Genetics and Adam and Eve

[amortalman]

I began to wonder about this after reading a post by rikuoamero wherein he made mention of it. It sounded like a worthy subject to explore.

So the question for debate is:

Does genetics disprove a literal Adam and Eve?

[alexxcJRO]

Math is hard. I understand.

Do the math it is all there.
Genet said it not me it is all in his paper.

Sir you lied before. I don’t believe anything you say.

Q: What if you lied again?!

One has to prove his claims, not the opponent.
So please provide the evidence.

I did post 55

You said this: “The lost of mutation is not the problem There are more mutations lost in heteroplastic mutations than there are in homoplastic mutations. The question is not the lost of mutations but which method is best at getting around the lost mutations. “

Q: "mutation lost in mutation" ?????

That does not make any sense. You are just babbling gibberish.

Sir the number 63(of variants) goes out the window under scrutiny.
The 3 outlined scenarios show Jeanson could have counted a somatic mutation as germline mutation.
He cannot be sure that any of that 63 variants represents a genuine germline mutation.

[alexxcJRO]

[Replying to post 57 by alexxcJRO]

Of course is true that the “by definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the scriptural record.� is a unfalsifiable claim.

And your joke of a scientist believes irrational things. Cool

Its still true.

Its still true that “by definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the scriptural record.� is an unfalsifiable claim.

Its still true that your joke of a scientist believes irrational things.

[DrNoGods]

[Replying to post 52 by EarthScienceguy]

The naturalist still has his "theology" veil it in anything you want to veil it in but it is still theology because it is based on a belief system not fact.

You obviously cannot distinguish between actual science, which is based on observations, measurements, experiments, etc., and religious-based pseudoscience which is based on false assumptions, god did this or that, etc.

There is no faith involved in the understanding of how chemical reactions proceed, how gravity works, how the fundamentals of mathematics, physics, chemistry, biology, etc. work. It is all based on observations and evidence that is repeatable and consistent.

The fact that you don't understand this, at all (clearly!), and think that people like Russell Humphreys can produce valid "theories" based on imaginary assumptions and god-did-it prerequisites just because of some purely coincidental numbers, is just more proof that you can't comprehend even the most basic and simple premises on which actual science is based.

The idea here is to debate real science and religion, but you fail to appreciate the difference between real science and creationist nonsense. Calling it creation "science" doesn't make it actual science of the type that is recognized around the world as the pursuit of understanding of the natural world. All you are doing is trying to support the biblical narrative (and preach) using not science, but bad pseudoscience. It is a standard creationist's tactic to claim that real science requires faith, which is a total cop-out resulting from the complete failure of creationist "science" to explain anything at all, and a complete misunderstanding of how real science works (ie. that is is based on observations, evidence, etc. ... not faith).

[DrNoGods]

[Replying to post 54 by EarthScienceguy]

Yes it does matter. If fact using Humphrey's equation you too can make a prediction. What it the magnetic field around Kepler 186f? We can calculate it using Humphrey's equation and his assumption of 6000 years.

You just don't get it do you? Humphreys' predictions are meaningless because his "theory" requires a god-did-it prerequisite (alignment of all the H-atom nuclear spins). That invalidates anything his "theory" predicts. Period. It is irrelevant if he happens to coincidentally land on a few close numbers. But you can't seem to understand this basic (fatal) problem.

Genetic theory does not say that.

What? Who said anything about genetic theory? The topic was Noah's flood and the structure of the Earth, and you reply with "genetic theory does not say that." Focus.

[EarthScienceguy]

[Replying to post 60 by alexxcJRO]

Sir the number 63(of variants) goes out the window under scrutiny.
The 3 outlined scenarios show Jeanson could have counted a somatic mutation as germline mutation.
He cannot be sure that any of that 63 variants represents a genuine germline mutation.

What would you suggest using

[EarthScienceguy]

[Replying to alexxcJRO]

You said this: “The lost of mutation is not the problem There are more mutations lost in heteroplastic mutations than there are in homoplastic mutations. The question is not the lost of mutations but which method is best at getting around the lost mutations. “

Q: "mutation lost in mutation" ?????

