestor with the chimpanzee. 36 of those were olfactory receptors"

Two other missing genes have been well studied as noted in the link.

Hair keratin gene KRTHAP1
A gene for type I hair keratin was lost in the human lineage. Keratins are a major component of hairs. Humans have still nine functional type I hair keratin genes but the loss of that particular gene might have had a dramatic effect (human body hair thinning). Interestingly, the gene loss apparently occurred in the recent human evolution (less than 240 000 years ago).[12]

Myosin gene MYH16
Stedman et al. (2004) stated in an article in Nature, that the loss of the sarcomeric myosin gene MYH16 in the human lineage led to smaller masticatory muscles. They estimated that mutation that led to the inactivation (a two base pair deletion) occurred 2.4 MYA right before Homo ergaster/erectus showed up in Africa. This period that followed was marked by a strong increase in cranial capacity. The loss of that gene may have removed an evolutionary constrain on brain size in the genus Homo.


Also from the first link, you can see that it is possible to measure different aspects of the genome difference.

"At the DNA level, the human and chimpanzee genomes are almost 99% identical at the DNA bases where the two genomes align to each other. By taking into account the insertions and deletions that have occurred in each species since their divergence from a common ancestor ~5 to 6 million years ago, they still share 96% of their sequence. At the protein level, 29% of proteins have the identical sequence and the average protein has accumulated just one human-specific amino-acid change."



The number you got regarding the 99.9% similarity may come from the line of thinking mentioned in the first link http://www.broad.mit...ckgrounder.html

We now have a nearly complete catalog of the 40 million genetic differences between the two genomes. Only ~3 million of these are in functional DNA sequence, significantly narrowing the search for what specific changes led to the evolution of human beings as well as those changes relevant to human-specific disease.



That is, we may have a smaller difference if we look at only the areas of the genome that are producing proteins. So depending on how you count and what you count and what you think is relevant, you can get numbers as low as about 95% similarity to higher than 99%.

Hope this helps.
James

#3 ikester7579

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Posted 06 January 2008 - 01:46 PM

Then why present all this with just numbers on some sites without where the numbers come from? Seems to me somebody is trying to sell the idea more than prove it.

#4 Phaedrus

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Posted 06 January 2008 - 03:05 PM

Evolutionist claim we are around 99.8% the same as Chimps in our DNA. That's a .2% difference. Does anyone know what that .2% actually means?

If you need help, you can read this article here: http://evolution.ber...ws/060301_crime

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Counting the indels and the Chromosomal rearrangements its close to 7%

It's not 1% and they have known that for years. Counting only the single base differences (sometimes referred to as point mutations, really just a single base pair difference) it's at least 1.23%. That comes to 35 million base pairs, then the indels (insertions and deletions sequences that are present in one and absent in the other). The indels account for 3%-4% of the divergence with some 90 million base pairs.

Oh, but wait it just keeps getting better and better. Those numbers came from the Initial Sequence of the Chimpanzee Genome (Nature Sept 2005). At that time they were reporting that there were 9 pericentic inversions (chromosomal rearrangements) from 2 million base pairs long to 4 million base pairs long, for a total of 20 million base pairs and that, mind you, are just the very large rearrangements.

I have been following the trends in Genetics and what I have been finding is that the differences between Chimpanzees and Humans are far larger then we have been led to believe.

Genomic DNA sequences of humans and chimpanzees differ by only 1.23% if considering only point mutations , a figure that grows up to 5% if small insertions and deletions are taken into account and up to a yet unknown percentage when segmental duplications are added to the picture Besides such relatively small-scale changes in their DNA sequences, the two species differ by large-scale rearrangements in their karyotypes. Human chromosome 2 results from the fusion of two acrocentric chromosomes that are independent in the great apes. In addition, there are at least 7 major (larger than 10 Mb) pericentric inversions (in human chromosomes 4, 5, 9, 12, 15, 17 and 18) that range in size between 16 and 77 Mb and many smaller ones. (Genome Biology 30 October 2007)

Indeed, Kimura's 1968 article begins with a discussion of the amino acid substitution rate obtained from ZUCKERKANDL and PAULING (1965). From this, Kimura estimated the nucleotide substitution rate on the basis of codon degeneracy and extrapolated this rate to the entire genome on the basis of the total number of base pairs estimated by MULLER (1958). This rate was too high to be accounted for by natural selection, according to HALDANE's (1957) cost of natural selection. Molecular Clock: An Anti-neo-Darwinian Legacy Genetics, Vol. 176, 1-6, May 2007

Look at the bolded part, I don't know if you seen Fred's debate in the debate section but he makes some good points based on Haldane's predictions. The fact is that he was working with a much lower amount of divergence. Counting the chromosomal rearrangements the mutation rate would have had to be off the charts.

The Human Genome is just under 300 Mb (million base pairs) long, as is the Chimpanzee Genome. The Chimpanzee Genome as compared to the Human Genome has about 35 million single bases that are different or 1.23%. When you add the indels (insertions/deletions) there are 90 Mb that are different which comes to 120 Mb. The Last Common Ancestor (LCA) for Chimpanzees and Humans is estimated to have lived between 5 million years ago (Mya) and 7 Mya. That means that since the split 125 Mb would have had to change in the respective genomes which comes to 25 per year (a mean average) for 5 million years. No add to that another 7 major pericentric inversions that are larger then 10 Mb ranging from 16 to 77 Mb long. That comes to at least 195 Mb in 5 Mya which is something like 29 base pairs permenantly changed in the respective genomes per year for 5 million years. The question could be asked, how is that a problem for evolution, the answer is simply the deleterious affects, or as the authors of this paper call it, codon degeneracy.

