Evolution as natural history is psuedo-science

mark kennedy · Nov 16, 2006

Deamiter said:
If the average bp per mutation is 9 (didn't we calculate about 7.7 WITHOUT the largest?) then the average number of base pairs could easily be 90M with a NUMBER of mutations of 5M. What about this doesn't make sense?

I know you are getting confused but just bear with me. There are 5 million indels that seperate us from chimpanzees. Taken together they are 90 million base pairs. This is the mutation used in the spontaneous mutation rate paper, you will find it is virtually identical to the one sfs gave:

"With 6.4 x 10^9 base pairs in the diploid genome, a mutation rate of 10^-8 means that a zygote has 64 new mutations. It is hard to image that so many new deleterious mutations each generation is compatible with life, even with an efficient mechanism for mutation removal. Thus, the great majority of mutations in the noncoding DNA must be neutral."(Spontaneous Mutation Rate, Genetics, 1998)

The genome is 3.2 billion base pairs long, or thought to be in 1998 when this paper was published. A diploid generation means that there are two copies of the genome during meiosis. The 10^-8 means 1 per 100,000,000 bases so out of 1 billion bases there will be ten mutations. Out of 3 billion there will be 30 and in the diploid generation there will be approximatly 60.

"caption: Each time a cell divides into two daughter cells, its full genome is duplicated; for humans and other complex organisms, this duplication occurs in the nucleus. During cell division the DNA molecule unwinds and the weak bonds between the base pairs break, allowing the strands to separate. Each strand directs the synthesis of a complementary new strand, with free nucleotides matching up with their complementary bases on each of the separated strands. Strict base-pairing rules are adhered to adenine will pair only with thymine (an A-T pair) and cytosine with guanine (a C-G pair). Each daughter cell receives one old and one new DNA strand. The cells adherence to these base-pairing rules ensures that the new strand is an exact copy of the old one. This minimizes the incidence of errors (mutations) that may greatly affect the resulting organism or its offspring.

For more on the science behind the Human Genome Project, see our Genetics 101 Website. "

(image credit: U.S. Department of Energy Human Genome Program, http://www.ornl.gov/hgmis.)

That is 64 base pairs per zygote and clearly they are measuring them in base pairs, sfs would seem to want us to believe otherwise. I'm going to tell you why, because 64 base pairs per generation is not what would have had to happen. 125 million base pairs (35 million base pairs + 90 million base pairs) in 5 million years is 25 base pairs per year or 500 per generation (estimated at 20 years). You don't believe me, don't take my word for it ask a geneticist who worked on the paper:

sfs said:
For starters, we should be able to predict how different the genomes should be. The seven million years of evolution in each lineage represents about 350,000 generations in each (assuming 20 years per generation). How many mutations happen per generation? Estimating mutation rates is not easy (at least without assuming common descent): it is hard to find a few changed nucleotides out of 3 billion that have not changed. By studying new cases of genetic diseases, individuals whose parents' do not have the disease, however, it is possible to identify and count new mutations, at least in a small number of genes. Using this technique, it has been estimated[1] that the single-base substitution rate for humans is approximately 1.7 x 10^-8 substitutions/nucleotide/generation, that is, 17 changes per billion nucleotides. That translates into ~100 new mutations for every human birth. (17 x 3, for the 3 billion nucleotides in the genome, x 2 for the two genome copies we each carry). At that rate, in 350,000 generations a copy of the human genome should have accumulated about 18 million mutations, while the chimpanzee genome should have accumulated a similar number.

Common ancestry of humans and chimpanzees: mutations

I know you are a science student so I don't need to dwell on the formula any further, you either have the concept or you don't.

As for the calculation of 500 base pairs per generation... whatever is wrong with that? If you've got a population of 10,000 that's 1/20 per member. Since we're only counting FIXED mutations, that seems entirely reasonable to me. Certainly within an order of magnitude or so.

There has to be a linear progression, parent A passes on to offspring B who passes on to offspring C. Each zygote has 60 base pairs worth of mutations not 500 which is what they would need. There are 350,000 generations in 7 million years, you do the math.

They are trying to say that the 60 mutations are not 60 base pairs but 60 mutations of indiscriminate length, at least two of us in this thread know for a fact that this is not true.

shernren · Nov 17, 2006

Your problem isn't genetics, mark, it's comprehension and the ability to consider for even a split second anything that disagrees with you.

mark kennedy said:
1 what per what number of base pairs=genome?
0.1 what, per what number of base pair in the genome?
1/300 what per what number of base pairs in the genome?
0.1-100 what, per what number of base pairs in the genome?
1/300 what, what cell is dividing, how many base pairs are effective in the genome?

That is precisely my point. If mutations were really measured in base pairs, wouldn't these units:

1 per genome per replication
0.1 per genome per replication
1/300 per genome per replication
0.1-100 per genome per sexual generation
1/300 per cell division per effective genome

be:

1 base pair per genome per replication
0.1 base pair per genome per replication
1/300 base pair per genome per replication
0.1-100 base pair per genome per sexual generation
1/300 base pair per cell division per effective genome

?

You are simply assuming that the "what" is base pair, even though the words "base pair" are simply not present at all in the measurement. You assume the result you want to prove and then wonder why everybody's laughing. There is a word that describes people who systematically see non-existent things that enforce their illogical beliefs, but I am too polite to use it to describe you.

mark kennedy said:
You make this huge effort to appear as if you are being precise and systematic when you are argueing in circles around the main point. The mutations are measured in base pairs and don't you think by now I know that I have to know my material cold? No creationist could get away with the flagerant misrepresentation you just posted here.