Yes mutations lost to selections processes.

Man, I hate paper written by biologist. But I finally think I understand what Genet did. Maybe. Wow, I did not realize he wrote so many papers on this subject. Doesn't mean I think he is correct but it does mean he can spin a tale really well.

1st of all he did not use 2000 mtDNA genomes for his paper he used 193.

We used a set of 193 human complete mtDNA sequences selected from the previous tree to represent all of the main branches both within and outside Africa, with two chimpanzee sequences and a bonobo sequence, to construct a maximum likelihood (ML) tree and estimate the rate of the mtDNA clock.

He also did not use all of the mtDNA data.

we used only mutations that were older than an overall � = 4, to avoid the proposed preponderance of weakly deleterious mutations in young branches, and younger than � = 18 (broadly corresponding to the age in mutations of macrohaplogroups M and N), to avoid a possible high degree of saturation in the deeper parts of the tree. For synonymous mutations, we used mutations that were younger than � = 18, because selection should not be an issue for these. We performed all of the simulations for each type of mutation at least six times, until the shape of the curve did not change with further analyses.

(we excluded position 16519, the fastest of all, from the main analyses),

Now whether or not that comes up to 7% I don't know and don't care.

3rd
If one would examine figure 3 in Genet's paper he makes it makes it abundantly clear that everything before position 4 had many synonymous mutations. Those after p= 18 had few synonymous mutations.

Sir the number 63(of variants) goes out the window under scrutiny.
The 3 outlined scenarios show Jeanson could have counted a somatic mutation as germline mutation.
He cannot be sure that any of that 63 variants represents a genuine germline mutation

What makes Genet's calculation valid you are are not accepting Jeanson's as valid. Genet has many more of his mutations selected out. So many that he could only use part of his data. This is a non issue. Otherwise you would also have to declare Genet's work as incorrect also.


4. His calculation nucleotides per year is very unclear. If you have an insight let me know. He could have divided .476 his ratio by the total number of nucleotides in his 2000+ sample. But he already said that he only used those between p-4 to p-18.

But if he did use the .476 it was at the cost of not being allowing for any values higher than what he calculated. His calculation is more than unclear. Oh for physics papers again.


Last edited by alexxcJRO on Tue Apr 16, 2019 10:29 am; edited 1 time in total

[EarthScienceguy]

[Replying to alexxcJRO]

1st of all Genet did not use 2000 mtDNA genomes for his paper he used 193.

We used a set of 193 human complete mtDNA sequences selected from the previous tree to represent all of the main branches both within and outside Africa, with two chimpanzee sequences and a bonobo sequence, to construct a maximum likelihood (ML) tree and estimate the rate of the mtDNA clock.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694979/#

He also did not use all of the mtDNA data.

we used only mutations that were older than an overall � = 4, to avoid the proposed preponderance of weakly deleterious mutations in young branches, and younger than � = 18 (broadly corresponding to the age in mutations of macrohaplogroups M and N), to avoid a possible high degree of saturation in the deeper parts of the tree. For synonymous mutations, we used mutations that were younger than � = 18, because selection should not be an issue for these. We performed all of the simulations for each type of mutation at least six times, until the shape of the curve did not change with further analyses. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694979/#

(we excluded position 16519, the fastest of all, from the main analyses),

Now whether or not that comes up to 7% I don't know and don't care.

2rd
If one would examine figure 3 in Genet's paper he makes it makes it abundantly clear that everything before position p= 4 had many synonymous mutations. Those after p= 18 had few synonymous mutations.

Sir the number 63(of variants) goes out the window under scrutiny.
The 3 outlined scenarios show Jeanson could have counted a somatic mutation as germline mutation.
He cannot be sure that any of that 63 variants represents a genuine germline mutation

Question: What makes Genet's calculation valid and Jeanson's not, when Genet's somatic mutation loss many more mutations to section than Jeanon's. Genet's somatic mutations had so many mutations that he could only use part of his data. This is a non issue? If you are trying to declare Jeanon's work invalid because mutations lost to selection. Then Genet's work would have to be declared invalid also.