Thanks for the link by the way, very interesting piece.

Grace and peace,
Mark

#5 jamesf

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Posted 06 January 2008 - 04:09 PM

Then why present all this with just numbers on some sites without where the numbers come from? Seems to me somebody is trying to sell the idea more than prove it.

View Post


Well, most scientific findings get simplified by the time they get to the popular press. Each of the numbers stated by the original study was very likely correct for the point they were making. A base pair subsitution is a very straightforward number. However, an insertion or deletion is a bit more complicated. Suppose you consider the extra chomosome in someone with Down's syndrome. Is that one mutation? Or do you count up all the base pairs in the extra chromosome and include that total in the extra mutated base pairs? They have found gene's in humans that are turned off, but are turned on in chimps. How should we count that?


Here is the way the big study in Nature stated the point.
http://www.nature.co...ature04072.html

Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements.


Each insertion/deletion event may represent one or several mutations. So if you are looking at total mutations we have something like 40 million and change. However, everyone likes to argue about what is the most relevant number. Clearly if you are trying to date how far back the human/chimp split is, the relevant number is how many independent mutations have occured: not the total differences in the number of base pairs.

By the way, about half (actually a bit more than half) of the difference between humans and chimps is argued to be due to the evolution of chimps away from the original ancestor of both chimps and humans. So if you want to ask how many mutations we have from the that base ancestor it is close to 20 million.

Along this general line, I would enjoy hearing an argument on how you can get all the diversity currently found in humans from one family 5000 years ago. Since there would only be one Y chromosome on the ark (the male Y chromosome of Noah), you need to have a tremendous number of non- harmful mutations each generation to get all the diversity we have today. It would be interesting to see the calculation. Sounds like very very fast evolution.

#6 ikester7579

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Posted 06 January 2008 - 09:28 PM

Well, most scientific findings get simplified by the time they get to the popular press. Each of the numbers stated by the original study was very likely correct for the point they were making. A base pair subsitution is a very straightforward number. However, an insertion or deletion is a bit more complicated. Suppose you consider the extra chomosome in someone with Down's syndrome. Is that one mutation? Or do you count up all the base pairs in the extra chromosome and include that total in the extra mutated base pairs? They have found gene's in humans that are turned off, but are turned on in chimps. How should we count that?


Since Down's syndrome is being used as a evolution example. Would you considered a person with Down's syndrome more or less evolved than the rest of us?

Here is the way the big study in Nature stated the point.
http://www.nature.co...ature04072.html
Each insertion/deletion event  may represent one or several mutations. So if you are looking at total mutations we have something like 40 million and change. However, everyone likes to argue about what is the most relevant number. Clearly if you are trying to date how far back the human/chimp split is, the relevant number is how many independent mutations have occured: not the total differences in the number of base pairs.


You are speaking as if you know for sure there was a split. Problem with implying that is that it makes the theory of evolution an absolute and not a theory. I say this to keep the debate in the right light, that evolution is still a theory.

By the way, about half (actually a bit more than half) of the difference between humans and chimps is argued to be due to the evolution of chimps away from the original ancestor of both chimps and humans. So if you want to ask how many mutations we have from the that base ancestor it is close to 20 million.

Along this general line, I would enjoy hearing an argument on how you can get all the diversity currently found in humans from one family 5000 years ago. Since there would only be one Y chromosome on the ark (the male Y chromosome of Noah), you need to have a tremendous number of non- harmful mutations each generation to get all the diversity we have today. It would be interesting to see the calculation. Sounds like very very fast evolution.

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Yes it does sound fast. And I would also like to know how survival traits are lost when survival of the fittest is a mechanism of evolution?

Example: Chimps and other primates have the ability to resist aids. Since that is a survival trait, why was not that trait past on to us?

This one thing disproves the mechanism called survival of the fittest. Because look how many die from this every year.

#7 rbarclay

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Posted 07 January 2008 - 02:53 PM

Then why present all this with just numbers on some sites without where the numbers come from? Seems to me somebody is trying to sell the idea more than prove it.

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You are correct evolutionists are trying to sell their religion.

When the Encode project started to release their results the human chimp DNA difference increased to 5% or if you are an evolutionist that would be 95% similar. However, if you include the major hiostocompatibility complex (MHC) that figure decreases to 86.7% similarity or increases to 13.7% difference. Also since they are finding that "junk DNA" is really not junk after all and further studies are done on them I believe this difference will increase.

When scientists compared 77,461 bacterial artificial chromosome (BAC) from chimps to that humans there was only 48.6% that matched.

All this is proofing what Creationists already know the 99% similar figure given in the 1970's was very misleading.

References:

Harrub, Brad and Bert Thompson. Do human and chimpanzee DNA indicate an evolutionary relationship? http://www.apologeti...g/articles/2070

Nelson, J. Warren. Human/chimp DNA similarity continues to decrease: counting indels. http://www.answersin.../similarity.asp

Bob Barclay

#8 jamesf

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Posted 08 January 2008 - 08:35 AM

Since Down's syndrome is being used as a evolution example. Would you considered a person with Down's syndrome more or less evolved than the rest of us?

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Hmmm. I was using Down's syndrome as an example of the difficulty in measuring genomic distance. Virtually everyone has a few new random mutations (relative to their parents). The estimates vary but each of us probably has on the order of 100. Down's syndrome is a particularly large mutation.
Afraid I don't know what you mean by 'more or less evolved'. One could say that those mutations that block you from having fertile children are harmful mutations. Since Down's syndrome individuals rarely have kids, the mechanism of evolution blocks this particular harmful mutation from multiplying through the genepool.