Show that you know your material cold, because this just isn't it:

mark kennedy said:
I want you to think about this because frankly, I am sick and tired of being told this when I know it's not true:

Mutation rates in RNA viruses, whose genomes contain ca. 104 bases, are roughly 1 per genome per replication
That's 1 base in the virus which is 104 bases long.

Mutation rates in microbes with DNA-based chromosomes are close to 1/300 per genome per replication; in this group, therefore, rates per base pair vary inversely and hugely as genome sizes vary from 6 x 103 to 4 x 107 bases or base pairs.
The rates per genome varies here because the genome sizes vary greatly. It is from 6 x 103 to 4 x 107 bases or base pairs.

Let's look at those statements again:

Mutation rates in RNA viruses, whose genomes contain ca. 104 bases, are roughly 1 per genome per replication.

For effective comprehension I parse this sentence to become:

RNA viruses' genomes contain ca. 104 bases.
Mutation rates in RNA viruses are roughly 1 per genome per replication.

These two sentences are informationally equivalent to the sentence above. From here it is clear that "104 bases" is a description of genome size, mutation rates are measured as [unitless] per genome per replication.

Next:

Mutation rates in microbes with DNA-based chromosomes are close to 1/300 per genome per replication; in this group, therefore, rates per base pair vary inversely and hugely as genome sizes vary from 6 x 10^3 to 4 x 10^7 bases or base pairs.

I don't even have to re-parse this to show that two separate things are being discussed:

Mutation rates in microbes with DNA-based chromosomes are close to 1/300 per genome per replication; in this group,
therefore, rates per base pair vary inversely and hugely
as genome sizes vary from 6 x 10^3 to 4 x 10^7 bases or base pairs.

The only things described in terms of base pairs are genome sizes. Are mutation rates measured in base pairs here? No, again the unit is [unitless] per genome per replication.

mark kennedy said:
The size of the effective genome is a very small fraction of the genome in eukaryotes (you are composed of eukaryotes by the way). Dispite that fact the per genome/per sexual generation rate is indisitiquishable.

The rate varies because the size of the target varies from 1 to greator then 1010. The b stand for base or base pair.

The mutability per base, do you understand that this is per base!!!???

I'm not "composed" of eukaryotes. I am a eukaryote.

Yes, mutability is per base. There is a fundamental difference in measuring things in bases, and measuring probabilities per base.

mark kennedy said:
Horse feathers!!! Everything is measured in base pairs, the length of the section being viewed, the length of the mutation and the length of the respective genomes.

(Yes, horse feathers would be a very good way to disprove evolution, as they violate nested hierarchy, but I doubt you're being literal here, or even serious.)

That is precisely what I said:

The only things described in terms of base pairs (italicized) are genome sizes and mutation lengths, not mutation rates or number of mutations.

Your statement, by omitting "mutation rates", implicitly agrees that mutation rates are not measured in base pairs.

mark kennedy said:
The quoted portion <snip> is in base pairs, everything in the paper is in base pairs, everything in every genome in every living system known to man is in base pairs.

But the probability of a given event happening to a certain genome or fragment of genome need not be measured in base pairs.

mark kennedy said:
Dude I love you but I have got to be honest here, you have bought and are trying to sell a lie. I really don't have a problem one with TEs, most of them express genuine Christian conviction and I enjoy exchanges with them. You have been told wrong and apparently bought it hook line and sinker. I know that you believe what you are saying, I can tell by your attitude. My problem is not with you, it's with the one who told the original falsehood.

This isn't evolutionism I'm trying to teach you here, it's basic junior high school math. You're the only person I've ever known who doesn't understand dimensional analysis.

mark kennedy said:
Stop right there, here you are looking at 2 x 10^-8 which is 2 times a decimal point followed by 9 zeros. I am no statistician but 2 cars having accidents out of 100 million cars is pretty darn good.

Well I picked an unreasonable rate, the point is in the units not the values.

mark kennedy said:
You are measureing you rate per day, you have 2 cars out of 10^8 or 1,000,000,000 cars.

You understand what I said better than I do? Brilliant.

mark kennedy said:
There were 73 cars involved in accidents that year, which by the way is some good driving for the number of cars on the road there.

At least we know that your problem is not with genetics, it's with basic comprehension and mathematics.

mark kennedy said:
I can't let you continue with the analogy, it's just too embarasing.

The only thing I'm embarrassed about is your response. If any of you have watched Happy Feet already, I feel exactly like that operatic madame penguin near the beginning of the movie who ends up bashing her head against an icy outcrop because for the first time in her life she can't teach a penguin to sing.

Look, let me make it direct, clear, and straightforward.

A statistician studies head-on collisions.
He comes to the conclusion that the rate at which head-on collisions occur are 0.001 per car per day.
Over one day I see one million cars on the road.
Over that day I therefore expect to see 1,000 head-on collisions.

Does that mean 1,000 cars will be destroyed?
No, 2,000 cars will be destroyed, because by definition a head-on collision involves at least two cars.

Compare this with:

A geneticist studies mutations.
He comes to the conclusion that the rate at which mutations occur are 10^-8 per base pair per reproduction.
In one diploid genome he sees 6.4 x 10^9 base pairs.
Therefore he expects that in a new diploid genome he will see 64 mutations.

Does that mean that 64 base pairs will be mutated?
No, more than 64 base pairs will be mutated, because by observation many mutations involve multiple base pairs.

This is what I have come to dispise about evolution, this is how comprehensive formulas turn into mindless gibberish.