3. The real issue between these two papers is not how many mutations there are but how these mutations are connected to time.

Jeanson calculated his mutation rate the following way.

(63 mutations)/(398 the number of pedigrees examined x 16,596 number base pairs per pedigree) = 9.55 x 10-6 mutations /base pairs * generation
(9.55 x 10-6 mutations/ base pairs * generation) x 16596 base pairs = 0.158 mutations /generation
(0.158 mutations / generation) x (1 generation/25.5 years) = 6.62 x 10-3 mutations / year.
63 mutations / 2x(6.62 x 10-3 mutations) / year = 4758 years.

Jeanson could have used Genet’s numbers but it really does not help.
Genet said that he had a total of 10,683 substitutions.
“There were, in total, 10,683 substitutions throughout the tree.�
He also said that he used only 193.
“We used a set of 193 human complete mtDNA sequences selected from the previous tree to represent all of the main branches both within and outside Africa�
Calculating time using these numbers. Genet has already said that he has not used all of the genome. So this estimate would be high.
10683 / (193 x 16596) = 3.33 x 10-3 mutations / base pairs *generation
(3.33 x 10-3 mutations / base pairs * generations) x 16596 base pairs = 55.4 mutations / generation
(55.4 mutations / generation) x ( 1 generation / 25.5 years) = 2.17 mutations / year
10683/ 2(2.17) = 2461 years.


The maximum possible number of years that his numbers could produce.
10683 substitutions / (2196 pedigrees x 16596 base pairs) = 2.93 x 10-4 substitutions / generation * base pairs
(2.93 x 10-4 substitutions/generations*base pairs) x 16596 base pairs = 4.86 substitutions/generations
(4.86 substitutions / generations) x (1 generation / 25.5 years) = 0.191 substitutions / year
mtDNA = 2 rate x time
10683 substitutions/2 (.191) = 27965 years
27965 years is a far cry of the 180,000 years needed for evolutionary theory.

In Genet’s 2009 paper, he makes it very unclear on how he arrived at a mutation rate of 1.665 x 10-8 substitutions / year.

It is at this point that Genet’s paper through me off because I assumed he was using a pedigree based system like Jeanson when he was using a phylogeny based system. Genet’s conversion to time did not come from using generations but from using the phylogenetic tree that he generated.

Brenna M. Henn Christopher R. Gignoux Marcus W. Feldman Joanna L. Mountain describe how the phylogeny based mutation rate is calculated in their 2008 paper "Characterizing the Time Dependency of Human Mitochondrial DNA Mutation Rate Estimates". https://watermark.silverchair.com/msn24 ... GFCVkTb2V3

“Phylogeny-based mutation rates are estimated by first constructing either a gene genealogy or a species phylogeny. In the latter case, one then calibrates the species split with external paleontological evidence. The number of mutations between two groups is subsequently computed, either by averaging the number of differences between species or by taking two sequences with the greatest number of differences. The number of mutations between two species lineages is then divided by the externally derived divergence date. This method has been applied to phylogenetic mutation rates obtained by comparing modern human and chimpanzee mtDNA sequences (Ward et al. 1991; Tamura and Nei 1993; Horai et al. 1995).�

A phylogeny based system cannot falsify Jeanson’s work because it is based not on the genome but on archeology.

4. The debate is not even the 5-6 thousand date that Jeanson came up with. This is a well known separation in predictions between the pedigree based and phylogeny-based estimates. That occurs at about 5000 years ago.

�Genealogy-based rate estimates between 2,500 and 5,000 years ago are indistinguishable from pedigree-based mutation rate estimate. This remains true across different haplogroups and populations from vastly different geographic locations, for example, Canary Islands versus Samoa.
The time period between 5,000 and ;15,000 years ago represents both a break in our data set and a sudden decline in estimated mutation rate�

https://watermark.silverchair.com/msn24 ... GFCVkTb2V3

In conclusion.