You are speaking as if you know for sure there was a split. Problem with implying that is that it makes the theory of evolution an absolute and not a theory. I say this to keep the debate in the right light, that evolution is still a theory.

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Yes, in that quote you reference, the scientists are quite confident that chimps and humans had the same ancestor. Scientists in this field consider this to be a fact. However, the theory of evolution will always be a theory. It can not go higher than the status of theory. That is the highest form of science. In the same way, the theory of gravitation will always be a theory. However, it will never be an 'absolute.'

But for the sake of this argument, I am happy to keep it an 'hypothesis' ...


Yes it does sound fast. And I would also like to know how survival traits are lost when survival of the fittest is a mechanism of evolution?

Example: Chimps and other primates have the ability to resist aids. Since that is a survival trait, why was not that trait past on to us?

This one thing disproves the mechanism called survival of the fittest. Because look how many die from this every year.

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First, I suspect that the chimps relative resistance to aids is not due to the common ancestor of humans and chimps. I suspect it is due to a more recent development. However, many humans have genes that make them resistant to AIDs

http://www.ncoic.com/0997obrien.html

So in those places in the world where there is a high death rate from aids, we would expect those individuals with the genes that help make them resistant will have more fertile children than those that do not have the genes. If you die from AIDs before you have children, you do not pass on the ineffective genes.

From this simple process, a higher and higher proportion of the population will end up with the resistant genes. Given the high rate of death in parts of africa, I suspect we will find a relatively large increase in these resistant genes in africa relative to the U.S.

Regarding your question as to how survival traits get lost, there are a number of answers. The simple answer is that the environment changes and the genes for some survival traits are no longer needed. Mutations to those genes no longer harm the organism and the genes can mutate away from the original function. For example, cave animals can lose those genes that produce eyes and skin pigments. In humans, the prevalence of red-green color blindness in caucasian males (around 8%) is around twice that of native american's, africans and aborigines (around 4%). One could argue that in a societies where the need for precise color distinctions is less important for survival, we are likely to see increases in color blindness.

I suppose this would be considered micro-evolution but it is all part of evolutionary theory.

#9 ikester7579

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Posted 08 January 2008 - 12:20 PM

I won't be responding right away to this because I am studying what everyone is saying, plus the references they leave. Plus some other stuff on DNA as well. I find this all fasinating.

Plus I'm debating this on youtube.

So thinks everyone for your responses. If you have more to add, I'm willing to read. Condense it if possible.

#10 trilobyte

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Posted 09 January 2008 - 05:31 AM

The evolutionary minded suggest that us humans and the chimps have a common ancestor.

Then they suggest there was a split something like 5 to 6 MY ago. (depending on your source)

Scientist tell us that we humans have somewhere around 3,000,000,000 base units in our genome. (nucleotides)

They also tell us that the difference between our base unit DNA and chimp DNA (our alleged closest relative) is only about 1.4% to 5% (Once again depending on your source)

Lets set up a scenario by winding the clock back 6 Million Years....which is close to the 5-6 MY suggested by the evos which will allow evolution more time... painting a more conservative evolutionary-friendly scenario.

Lets also say that a generation is 13 years.
This means in 6 MY's time there will only be 461,538 generations.

For the sake of the argument and to tilt the scale in favor of evolution, lets say that each generation has 3 beneficial mutation and it is selected and added to the gene pool.

Also for the sake of the argument lets say that this offspring that has received 3 beneficial mutation, in 13 years, has offspring that will also contain 3 beneficial mutation that adds to the last and makes it more human like...and so on and so on for 461,538 generation creating a more and more human like offspring.

BUT then we do the math.
461,538 generations X 3 mutations =1,384,614 total mutations

1,384,614 changes is only 0.00046 % of the 3,000,000,000 base pairs.

....which STILL presents quite a problem for the evos considering the supposed 1.4% to 5% difference in base pairs.

Remember, the scenario assumes 3 beneficial mutation occurs, is selected and adds to the previous 3 beneficial mutation each generation...which we all know the evolutionist claim doesn't happen.

But some evolutionist may claim, “only the coding DNA should be used in the scenario calculations”.

The argument should stop here, as the differences between humans and chimps count the base pairs and not just coding DNA.

Soooooooo, lets run the figures again only using the coding DNA...or about 5% of the DNA which represents our difference.....that would be about 150,000,000.

Out of 150,000,000 coding DNA, a change of 1,384,614 would represent about 0.009%..... STILL SHORT

Still the evolutionist may argue that those numbers should be split because the chimps took one path and the humans took another with a theoretical equal number of changes on both sides of the common ancestor split.

That would now mean 75,000,000 changes of the human half of the coding DNA required from the split and 75,000,000 for the chimp side.

As we see, 1,384,614 mutations would also fall short with a 0.018% difference between human and chimp...considering our 1.4% to 5% difference in base pairs.

The bottom line, it seems as if there wasn’t enough time or mutations to “evolve” man from a common ancestor in 5-6 MY’s.

#11 jamesf

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Posted 09 January 2008 - 09:25 AM

Dear Trilobyte,
You seem to be making an error regarding the number of mutations. When that is fixed, the math seems to work just fine. As I mentioned in my previous post (links available if you want), each generation has on the order of 100 new mutations.

Lets also say that a  generation is 13 years.
This means in 6 MY's time there  will only be 461,538 generations.

For the  sake of the argument and to tilt the scale in favor of evolution, lets say that each generation has  3 beneficial mutation and it is selected and added to the gene pool.

Also for the sake of the argument lets say that this offspring that has received 3 beneficial mutation, in 13 years, has offspring that will also contain 3 beneficial mutation that adds to the last and makes it more human like...and so on and so on for 461,538 generation creating a more and more human like offspring.