With 6.4 x 10^9 base pairs in the diploid genome, a mutation rate of 10^-8 means that a zygote has 64 new mutations. It is hard to image that so many new deleterious mutations each generation is compatible with life, even with an efficient mechanism for mutation removal. Thus, the great majority of mutations in the noncoding DNA must be neutral.

The genome is 3.2 billion base pairs long, or thought to be in 1998 when this paper was published. A diploid generation means that there are two copies of the genome during meiosis. The 10^-8 means 1 per 100,000,000 bases so out of 1 billion bases there will be ten mutations. Out of 3 billion there will be 30 and in the diploid generation there will be approximatly 60.

[/quote]

mark kennedy · Nov 19, 2006

shernren said:
Your problem isn't genetics, mark, it's comprehension and the ability to consider for even a split second anything that disagrees with you.

My problem is that evolutionists want to make dramatic points over semantics while argueing in circles around the central issue. I understand that the genomes of every living thing consists of pairwise nucleotide sequences. It is absurd to insist that a mutation of a million bases is quantativly the same as a single base.

That is precisely my point. If mutations were really measured in base pairs, wouldn't these units:

1 per genome per replication
0.1 per genome per replication
1/300 per genome per replication
0.1-100 per genome per sexual generation
1/300 per cell division per effective genome

Quote things in context

Still argueing around the central point I see, try taking these ratios in their proper context:

"RATES of spontaneous mutation per replication per measured target vary by many orders of magnitude depending on the mutational target size (from 1 to >1010 b, where b stands for base or base pair as appropriate), the average mutability per b (from 10-4 to 10-11 per b per replication), and the specific mutability of a particular b (which can vary by >104-fold). "

I know that this isn't an arguement you came up with but I know it's wrong. Sure, it's an estimate and a pretty general one but there are reasons for that. To say that the unit of measurement is not base pairs makes the whole equation utterly meaningless.

be:

1 base pair per genome per replication
0.1 base pair per genome per replication
1/300 base pair per genome per replication
0.1-100 base pair per genome per sexual generation
1/300 base pair per cell division per effective genome

?

The ratios you are looking at here are the mutation compared to the overall genome.

You are simply assuming that the "what" is base pair, even though the words "base pair" are simply not present at all in the measurement. You assume the result you want to prove and then wonder why everybody's laughing. There is a word that describes people who systematically see non-existent things that enforce their illogical beliefs, but I am too polite to use it to describe you.

I keep going over it again and again in my mind and I honestly don't get what is so hard to grasp about this. The estimate is per base pair, I'm not making this up it's in the paper again and again:

Mutation rates in lytic RNA viruses:

The mutant frequencies were 26/16158 b sequenced (16.1 x 10-4)

6.3 x 10^-4 per b

3 x 10^-4 per b

Drosophila melanogaster

about 0.3 of all amino acid changes were detectable as band shifts. In addition, only about 2/3 of base pair substitutions change an amino acid.Thus, the mutation rate per locus per generation is (3/1, 658,308)(0.3)/(2/3) = 9.0 x 10^-6

10^3 gives 8.5 x 10^-9 mutations per b per generation.

I'm not "composed" of eukaryotes. I am a eukaryote.

What could that possibly mean? More of the semantical shell game evolutionist use to evade that central point.

Yes, mutability is per base. There is a fundamental difference in measuring things in bases, and measuring probabilities per base.

The biggest difference is being able to actually sequence the nucleotides. That is probably why we were thought to be 99% ape in our DNA, the molecular analysis was not as precise as the sequenced genomes we have now.

(Yes, horse feathers would be a very good way to disprove evolution, as they violate nested hierarchy, but I doubt you're being literal here, or even serious.)

A nested hierarchy is little more then a more elaboate version of Darwin's tree of life.

That is precisely what I said:

The only things described in terms of base pairs (italicized) are genome sizes and mutation lengths, not mutation rates or number of mutations.
Your statement, by omitting "mutation rates", implicitly agrees that mutation rates are not measured in base pairs.

Oh for crying out loud, they are multiplying a mutation rate by the number of base pairs in the section or genome using a negative integer. That indicates that the measure is in base pairs. Now I realize this isn't an exact measurement but it is still in base pairs.

But the probability of a given event happening to a certain genome or fragment of genome need not be measured in base pairs.

You really don't know where this line of reasoning came from do you? The real issue is the indels in the Chimpanzee Genome comparision and it's time to move on to that.

This isn't evolutionism I'm trying to teach you here, it's basic junior high school math. You're the only person I've ever known who doesn't understand dimensional analysis.

Your not getting the big picture here, mutations are accumulated at a steady rate. It fluctuates but it is none the less discernable ratio between the overall genome and the base pairs altered as the result of transcript errors. You keep preaching this fundamentalist evolutionism but I don't buy a mutation being a million base pairs long is that same as a single substitution.

This is what I have come to dispise about evolution, this is how comprehensive formulas turn into mindless gibberish.

With 6.4 x 10^9 base pairs in the diploid genome, a mutation rate of 10^-8 means that a zygote has 64 new mutations. It is hard to image that so many new deleterious mutations each generation is compatible with life, even with an efficient mechanism for mutation removal. Thus, the great majority of mutations in the noncoding DNA must be neutral.

The genome is 3.2 billion base pairs long, or thought to be in 1998 when this paper was published. A diploid generation means that there are two copies of the genome during meiosis. The 10^-8 means 1 per 100,000,000 bases so out of 1 billion bases there will be ten mutations. Out of 3 billion there will be 30 and in the diploid generation there will be approximatly 60.