I understand that naturalist are going to describe phylogeny-based systems is the accurate system because it matches up with archaeology. But this would be circular reasoning because archeology was used to create the mutation rate.

It is indisputable that pedigree-based mutation rate estimates, all give very young dates that fall right in line with Young Earth Theory. This is the reason for the less than straight forward approach that Genet has in his 2009 paper when he calculates his mutation rate.

Thanks, alexxcJRO it was a great discussion and it gave me another paper to submit for publication also. I can put your name on it if you wish since your input did help me write it. Mr. AlexxcJRO will be the talk of young earth creationist circles. I will also be publishing this information (probably not in this form.) on my other platforms also. Just let me know if you want your name on the paper I am going to write. Mr. AlexxcJRO could be the next Ken Ham maybe.

Thanks again. And let me know yes or no.

[EarthScienceguy]

[Replying to post 63 by DrNoGods]

You just don't get it do you? Humphreys' predictions are meaningless because his "theory" requires a god-did-it prerequisite (alignment of all the H-atom nuclear spins). That invalidates anything his "theory" predicts. Period. It is irrelevant if he happens to coincidentally land on a few close numbers. But you can't seem to understand this basic (fatal) problem.

No, because you still have not explained why his numbers were close, more than one time. Out to the millions of values out there why were his correct and naturalist wrong.

Now what a good naturalist would do is make up a naturalistic explanation of how the magnetic field could have been generated say like during maybe "inflation". There you go I just gave you a million dollar idea and your name in the history books. And all I ask is that you put my name "earthscienceguy" in the contribution section and maybe a little kick back.

Quote:
Genetic theory does not say that.

Oh yes it does all pedigree based estimations say this.

What? Who said anything about genetic theory? The topic was Noah's flood and the structure of the Earth, and you reply with "genetic theory does not say that." Focus.

Wow did you forget what the above quote was referring to 1500 years before Noah's flood was creation. "that what genetic theory says."

[DrNoGods]

[Replying to post 65 by EarthScienceguy]

No, because you still have not explained why his numbers were close, more than one time. Out to the millions of values out there why were his correct and naturalist wrong.

And you still don't understand why the required initial condition "god aligned all of the H atom nuclear spins" invalidates virtually anything that may come after it. The fact that you don't understand this says everything about your lack of understanding of how real science works.

But I can see in your post above to allexxJRO that you play entirely in the amateur ranks. Where are you going to "publish" your "work"? On your own website, or some creationist website or publication? Certainly no real science journal would even send it out for review or consider wasting time on anything that requires the biblical creation myth to be accepted as reality. You really should remove the word "science" from your handle ... the nonsense you are trying to sell has virtually no relationship to actual science.

[alexxcJRO]

1st of all Genet did not use 2000 mtDNA genomes for his paper he used 193.

So funny how you are changing your claims. )

Sir you said: “All of Am J Hum Genet 2000 mtDNA were generated by a computer program they were not actually mapped from actual individuals. They are made up. “

The papers says: "We compiled a database containing published complete mtDNA sequences from NCBI with the Geneious software. These included the complete mtDNA sequences from several papers6–9,11–25,41–52 and several deposited by Family Tree.
...
A list of the published complete mtDNA genomes used is shown in Table S1, available online. A total of 2196 complete mitochondrial genomes were used in the final analyses.
For comparative and calibration purposes, we used two sequences of Pan troglodytes,57,58 one of Pan paniscus,58 and two of Gorilla.58,59 Additionally, all of the available complete mtDNA genomes from primates were retrieved from NCBI, again with the Geneious software. A list is shown in Table S2. We later included the complete mtDNA sequence of the Neanderthal for comparison.60
...
We constructed phylogenetic trees by using the reduced-median algorithm61 of the Network 4 software"
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694979/#


You said fake/generated 2000 mtDNA genomes(not from real individuals) and the paper says he used 2000 mtDNA complete genomes(from real individuals) which were retrieved from NCBI.