BUT then we do the math.
461,538 generations X 3 mutations =1,384,614 total mutations

View Post


With 100 new mutations we have

461,538 x 100 = 46,153,800

Chimps have a 35 million base pair difference from humans so this seems on the right order. In fact, it gives plenty of mutations for this simple calculation since chimps presumably have about the same number of mutations away from the common ancestor. It should be noted, however, that a full account must include a discussion on how each mutation gets 'fixed' into the population.

Of these 35 million, we do not know how many are 'beneficial'. Certainly the vast majority are neutral since they either occur in the non-coding regions or do not change the protein. Negative mutations are removed either at birth (e.g., through miscarriages), susceptibility to disease or simply result in reduced fertility - effectively removing them from the genome.

Hope that helps,
James

#12 numbers

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Posted 09 January 2008 - 10:45 AM

When scientists compared 77,461 bacterial artificial chromosome (BAC) from chimps to that humans there was only 48.6% that matched.


Here's a link to the paper you are referring to. Link (Free Registration Required)

That study arrived at a 98% overall similarity figure for chimp/human genome sequences

The BESs mapped with high confidence (13) were used to calculate the difference between the chimpanzee and human genomes at the nucleotide level. The number of sites in valid alignments (nucleotide sites that have PHRED quality values q ≧ 30) was 19,813,086. Out of this number, 19,568,394 sites were identical to their human counterparts for a mean percent identity of 98.77. This value is consistent with previous observations (3, 9, 10); however, our calculation comes from a much larger random comparison of slightly less than 1% of the total genome.


The study explains where that 48.6% number came from and why it doesn't contradict the 90+% similarity number for chimp/humans.

We found that 48.6% of the whole human genome was covered by the chimpanzee BACs (Table 2). One of the reasons for this apparently low coverage is that we used rather stringent conditions for the calculation; that is, BAC clones were incorporated into the calculation only when they had two sequenced ends in the same NT contig with the correct orientation. Probably because the orientation of draft sequences within the NT contig is sometimes incorrect, 70% of the total paired ends fit the condition. The coverage for chromosomes 14, 20, 21, and 22 was substantially higher. This difference correlates closely with the quality of the human genome sequences used as reference where finished chromosomes and those with longer contigs display higher BAC coverage. We also tested 1 Mb of the human draft sequences corresponding to positions 8012178 to 8426236 and 18502342 to 19012063 of chromosome 21, which we were able to retrieve from the public portion of the Celera database; however, we observed no substantial differences between the mapping results obtained through the public database and that of Celera. Theoretically speaking, the probability of coverage assuming totally random nucleotide distribution was calculated at around 0.7 (15); thus, we concluded that the actual coverage of about 70% for these essentially finished chromosomes is reasonable

Basically what that means is that they ended up using 70% of the chimp DNA clones against a partial map of the human genome (the study is from 2002, the human genome project didn't finish until 2003). When they found matches between the two the matched parts averaged 98% similarity. When they used maps of almost completely sequenced human chromosomes they had near 70% coverage which was reasonable from counting only 70% of the BAC clones.

#13 Guest_George R_*

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Posted 09 January 2008 - 04:12 PM

Clarification needed on this topic:

I have a few simple questions about the "100 beneficial mutations per generation".


Not to challenge the numbers, but to understand what they mean....

(1) is that 100 surviving beneficial mutations ... each of them spreads throughout the gene pool? Or does that 100 get wittled down to a smaller number of prevalent surviving mutations (e.g. some are dropped since they don't successfully cover the whole gene pool)?

(2) Is the number 100 dependent on the size of the population for each generation? Or is it a standard regardless of population size and family size?

(3) If the population goes through periods of population size change - (such as occurs cyclically or catastrophically with natural populations of mammals) ... Does that filter out some of the beneficial mutations and reduce the number of surviving mutations?

(4) There is only a small chance that a specific individual will have his genes represented many generations in the future (it depends on individual survivorship and gene predominance for survivors). Does this affect the assumption about 100 accumulating beneficial mutations for each generation?

Anybody can answer if you want.

#14 jamesf

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Posted 09 January 2008 - 05:22 PM

Clarification needed on this topic:

I have a few simple questions about the "100 beneficial mutations per generation".
Not to challenge the numbers, but to understand what they mean....

(1) is that 100 surviving beneficial mutations ... each of them spreads throughout the gene pool? Or does that 100 get wittled down to a smaller number of prevalent surviving mutations (e.g. some are dropped since they don't successfully cover the whole gene pool)?

(2) Is the number 100 dependent on the size of the population for each generation? Or is it a standard regardless of population size and family size?

View Post


I can't tell where you are directing this post. However, I must repeat that it is extremely difficult to identify which mutations are beneficial, which are neutral and which are slightly harmful. The number 100 is a very rough estimate of the total number of mutations in each generation. When we compare chimps and humans, we can not precisely say which are the beneficial mutations - we have only the total numbers.

We can say that most of these are neutral. Of the 100 mutations, (from what I read) there are something like 90 in non-coding DNA and have no effect on proteins (neutral). Of the remaining 10, around 5 will be neutral because although the codon changes, the same amino acid is produced and therefore the same proteins are produced.
Of the remaining 5, they are likely to be harmful or neutral. If particulary harmful, the owner dies and does not pass on the gene. They can be weakly harmful. For example, if the mutation is on a recessive gene, the mutation may remain invisible until the owner mates with another that has that gene. For example, 1 in 70 humans have the recessive albino gene, but the incidence of albinism is much rarer since it is recessive.