My problem is not that I don't understand genetics or math for that matter. My problem is that I am not supposed to question the central thesis of Darwinian evolution. I'm supposed to analyze everything I learn about genetics and biology in light of the assumption of a single common ancestor. That is the fundamental error I'm making and it has nothing to do with math and very little to do with genetics.

sfs · Nov 19, 2006

mark kennedy said:
My problem is not that I don't understand genetics or math for that matter. My problem is that I am not supposed to question the central thesis of Darwinian evolution. I'm supposed to analyze everything I learn about genetics and biology in light of the assumption of a single common ancestor. That is the fundamental error I'm making and it has nothing to do with math and very little to do with genetics.

Sorry, Mark, but the fact that you don't understand math or genetics means that your analysis of everything you're talking about is meaningless. That has nothing to do with accepting or rejecting common ancestry.

shernren · Nov 19, 2006

mark kennedy said:
The genome is 3.2 billion base pairs long, or thought to be in 1998 when this paper was published. A diploid generation means that there are two copies of the genome during meiosis. The 10^-8 means 1 per 100,000,000 bases so out of 1 billion bases there will be ten mutations. Out of 3 billion there will be 30 and in the diploid generation there will be approximatly 60.

My problem is not that I don't understand genetics or math for that matter. My problem is that I am not supposed to question the central thesis of Darwinian evolution. I'm supposed to analyze everything I learn about genetics and biology in light of the assumption of a single common ancestor. That is the fundamental error I'm making and it has nothing to do with math and very little to do with genetics.

"10^-8 means 1 per 100,000,000 bases so out of 1 billion bases there will be ten mutations. Out of 3 billion there will be 30 and in the diploid generation there will be approximatly 60"

fair enough.

Now, if 60 indels happen, and each indel causes 20 base pairs to change,

How many mutations have occurred? 60.
How many base pairs have been changed? 1200.

If 30 indels happen, each causing 20 base pairs to change, and 30 single-base substitutions happen,

How many mutations have occurred? 60.
How many base pairs have been changed? 630.

If 60 single-base substitutions happen,

How many mutations have occurred? 60.
How many base pairs have been changed? 60.

In each case 60 mutations happen. In each case a different number of base pairs is changed. It's entirely possible for 60 mutations per generation to change more than 60 base pairs per generation. And this has nothing to do with the "central thesis of Darwinian evolution", or even the Central Dogma. It's basic math and genetics, and calling it Darwinian propaganda just because you won't accept it doesn't help you much at all.

MatthewDiscipleofGod · Nov 19, 2006

sfs said:
Sorry, Mark, but the fact that you don't understand math or genetics means that your analysis of everything you're talking about is meaningless. That has nothing to do with accepting or rejecting common ancestry.

A fact that you have yet to prove. Mark certainly is doing well at holding his own in this thread. I'll have to go back and read it closer when I have more time since there is such a wealth of information being posted here.

It's posts like this though that have stopped my from posting in this forum to begin with. Posts like this by sfs are pointless and don't further any argument except for those that is being posted against. If you honestly believe Mark doesn't understand math and genetics please prove it. Don't make assertions that have no backing in reality.

mark kennedy · Nov 19, 2006

Project 86 said:
A fact that you have yet to prove. Mark certainly is doing well at holding his own in this thread. I'll have to go back and read it closer when I have more time since there is such a wealth of information being posted here.

It's posts like this though that have stopped my from posting in this forum to begin with. Posts like this by sfs are pointless and don't further any argument except for those that is being posted against. If you honestly believe Mark doesn't understand math and genetics please prove it. Don't make assertions that have no backing in reality.

Actually there was a pretty good point in there but it gets buried in the mix. Mostly it's a minor point about mutation rates being a general estimate but they tend to blow things out of proportion. The real problem is that when the truth came out that the divergence between chimapnzees and humans was finally revealed it was much greater then predicted. They have been saying it's 99% and it turns out that it's 95% and creationists are saying it's actually closer to 90%.

What's it all mean? If the difference is 1%, its something like 35 million base pairs. If it's 95% then it's more like 150 million and those two percentages have rates at which the DNA was changed. The fact is that if mutations are being accumulated just slightly above the rate we see them in modern times it would produce a great deal more disease and death and very little in the way of improved attributes. The contention is that the mutation rate doesn't change because there are more differences it just means bigger mutations and a mutation a million base pairs long counts the same as one that is 1 base long which is absurd.

The bottomline here is that the truth about the differences between chimpanzees are becoming increasingly obvious. If human ancestry cannot be traced back to apes then that's pretty much it for evolution as we know it. The science would not change but the philosophy of the ABCs of evolution (anything but creationism) would change. Then the possibility of God acting in time and space to create man fully formed must be considered. For a secular humanist that is simply unthinkable.

I appreciate your vote of confidence.

Grace and peace,
Mark

shernren · Nov 20, 2006

Project 86 said:
A fact that you have yet to prove. Mark certainly is doing well at holding his own in this thread. I'll have to go back and read it closer when I have more time since there is such a wealth of information being posted here.

It's posts like this though that have stopped my from posting in this forum to begin with. Posts like this by sfs are pointless and don't further any argument except for those that is being posted against. If you honestly believe Mark doesn't understand math and genetics please prove it. Don't make assertions that have no backing in reality.

Now, at least you explicitly mentioned that you hadn't really read through the thread. Because if you had, you would have noticed in this thread alone these two posts by sfs all the way back in page 3:

sfs said:
Mark has been corrected on this point literally dozens of times, but he keeps repeating it anyway. I guess he doesn't like the answer, since he insists that everyone (including the scientists) is lying to him.