Therefore we can conclusively say that you lied.

He also did not use all of the mtDNA data.


Quote:
we used only mutations that were older than an overall � = 4, to avoid the proposed preponderance of weakly deleterious mutations in young branches, and younger than � = 18 (broadly corresponding to the age in mutations of macrohaplogroups M and N), to avoid a possible high degree of saturation in the deeper parts of the tree. For synonymous mutations, we used mutations that were younger than � = 18, because selection should not be an issue for these. We performed all of the simulations for each type of mutation at least six times, until the shape of the curve did not change with further analyses. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694979/#




Quote:
(we excluded position 16519, the fastest of all, from the main analyses),


Now whether or not that comes up to 7% I don't know and don't care.

2rd
If one would examine figure 3 in Genet's paper he makes it makes it abundantly clear that everything before position p= 4 had many synonymous mutations. Those after p= 18 had few synonymous mutations.

You said: “The 2009 study only looked at 7% of the mitochondrial DNA genome�.

The paper said:
“A total of 2196 complete mitochondrial genomes were used in the final analyses.
…
“This relative mutation rate was calculated with mutations with relative ages lower than � = 18 (in order to avoid the African long branches, where saturation could be an issue) and older than � = 4 (in order to avoid the majority of the deleterious mutations in both control and coding regions). This ratio of coding-region mutations to control-region mutations yielded a value of 1.57.�
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694979/#

Sir not using mutations (>� = 18, to avoid the African long branches, where saturation could be an issue) and (< � = 4 to avoid the majority of the deleterious mutations in both control and coding regions) in their calculations does not equate they used “The 2009 study only looked at 7% of the mitochondrial DNA genome�.

While they did not used all of their mutations in their calculations because of good reasons that does not mean the “The 2009 study only looked at 7% of the mitochondrial DNA genome.�

While they did not select all mutations for their calculations, they looked at all the mtDNA genome before this selection. Therefore the claim:“The 2009 study only looked at 7% of the mitochondrial DNA genome.� is still false.

The lie is obvious.

Question: What makes Genet's calculation valid and Jeanson's not, when Genet's somatic mutation loss many more mutations to section than Jeanon's. Genet's somatic mutations had so many mutations that he could only use part of his data. This is a non issue? If you are trying to declare Jeanon's work invalid because mutations lost to selection. Then Genet's work would have to be declared invalid also.
(63 mutations)/(398 the number of pedigrees examined x 16,596 number base pairs per pedigree) = 9.55 x 10-6 mutations /base pairs * generation
(9.55 x 10-6 mutations/ base pairs * generation) x 16596 base pairs = 0.158 mutations /generation
(0.158 mutations / generation) x (1 generation/25.5 years) = 6.62 x 10-3 mutations / year.
63 mutations / 2x(6.62 x 10-3 mutations) / year = 4758 years.
It is at this point that Genet’s paper through me off because I assumed he was using a pedigree based system like Jeanson when he was using a phylogeny based system. Genet’s conversion to time did not come from using generations but from using the phylogenetic tree that he generated.
A phylogeny based system cannot falsify Jeanson’s work because it is based not on the genome but on archeology.

4. The debate is not even the 5-6 thousand date that Jeanson came up with. This is a well known separation in predictions between the pedigree based and phylogeny-based estimates. That occurs at about 5000 years ago.

I don’t know if it makes Genet’s work invalid.

And it’s irrelevant to my argument sir.

All I know it’s invalidates Jeanson’s number of 63 variations. All his calculation go out the window. Therefore his rate goes out the window. Sayonara. Asta la vista, bye bye. Ciao.

Again I say, I do not care what happens with Genet work whatsoever.
All I care is that it invalids Jeanson’s work.
The fact that it may negate Genet’s works does not make the objections against Jeanson’s work therefore invalid. That is non-sequitur.
I hope you know this.

Conclusion: My objections stand firm.