As far as your second question, I have read that different species and different parts of the genome have different rates of mutation. I have not heard that it depends on the size of the population. However, with a large population and with everyone producing mutations, the chance of at least one beneficial mutation must go up.


(3) If the population goes through periods of population size change -  (such as occurs cyclically or catastrophically with natural populations of mammals) ... Does that filter out some of the beneficial mutations and reduce the number of surviving mutations?

(4) There is only a small chance that a specific individual will have his genes represented many generations in the future (it depends on individual survivorship and gene predominance for survivors). Does this affect the assumption about 100 accumulating beneficial mutations for each generation?

Anybody can answer if you want.

View Post


I have read that when a population goes through a bottleneck, one does get more drastic changes. If the small population happened to have a rare beneficial mutation, then from what I understand it will propagate through that small population at a relatively high rate. However, even neutral mutations have a greater chance of propogation. This is a basic feature of 'genetic drift'
http://en.wikipedia....i/Genetic_drift

Again, your last point seems to be assuming that the 100 mutations are beneficial. Only a very small percentage of these are beneficial. However, these beneficial genes can multiply through the population depending on how beneficial they are. For example, 70% of humans are lactose intolerant as adults. The genetic mutations that allowed for adult lactose tolerance are relatively recent but it has multiplied relatively quickly through the population.

http://www.nytimes.c...r=1&oref=slogin

Hope that helps.
James

#15 Guest_George R_*

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Posted 10 January 2008 - 03:09 PM

Thanks for the reply. A really appreciate your sharing your expertise and also gently pointing out where I made false steps.

You have correced me from assuming that these 100 were beneficial.

That means we have less potential to "do good" with those mutations

I would have to make a high level assumption that the detrimental ones have nil to zilch chance of persisting - and thus cannot account for net differences in surviving populations.

That leaves the neutral ones - and I have no idea why thet would generally tend to accumulate across an entire population unless there was (as you say) a bottleneck that focussed on some individuals with these neutral mutations ... and effectively closed the door to the (many?) non-survivor's neutral mutations.

That's a lot fewer surviving mutations in the end population.

Based on that I cannot see how a high enough number of surviving mutations would be accounted for to make up the observed diffrence in DNA.

I am also concerned that some of the mutations frittered themselves out in population subsets that painted themselves into a corner, and are "no shows" in the surviving subsets,.

Without doing the math... thats a lot of "mutation leakage" ... that cannot build up to the final sepcies pairs that we are comparing.

#16 jamesf

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Posted 10 January 2008 - 05:52 PM

Thanks for the reply. A really appreciate your sharing your expertise and also gently pointing out where I made false steps.

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Hi George,
Glad to help, but I am certainly not an expert on genetics - although my wife works in genetics so I can always get help if I need it.

You have correced me from assuming that these 100 were beneficial.

That means we have less potential to "do good" with those mutations

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Yes, beneficial mutations are quite rare. I don't know how common they are. I have heard of numbers 1 beneficial mutation for every harmful 1000 mutations, but I think that is a wild guess. Certainly, the vast number of these are neutral. The most harmful ones block the fetus from developing, so there is never even a birth.

I would have to make a high level assumption that the detrimental ones  have nil to zilch chance of persisting - and thus cannot account for net differences in surviving populations.

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Actually, quite a number persist. Most everyone has some pretty nasty recessive mutations which is why it is a bad idea to marry someone that is genetically close. Most all cultures have bans against incest. Any even without the cultural influence, most individuals are not attracted to their siblings or children - for this very good reason. I had a Pakistani friend that married a cousin and unfortunately, although it was a great kid, he suffered from several recessive mutations.

In addition, some genes, like those for sickle cell, are actually beneficial (in areas with malaria) as long as they are heterozygous (you get the gene from only one parent). If the gene becomes too frequent in the population and you get it from both parents (homozygous), then it can be quite harmful.

That leaves the neutral ones - and I have no idea why thet would generally tend to accumulate across an entire population unless there was (as you say) a bottleneck that focussed on some individuals with these neutral mutations ... and effectively closed the door to the (many?) non-survivor's neutral mutations.

That's a lot fewer surviving mutations in the end population.

Based on that I cannot see how a high enough number of surviving mutations would be accounted for to make up the observed diffrence in DNA.

I am also concerned that some of the mutations frittered themselves out in population subsets that painted themselves into a corner, and are "no shows" in the surviving subsets,.

Without doing the math... thats a lot of "mutation leakage" ... that cannot build up to the final sepcies pairs that we are comparing.

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The neutral mutations can accumlate because there is nothing to get rid of them. If you and your mate are not genetically close, then the mutations will almost certainly not be at the same sites. So you pass those on to your mutations onto your kids and each kid adds another 100 - again in completely new set of locations. Relative to your parents, your kids will have significantly more neutral mutations than you will.

However, I have seen a bunch of papers on the role of population bottlenecks on gene populations. It certainly plays a big rule.

One thing seems clear from the fossil record. Evolution 'appears' faster after major catastrophes (although this is debated). After the great Permian extinction which killed off the trilobites and 95% of all species alive at the time, we see the rise of the dinosaurs and a variety of other species. After the KT extinction event which killed of the dinosaurs we see the rise of the great variety of the modern mammal species. One argument is that this relatively fast evolution occurs because the death of the old dominant species provides new opportunities for the surviving species. There are more possible environments where mutations can be beneficial. In addition, the small isolated populations that survive are more likely to suffer from genetic drift.