Here's the situation: we do think that there are about 60 new mutations per generation in each copy of the genome. We also think there have been about 300,000 generations between us and the chimp-human common ancestor, so we would expect about 18 million new mutations have occurred since the common ancestor in our lineage, and another 18 million in the chimp lineage. So we would expect the human and chimpanzee genomes to differ by 35 or 40 million mutations (more or less -- with the uncertainty on the numbers, anything between 20 and 60 million would not have been very surprising). What we actually found when we compared the genomes was 40 million differences, i.e. just about exactly what we expected.

Those 40 million differences affected more than 40 million base pairs, however, since some of them (~5 million) were insertions or deletions of bits of DNA, which can affect many more than 1 base pair at a time. The total number of bases that differed was about 125 million (35 million single-base differences + 5 million insertions and deletions, with an average insertion/deletion size of 18 base pairs). Since 125 million (or 145 million, since Mark insists on including inversions for some reason) is larger than 40 million, Mark has decided there must be a terrible flaw in evolution here and that all of the scientists are lying to cover it up.

sfs said:
Nature says lots of things -- I'm not sure what you're asking about. The chimpanzee genome paper in Nature said, "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.

The figure of 60 can include the insertions/deletions (usually known as "indels", since it's less to type) or not, according to taste. The total mutation rate includes single-base substitutions and indels. The single-base substitution rate was known to be 60 plus or minus at least 20. The indel rate was thought to be about one tenth the substitution rate, but is now estimated to be closer to 20% of the substitution rate. So you could use 50 as the substitution rate and 10 as the indel rate (giving 60 total), or 60 as just the substitution rate with 70 as the total. As I said originally, there was plenty of uncertainty about the exact numbers. The inversion rate can be ignored, since it is even lower than the indel rate.

As for the figure of 400 mutations per generation, that doesn't exist. Look back at what Mark wrote: he talked about "400 per generation", without saying what it was that was happening at a rate of 400 per generation. What he means is 400 base pairs per generation, not 400 mutations. Since a single indel can be hundreds, thousands or even hundreds of thousands of base pairs long, the number of base pairs mutated is generally larger than the number of mutations. (Presumably the 400 means 200 per generation in humans and 200 in chimpanzees, since that would add up to the total difference seen in the genome comparison.)

I'm sorry, but I don't know what you mean. 40M and 145M are measuring different things. It's like comparing "number of car trips taken per year" and "miles travelled per year". There's no reason they should be the same.

where he clearly makes his case against what mark is saying. The fact that he even bothers to do this is astounding, as surely a geneticist has better things to do with his time than to type up a fresh rebuttal to someone who has been bringing up this point countless times for many months in multiple forums and been told why he's wrong again and again, each time dismissing the corrections as "semantic" or "obscure" or whatever politely derogatory word happens to be on his mind at the moment.

Mark's argument-from-incredulity is already a lot weaker than it was back in June when these howlers occurred:

mark kennedy said:
The mutation rate is 10^-8, it is not a difficult statistic to find if you make any kind of an effort at all. What is more, well over 98% will be neutral which is to say they do nothing at all with the vast majority of the balance being deleterious which means they are harmfull. We have a great disparity between the known divergance rate which is a decimal point followed by 8 zeros. Then there is the rate of fixed nucleotide sequences which comes to 9 per year for 10 million years and that is twice the amount of time scientists five it.

Try typing mutation rate for Homo sapians and you will confirm what I have allready told you for months. Try the Wikepedia article on the subject of mutations as a primer.

shernren said:
The actual rate is:

10^-8 / nucleotide / generation
* 3.2*10^9 base pairs

~= 32 nucleotides per generation.

Does it still seem minute to you?

Come to think of it, looking back, I have no idea what mark was trying to say. But the main point of dredging these posts up is that yep, that was me, making the same idiotic mistake mark has made: equating the number of mutations to the number of base pairs (bolded part; emphasis in original). So go ahead, chastise me for not knowing my basic math and genetics.

But at least I (quite fortuitously) cleaned up my own mess:

shernren said:
Secondly, in terms of units, the unit solves the problem. 10^-8 mutations per nucleotide per generation has to be multiplied by the length of the human genome, 3.2 x 10^9 base pairs, to get the average expectation of 32 mutations a generation. Also, the unit denotes that we are actually applying a rate for individual nucleotide substitutions, to which the rate for indels has to be added separately. (And an expected indel rate hasn't been supplied. Is 1 indel a year too many?) IOW, the mutation rate only has to apply to the nucleotide divergence, which is 1.06% x 3.2x10^9 = 3.4 million nucleotides.

Note that "32 mutations a generation" - that's me narrowly missing the nucleotide error by an inch. The reason I'm bringing this up is to say that we are not being so hostile to mark merely for making an error, as I myself made that same error quite a while back. Nor is it merely about his rejecting evolution, as we have been quite civil to creationists in general (at least before they left). It is simply that his basic errors compound upon themselves to create the illusion of an edifice of Darwin-defying arguments, and that he is convinced that everyone (including multiple geneticists) who disagrees with him is following some Darwinian secret agenda to persecute creationists, and when numerous cogent arguments are given to show how he is wrong (and in this case of mutations being measured in base pairs, almost none of them require the assumption of common ancestry, or indeed of natural selection in any way at all), he handwaves them all away and refers back to his aforementioned Darwinian secret agenda to persecute creationists.

sfs' ensuing dismissal is perfectly understandable in the light of all this.

Mallon · Nov 20, 2006

Given the choice, I'm going to have to go ahead and agree with those who actually have a formal education in biology/genetics. Credentials aren't meaningless.

sfs · Nov 20, 2006

Project 86 said:
A fact that you have yet to prove. Mark certainly is doing well at holding his own in this thread. I'll have to go back and read it closer when I have more time since there is such a wealth of information being posted here.

It's posts like this though that have stopped my from posting in this forum to begin with. Posts like this by sfs are pointless and don't further any argument except for those that is being posted against. If you honestly believe Mark doesn't understand math and genetics please prove it. Don't make assertions that have no backing in reality.

I have spent many hours over the last year or more replying to Mark's posts in great detail, often correcting the same errors over and over. At some point I simply have to say that enough is enough. I will still correct specific points for the sake of others who are reading, but I do not think it is possible for anyone to convince Mark that he is wrong even on the simplest of errors, so I am not going to try.

Go back and read all of my responses to Mark over the last two years before you tell me that I haven't backed up my assertions. (Hey, if I went to the trouble of writing them, you can go to the trouble of reading them.)

sfs · Nov 20, 2006

Mallon said:
Given the choice, I'm going to have to go ahead and agree with those who actually have a formal education in biology/genetics. Credentials aren't meaningless.

I do have credentials (I get paid to do genetics by a major university, and I publish peer-reviewed papers on the subject), but I don't have a formal education in genetics: my PhD is in physics. Switching fields like that is not uncommon.

random_guy · Nov 20, 2006

I have problems understand Mark's recent posts, and the followup posts since biology isn't my strongest subject, but is the gist of the argument this:
Mark: DNA sequencing analysis shows that there's too much base pair difference between humans and chimps to account for a common ancestor within the last xxx years. It would be impossible to have such a high mutation rate and sustain species viability. Here are the scientific sources to back the claims up. Therefore common ancestory is false.
Everyone else: The numbers cited in the papers use difference units to measure mutation rates/base pairs changed per mutation. Therefore the argument is wrong due to faulty units.

Is this the correct way of viewing this debate?

mark kennedy · Nov 20, 2006

Mallon said:
Given the choice, I'm going to have to go ahead and agree with those who actually have a formal education in biology/genetics. Credentials aren't meaningless.

I would to if this was about genetics and biology but it's not. Nothing causes an evolutionist to question universal descent. It's not falsifiable in any real sense and my interest has allways been in the attitutde of the arguement, the content is most often irrelevant.

rmwilliamsll · Nov 20, 2006

mark kennedy said:
I would to if this was about genetics and biology but it's not. Nothing causes an evolutionist to question universal descent. It's not falsifiable in any real sense and my interest has allways been in the attitutde of the arguement, the content is most often irrelevant.

the fact that Hoyle and company believe that panspermia is the answer to evolutionary problem means simply that evolutionists do challenge and disbelief significant pieces of the TofE, contrary to your assertation that "Nothing causes an evolutionist to question universal descent"

"It's not falsifiable in any real sense"
wrong-
1.chimeras would falsify common descent and probably the whole edifice of the TofE.
2.grossly misplaced fossils would as well.
3.so would have a genetic code mapping codons to tRNA in multiple forms, especially if each represented a biblical kind.
it is not only falsifiable, there are lots of people looking to overturn their little piece of the puzzle. i'd imagine that would be instant scientific stardom.

mark kennedy · Nov 20, 2006

random_guy said:
I have problems understand Mark's recent posts, and the followup posts since biology isn't my strongest subject, but is the gist of the argument this:
Mark: DNA sequencing analysis shows that there's too much base pair difference between humans and chimps to account for a common ancestor within the last xxx years. It would be impossible to have such a high mutation rate and sustain species viability. Here are the scientific sources to back the claims up. Therefore common ancestory is false.
Everyone else: The numbers cited in the papers use difference units to measure mutation rates/base pairs changed per mutation. Therefore the argument is wrong due to faulty units.

My arguement is not a complicated one, the known divergance does not line up with the known mutation rate by a longshot. This is the known mutation rate:

"With 6.4 x 10^9 base pairs in the diploid genome, a mutation rate of 10-8 means that a zygote has 64 new mutations. It is hard to image that so many new deleterious mutations each generation is compatible with life, even with an efficient mechanism for mutation removal. Thus, the great majority of mutations in the noncoding DNA must be neutral. " (Rates of Spontaneous Mutation, Genetic 1998 available online)

Now these mutations, or so I'm being told, are not measured in base pairs so apparently they can include hundreds of base pairs. The Chimpanzee Genome paper sfs worked on identified 35 million nucleotides that diverged between the two genomes along with 5 million indels. The indels are something like 90 million base pairs collectively. That comes to 125 million base pairs. I was wondering at what rate they would have had to be accumulated.

Notice the mutation rate says 64 mutations, if you do a little math thats 125 million base pairs in 5 million years (depending on the estimate since the last common ancestor). That comes to 25 base pairs per year which seems a little high to my uneducated mind. They keep telling me this is an arguement from incredulity and maybe they are right. Steve (sfs) and I discussed this regularly for quite some time and he exercised great restraint in trying to show me this creates no problem. I finally concluded that the neutral mutations might not be a big deal after all. Then I happened upon this article.

"Not very much, when you look at our DNA. But those few tiny changes made all the difference in the world...Scientists figured out decades ago that chimps are our nearest evolutionary cousins, roughly 98% to 99% identical to humans at the genetic level. "

How We Became Human

The fact is that this is wrong, we are 95% the same at best but we are talking about Time magazine. Then I googled 'Chimpanzee Genome' and found this 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."