Again, I hope this helps.
James

#17 rbarclay

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Posted 11 January 2008 - 09:30 AM

Here's a link to the paper you are referring to. Link (Free Registration Required) 

That study arrived at a 98% overall similarity figure for chimp/human genome sequences

The BESs mapped with high confidence (13) were used to calculate the difference between the chimpanzee and human genomes at the nucleotide level. The number of sites in valid alignments (nucleotide sites that have PHRED quality values q ≧ 30) was 19,813,086. Out of this number, 19,568,394 sites were identical to their human counterparts for a mean percent identity of 98.77. This value is consistent with previous observations (3, 9, 10); however, our calculation comes from a much larger random comparison of slightly less than 1% of the total genome.
The study explains where that 48.6% number came from and why it doesn't contradict the 90+% similarity number for chimp/humans.

We found that 48.6% of the whole human genome was covered by the chimpanzee BESs (Table 2). One of the reasons for this apparently low coverage is that we used rather stringent conditions for the calculation; that is, BAC clones were incorporated into the calculation only when they had two sequenced ends in the same NT contig with the correct orientation. Probably because the orientation of draft sequences within the NT contig is sometimes incorrect, 70% of the total paired ends fit the condition. The coverage for chromosomes 14, 20, 21, and 22 was substantially higher. This difference correlates closely with the quality of the human genome sequences used as reference where finished chromosomes and those with longer contigs display higher BAC coverage. We also tested 1 Mb of the human draft sequences corresponding to positions 8012178 to 8426236 and 18502342 to 19012063 of chromosome 21, which we were able to retrieve from the public portion of the Celera database; however, we observed no substantial differences between the mapping results obtained through the public database and that of Celera. Theoretically speaking, the probability of coverage assuming totally random nucleotide distribution was calculated at around 0.7 (15); thus, we concluded that the actual coverage of about 70% for these essentially finished chromosomes is reasonable

Basically what that means is that they ended up using 70% of the chimp DNA clones against a partial map of the human genome (the study is from 2002, the human genome project didn't finish until 2003).  When they found matches between the two the matched parts averaged 98% similarity.  When they used maps of almost completely sequenced human chromosomes they had near 70% coverage which was reasonable from counting only 70% of the BAC clones.

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If you notice they phrase "stringent conditions." I take that to mean they were not so stringent then on the rest of the study. In other words they were, for example, stringent to pick out only Ford Taurus' but the they relaxed their constraints and allowed some Ford Tempo's through because they did look like Taurus's they were just a little smaller. This is verified by their disclaimer at the end of the paper:

"Users of this map should be careful in applying the information because the possibility remains that assignment of particular clones in the NT contig is incorrect or that inter- or intrachromosomally duplicated regions may be included within an insert."

If they are stating that there might be incorrect information in this study they have cast doubt as to the validity of the study. So the 70% is what fits their studies NT contig and using the "stringent conditions" came up with 48.6% that is the figure that correctly shows what they arrived at. If you are only going to be stringent on one aspect of the study and the rest of the study has lacked conditions the results are misleading. Either they match or they do not.

Also your 70% is preceded by a big "probably" because they were looking for the correct orientation in the NT contig and they could only find 70% that could be used, that in it's self is telling us there are more differences than we are being told. Maybe the dfferences are too vast to make an accurate comparision. This might be why they state that out of the 77,461 BACs 36,960 (that is 47.7% were not used but the insinuation is that they mapped 77,461 BACs) were not mapped because they were categorized into 3 different classes and they list three reasons for this and they are important to note:

1. they corresponded to repeat sequences or showed hits to human sequences not included in the NT contigs.
2. They matched only with sequences from several species other than human.
3. They did not match with human sequences, which either correspond to unsequenced human regions or are from chimpanzee regions that have diverged substantially from humans or did not match for other unknown reasons.

"Construction and Analysis of a Human-Chimpanzee Comparative Clone Map." Vol. 295 January 4, 2002. http://www.sciencemag.org

There was a comparison of mRNA expression levels between human and chimpanzees from the brain and liver. This study found that only 31.4% of the mRNA were similar between humans and chimpanzees. It appears that the more they study the more they find the difference between the two increase.

The 95% I stated in my earlier post is closer to the actual for now I say for now because I believe differences will increase as more studies are done. One such area is the study of "junk" DNA. Since they have found the term "junk" is not correct they do have a function and these functions need to be studied to find their importance in life.

Intar- and interspecific Variation in Primate Gene Expression Patterns. Vol. 296 Apirl 12, 2002. http://www.sciencemag.org

There is still the hiostocompatibility complex (MHC) that figure decreases to 86.7% similarity or increases to 13.7% difference. As I have said before maybe the differences are more than we have been led to believe.

"Human/chimp DNA similarity continues to decrease: counting indels." http://www.answersin.../similarity.asp

Bob Barclay

#18 numbers

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Posted 11 January 2008 - 10:16 PM

If you notice they phrase "stringent conditions." I take that to mean they were not so stringent then on the rest of the study. In other words they were, for example, stringent to pick out only Ford Taurus' but the they relaxed their constraints and allowed some Ford Tempo's through because they did look like Taurus's they were just a little smaller.  This is verified by their disclaimer at the end of the paper:

"Users of this map should be careful in applying the information because the possibility remains that assignment of particular clones in the NT contig is incorrect or that inter- or intrachromosomally duplicated regions may be included within an insert."

If they are stating that there might be incorrect information in this study they have cast doubt as to the validity of the study. So the 70% is what fits their studies NT contig and using the "stringent conditions" came up with 48.6% that is the figure that correctly shows what they arrived at. If you are only going to be stringent on one aspect of the study and the rest of the study has lacked conditions the results are misleading. Either they match or they do not.