The chimpanzee genome, Nature Web Focus

I am somewhat familar with the paper they are announcing and it says 125 million base pairs not counting the 9 chromosomal rearrangements (20 Mb). Time magazine I can accept not realizing but this is Nature magazine and if you Google 'Chimpanzee Genome' this is the first thing you will find. Nature is a well respected magazine I cannot believe they would make such a ridiculasly inaccurate statement.

Currently they are beating me down with this mutation rate thing. I was just looking for a rough estimate of what the mutation rate would be for 98% as opposed to 95% which is close to 100 million base pairs. I am told that I don't know the first thing about mutation rates so I need not bother.

Is this the correct way of viewing this debate?

I don't think so, in fact I think this thread has been effectivly derailed. Steve and I got into it over the mutation rate that I considered a rough estimate of the number of base pairs involved. He seems to think otherwise and when it comes to comparing credentials I really don't have much to offer.

The fact is that this is not a hugely complicated issue, either the known mutation rate accounts for the divergence or it doesn't. If it does then it's just a matter of comparing what it would be for 98% and 95%. Call it an arguement from incredulity if you will but until there is clarification on this I am skeptical to in a profound way.

mark kennedy · Nov 20, 2006

rmwilliamsll said:
the fact that Hoyle and company believe that panspermia is the answer to evolutionary problem means simply that evolutionists do challenge and disbelief significant pieces of the TofE, contrary to your assertation that "Nothing causes an evolutionist to question universal descent"

"It's not falsifiable in any real sense"
wrong-
1.chimeras would falsify common descent and probably the whole edifice of the TofE.
2.grossly misplaced fossils would as well.
3.so would have a genetic code mapping codons to tRNA in multiple forms, especially if each represented a biblical kind.
it is not only falsifiable, there are lots of people looking to overturn their little piece of the puzzle. i'd imagine that would be instant scientific stardom.

It's remarkable that there is no basis for rejecting a common ancestor for men and apes. Scientific inquiry aside there is no real basis for rejecting it. The evolution of the human brain would have had to be remarkably vigerous adaptive evolution. The problem is that it would have had to happen very quickly and the genetic mechansims like natural selection do not account for it.

I have found that it is not in the minute and precise details that the heart of the controversy exists. It is in sweeping generalities like the expansion of the human brain from apes. If this can be demonstrated to be impossible then there is no real basis for common ancestry. This will all come down to adaptive evolution one way or the other, as a creationist I can only see one outcome. Nature will differ to the Creator since there is not providential agency that can produce something as complicated as the human brian.

We are not simply modified apes and that will hold true whether we agree on a common ancestor or not. We are clearly catagorically different and I am not one to dismiss the profound differences because the scientific establishment says its unscientific to do otherwise.

rmwilliamsll · Nov 20, 2006

Nature will differ to the Creator since there is not providential agency that can produce something as complicated as the human brian.

often i think that the divide between YECism and OECism is exactly this. YECists are most often charismatic and see God's creative hand everywhere. The idea being that the creative, the supernatural, the miraculous, the spectacular is more in keeping with the nature of God and His interaction with creation. Where most OECist are more providentially orientated, that God works through ordinary means of grace, that education and preaching change people without spectular, easy to see results. This orientation is a fundamental difference in how people see God's action in the world and marks a real divide in the conservative Church. Alignment of YECism with premil and OEC with amil just goes along this fissure.

btw, providence is as much God's hand in the world as creative miraculous activity, just because God chooses to do things with natural and secondary means does not mean He is inactive or not really involved. Providential care is certainly sufficent to explain the rise of humanity from proto-apes.

Mallon · Nov 20, 2006

mark kennedy said:
I would to if this was about genetics and biology but it's not.

8 pages of you debating the details of primate genetics and now you say it's not about genetics. Sorry if I don't believe you.

Nothing causes an evolutionist to question universal descent. It's not falsifiable in any real sense and my interest has allways been in the attitutde of the arguement, the content is most often irrelevant.

Nothing causes evolutionists to question univeral descent?
On what basis do you make such a claim?
The TEs I've come to know on these forums alone are quite possibly the most inquisitive bunch I know. It was questioning their beliefs that led them to cross the floor to begin with, afterall. And many here, myself included, question universal descent frequently (as did Darwin). The bottom line is that, whether or not you like it or accept it, common descent is scientifically well-supported. From humans and monkeys, and placentals, and mammals, and tetrapods, and vertebrates, etc. Denying it without some substantial evidential support is fruitless, and unfortunately, as sfs and others have shown, your statements thus far are baseless (no pun intended).
And as rmwilliamsll has shown, evolution is indeed falsifiable. It just so happens that none of the exceptions he lists are seen in nature. What does this mean? It means that the modern ToE is so well delinated as to explain everything we DO see in nature. That's the sign of a good theory. Unfortunately, I know of NO good creationist theory that does the same.

mark kennedy · Nov 20, 2006

Mallon said:
8 pages of you debating the details of primate genetics and now you say it's not about genetics. Sorry if I don't believe you.

It is a great deal more then 8 pages, this has been going on for at least a year. You can believe whatever you think is right but I'm telling you this is about philosophy and the actual science is a forgone conclusion.

Nothing causes evolutionists to question univeral descent?
On what basis do you make such a claim?

Personal experience in literally thousands of exchanges I have yet to see an evolutionist question any aspect of TOE as natural history. Nor have they offered a basis for it being falsified unless it was allready conclusivly decided what the facts are. It's an a priori assumption and there is no real reason to support it being a conclusion.

The TEs I've come to know on these forums alone are quite possibly the most inquisitive bunch I know. It was questioning their beliefs that led them to cross the floor to begin with, afterall. And many here, myself included, question universal descent frequently (as did Darwin).

Hold on a minute because I am not a newbie. TEs are the most vocal proponents for evolution on these boards. If they are questioning any of the major tenants for common ancestry I have yet to see the slightest glimmer of it. You might know something about TEs I don't but there is no indication that Darwin seriously questioned common ancestry. He accepted without question the natural theology of Paley and others, after developing his theory based on natural selection he abandoned it entirely and there was no real questioning involved.

You don't believe this has nothing to do with genetics and I don't happen to believe Darwin and the TEs are open minded. I don't see Darwinians or TEs asking any of the hard questions about human ancestry. They simply dismiss objections to the common ancestry and claim fundamental errors on the part of creationists. It allways goes back to the fundamentals, I have never seen an exception.

The bottom line is that, whether or not you like it or accept it, common descent is scientifically well-supported. From humans and monkeys, and placentals, and mammals, and tetrapods, and vertebrates, etc. Denying it without some substantial evidential support is fruitless, and unfortunately, as sfs and others have shown, your statements thus far are baseless (no pun intended).

That is exactly what drew me to these debates in the first place, the catagorical rejection of creatoinism. It would have been a passing curiosity had differences been discussed and left at that. Again and again the conclusion is that creatoinism, mine or anybodys version, is baseless. It does not matter what the problem is like the evolution of the human brian. Creationism is unscientific so it must be due to incompetance or willfull deception. This is not an open exchange, this is argueing against a foregone conclusion.

It just doesn't matter if Chimpanzees and humans share 98% of their DNA, 95% of their DNA or even 90% of their DNA. Nothing changes, not even the estimated mutation rate. There are no hard questions when the divergance jumps by 100 million nucleotides, no problem with an unprecedented expansion and development of the most highly conserved organ in creation.

No, there is just the constant insistance that evolution is true and creationism is false. If you guys are asking any questions, let alone the tough one you are not doing it on these boards.

Darwin said that the development of something as complicated as the eye by natural selection seemed unlikely. If Charles Darwin himself question natural selection as an explanation for the eye then why can't TEs question the divergence of our DNA and the development of the human brain from that of apes?

I say they have embraced the a priori assumption on common ancestry as universally applied to natural history. That is the fundamental flaw evolutionists see in creationism, not how living systems work and reproduce. They are preaching a gospel of universal naturalistic causation and calling it science.

Had you or any of the TEs dismissed my objections as a difference of opinion I would have left it at that. But no, you guys have to prove that the creationist is wrong at the most fundamental level, never conceding a single point. That is not genetics or biology, that is pure undiluted attitude.

And as rmwilliamsll has shown, evolution is indeed falsifiable. It just so happens that none of the exceptions he lists are seen in nature. What does this mean? It means that the modern ToE is so well delinated as to explain everything we DO see in nature. That's the sign of a good theory. Unfortunately, I know of NO good creationist theory that does the same.

No sir, it is not falsifiable, there has not been one propositional basis for falsification. What you get is syllogistic logic which is a rethorical device where no matter how the question is answered it will give the same conclusion. Modern TOE is a part of a much larger philosophy that is virtually identical to aristotlean philosophy and Medieval Rome. The status quo was maintained then with rethorical dogma and it's being maintained now but the same devices. Sure the particulars have changed but the pro status quo still demands unwaivering affirmation. TOE is not a theory, it is an a priori self existing fact supported by rethorical device, not empirical testing.

mark kennedy · Nov 20, 2006

rmwilliamsll said:
Nature will differ to the Creator since there is not providential agency that can produce something as complicated as the human brian.

often i think that the divide between YECism and OECism is exactly this. YECists are most often charismatic and see God's creative hand everywhere. The idea being that the creative, the supernatural, the miraculous, the spectacular is more in keeping with the nature of God and His interaction with creation. Where most OECist are more providentially orientated, that God works through ordinary means of grace, that education and preaching change people without spectular, easy to see results. This orientation is a fundamental difference in how people see God's action in the world and marks a real divide in the conservative Church. Alignment of YECism with premil and OEC with amil just goes along this fissure.

Most often the only difference I see between OEC and YEC is when the earth itself was created, biological creation is not questioned. I don't know, maybe you use the term differently but the question of the actual age of the earth does not interest me in the slightest.

I don't know that I am charasmatic but I do get a lot of my theology from Pentecostalism, actually from Weslyan Methodism. I do see God was working miracles throughout history and being active in the world in a profoundly supernatural way. I'm not really into the faith healer or snake handling stuff but everytime a person becomes a new creature in Christ, it's a miracle that dwarfs the feeding the 5,000.

btw, providence is as much God's hand in the world as creative miraculous activity, just because God chooses to do things with natural and secondary means does not mean He is inactive or not really involved. Providential care is certainly sufficent to explain the rise of humanity from proto-apes.

Frankly, no it's not sufficent at least not by normative mechainisms. It sounds like the whole thing is cut and dried for you but just consider one thing. Genetic mutations have occured in genes involved in the development of the human brain. They result in Parkinsons, Alzheimers, Schizophrenia, Epilepsy and the like. What is important to realize is that it is impossible for the human brain to make it's unprecedented expansion apart from dramatic changes in the genes,(protein coding, regulatory..etc.). The question come up what genetic mechanism provided this and the answers are not forthcoming. Natural Selection acting on beneficial effects is worthless since there are none observed or demonstrated.

When it comes to the evolution of the human brain evolution begs to question of proof on it's hands and knees. But let's just pretend this problem does not exist and any question raised is an argument from incredulity or something worse.

Evolution as natural history is psuedo-science

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