There's always doubt about the results of a study, that's nothing unusual. You are the one that introduced that study into the conversation, I was simply pointing out that the study you are using to say chimps are not ~98% genetically similar actually states point blank that they found 98% DNA similarity between chimps and humans. It's unusual to use one finding of a study and reject another finding from the exact same study.

You're also ignoring that the low coverage% was due to incomplete data on the human genome. Where the data was close to complete the coverage% was substantially higher.

Also your 70% is preceded by a big "probably" because they were looking for the correct orientation in the NT contig and they could only find 70% that could be used, that in it's self is telling us there are more differences than we are being told. Maybe the dfferences are too vast to make an accurate comparision.  This might be why they state that out of the 77,461 BACs 36,960 (that is 47.7% were not used but the insinuation is that they mapped 77,461 BACs) were not mapped because they were categorized into 3 different classes and they list three reasons for this and they are important to note:

1.  they corresponded to repeat sequences or showed hits to human sequences not included in the NT contigs.
2. They matched only with sequences from several species other than human.
3. They did not match with human sequences, which either correspond to unsequenced human regions or are from chimpanzee regions that have diverged substantially from humans or did not match for other unknown reasons.

"Construction and Analysis of a Human-Chimpanzee Comparative Clone Map." Vol. 295 January 4, 2002. http://www.sciencemag.org


Read the study more carefully, they didn't map 47% of 77641, they mapped 77641 out of 114,421 sequences. The 36960 is the number that weren't mapped out of the 114k, not out of the 77k.

There were actually 4 catagories of unmapped sequences and they show the breakdown of categories in a chart.

Repeats 1,168
Human¶ 20,376
Nonhuman 515
No hit 14,901

Notice that the majority of those they didn't map fell into the showing hits to human sequences not included in the NT contigs(20,376 BESs).
Also note that these are sequences not individual nucleotides so the fact that ~10% didn't map to human DNA doesn't have any impact on the 98% nucleotide similarity figure.

There was a comparison of mRNA expression levels between human and chimpanzees from the brain and liver.  This study found that only 31.4% of the mRNA were similar between humans and chimpanzees. It appears that the more they study the more they find the difference between the two increase.

The 95% I stated in my earlier post is closer to the actual for now I say for now because I believe differences will increase as more studies are done. One such area is the study of "junk" DNA. Since they have found the term "junk" is not correct they do have a function and these functions need to be studied to find their importance in life. 

Intar- and interspecific Variation in Primate Gene Expression Patterns. Vol. 296 Apirl 12, 2002. http://www.sciencemag.org


I'm assuming the "Intra......" study is where you get that 31.4% number. I'd suggest you re-read the study. They find that there was 31.4% difference, not similarity and the difference was in protein levels, not mRNA sequences. The initial topic of this thread was about dna similarity not protein level similarity, so this study really has nothing to do with the topic.

Qualitative differences represent changes in electrophoretic mobility of spots, which likely result from amino acid substitutions, whereas quantitative differences reflect changes in the amount of protein.

Comparison Analyzed spots Differences
...............................................Qualitative Quantitative
Human-chimpanzee 538 41 (7.6%) 169 (31.4%)


Just to illustrate the difference between DNA similarity and what that study was about, the study found that one of the human brains was more different from the other human brains that the other human brains were different from the chimp brains.

The results (Fig. 1A) show that the variation in gene expression between individuals within the species is substantial, relative to the differences between humans and chimpanzee. For example, one human brain sample differs more from the other human samples than the latter differ from the chimpanzee samples


There is still the hiostocompatibility complex (MHC) that figure decreases to 86.7% similarity or increases to 13.7% difference. As I have said before maybe the differences are more than we have been led to believe.

"Human/chimp DNA similarity continues to decrease: counting indels." http://www.answersin.../similarity.asp

Bob Barclay

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Link to Study

The MHC is involved in the immune system and is known to be one of the most variable parts of the genome so it's not exactly surprising that it'd be less similar than other parts of the genome.

But let's imagine for a moment that tomorrow a complete sequencing of the chimp and human genomes showed that not just the MHC region but the entire genome of chimps was only 87% genetically similar to us when counting indels. What exactly do you think that would mean for evolution or creationism? It wouldn't have much effect on the number of mutations required to accumulate the changes since a single indel affects many nucleotides at a time (that study gave an example of a 95,000 base deletion). Additionally, unless there's another animal with higher genetic similarity counting indels it wouldn't have any effect on whether we were most closely related to chimps. Since evolution expects that chimps are the most genetically similar animal to us but doesn't require a specific percentage similarity I fail to see the significance of a change in the percentage similarity. I suppose creationists could point and say see scientists had an incorrect estimate, but that's not unusual as most estimates turn out to be incorrect. It wouldn't have any relevance on whether chimps and humans shared a common ancestor which is what creationist actually have a problem with.

#19 Dave

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Posted 12 January 2008 - 06:08 PM

I'm a little confused. Maybe a lot confused.

In reading all this about genomic similarities and differences I'm struck with the question: "So?"

Other than its usefulness in letting us use mice as guinea pigs for medical research, etc., what does genomic similarity have to do with evolution?

I know, I know. Common ancestors, and all that. But, isn't this really just another classic case of scientists with a particular worldview leaning on their presuppositions, and assuming common ancestry? Classic circular reasoning.

You'll find genomic similarities between humans, mice, bananas, and virtually everything else. Every living creature has some DNA similarities to every other living creature. In fact, isn't everything in the universe made up of a similar set of building blocks called chemical elements?

Personally, I have no problem with research finding out that all living creatures share genetic similarities. Proves a common designer, and common creator. In order to think otherwise, you have to assume the vastly unproven, and unprovable, hypothesis of evolution.

Dave

#20 rbarclay

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Posted 13 January 2008 - 09:11 AM

There's always doubt about the results of a study, that's nothing unusual.  You are the one that introduced that study into the conversation, I was simply pointing out that the study you are using to say chimps are not ~98% genetically similar actually states point blank that they found 98% DNA similarity between chimps and humans.  It's unusual to use one finding of a study and reject another finding from the exact same study.

You're also ignoring that the low coverage% was due to incomplete data on the human genome.  Where the data was close to complete the coverage% was substantially higher.
Read the study more carefully, they didn't map 47% of 77641, they mapped 77641 out of 114,421 sequences.  The 36960 is the number that weren't mapped out of the 114k, not out of the 77k.

There were actually 4 catagories of unmapped sequences and they show the breakdown of categories in a chart.

Repeats  1,168
Human¶ 20,376
Nonhuman 515
No hit 14,901

Notice that the majority of those they didn't map fell into the showing hits to human sequences not included in the NT contigs(20,376 BESs).
Also note that these are sequences not individual nucleotides so the fact that ~10% didn't map to human DNA doesn't have any impact on the 98% nucleotide similarity figure.
I'm assuming the "Intra......" study is where you get that 31.4% number.  I'd suggest you re-read the study.  They find that there was 31.4% difference, not similarity and the difference was in protein levels, not mRNA sequences.  The initial topic of this thread was about dna similarity not protein level similarity, so this study really has nothing to do with the topic.

Qualitative differences represent changes in electrophoretic mobility of spots, which likely result from amino acid substitutions, whereas quantitative differences reflect changes in the amount of protein.

Comparison Analyzed spots Differences
...............................................Qualitative  Quantitative
Human-chimpanzee  538 41 (7.6%)  169 (31.4%)


Just to illustrate the difference between DNA similarity and what that study was about, the study found that one of the human brains was more different from the other human brains that the other human brains were different from the chimp brains.

The results (Fig. 1A) show that the variation in gene expression between individuals within the species is substantial, relative to the differences between humans and chimpanzee. For example, one human brain sample differs more from the other human samples than the latter differ from the chimpanzee samples
Link to Study

The MHC is involved in the immune system and is known to be one of the most variable parts of the genome so it's not exactly surprising that it'd be less similar than other parts of the genome.

But let's imagine for a moment that tomorrow a complete sequencing of the chimp and human genomes showed that not just the MHC region but the entire genome of chimps was only 87% genetically similar to us when counting indels.  What exactly do you think that would mean for evolution or creationism?  It wouldn't have much effect on the number of mutations required to accumulate the changes since a single indel affects many nucleotides at a time (that study gave an example of a 95,000 base deletion).  Additionally, unless there's another animal with higher genetic similarity counting indels it wouldn't have any effect on whether we were most closely related to chimps.  Since evolution expects that chimps are the most genetically similar animal to us but doesn't require a specific percentage similarity I fail to see the significance of a change in the percentage similarity.  I suppose creationists could point and say see scientists had an incorrect estimate, but that's not unusual as most estimates turn out to be incorrect.  It wouldn't have any relevance on whether chimps and humans shared a common ancestor which is what creationist actually have a problem with.

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I want to thank you for pointing out my errors in that post. I typed it after along day, was very tired, and really should have waited until the next day to post it with a clear head.

The number 77641, is wrong it should have been 114,421 sequences and 36960 was suppose to come out of the 114,421. Also I meant different not similar with the 31.4%.

I have re-read my post and it was confusing to me so I can imagine what it was to the rest of you.

Again I am sorry for the errors and can only say I will not to let this happen again.


Now as to your what I was trying to say. When papers are published they are presented to the public as though they are inerrant and that all the facts have been included. It was not until I read the paper that I found the whole story of the study. For instance you pointed out that this paper only used a small portion of human DNA of the total and not even the study mentioned how much of a percentage of human DNA was used of the total. I brought up the unmapped 36,960 BESs to show that even with only a small fraction of the human DNA used only a fraction of that could be used. Yet the news releases I have read made it sound like all the DNA has been mapped and that there is only a 98% similarity. The 98% is misleading since it is an average and the 48.6% similarity of the BES and the 31.4% difference in brain and liver genes simply means that there are areas that are vastly different from the 98% stated. But then the afore mentioned numbers would not support the evolutionists point of view like the 98% would.

The refers to indels is also very interesting. If you are putting this much importance on them then the 95% average similarity is correct. As I have said since they have found that "junk" DNA can no longer be considered "Junk" meaning they have a purpose studies of this DNA will most likely widen the differences making common ancestry impossible to prove.

You also use a standard ploy of the evolutionists, that is, so what if the similarity number decreases from 98% to 87% that does not prove anything. Well it was the evolutionists that wanted these studies done because the original 99% similarity meant that they could prove we have evolved from a primate. Now that the numbers are not working for them it is just like the useless organs, the probability factors, recapitulation, etc. evolutionists say they do not mean a thing in the grand scheme of things. I have to just shake my head and smile when evolutionists have to backtrack because something did not work out for them. You try so hard to prove your religion, fighting for it as hard as you can, and when it does not pan out the way you want you try to cover the facts with such an out landish ploy to say that it does not mean a thing. Since mutations are needed to make the evolutionary religion work a larger difference makes the mutation hypothesis impossible. Since mutations, especially the so-called beneficial ones needed by evolution, are far and few in between it is a matter of kissing the common ancestry good-bye.

I have to ask then why do you present the 98% in the first place if it really does not mean that much to your religion? To assert such a scenario means you know that evolution is simply a faith based religion that means no matter what the facts say our religion it infallibly true and correct.

Bob Barclay




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