SFT: Is Genetic Diversity a Problem for a Literal Adam and Eve? Joshua Swamidass and Biologos Debunked

Actually I challenge anybody to go back and read through this comment thread to see just who is dodging 99% of everything. You guys ignore most of what is said and then cherry pick one small detail that you THINK you can address while ignoring all the other empical data presented. I have yet to see any response to any of the data and facts I have presented in both this thread and the video thread.

Soon as you explain how the single mating pairs of unclean “kinds” on the Ark managed to have all the supposed super-heterozygosity, as well as explaining how the single mating pairs had all the genetic information for the multiple different species (dog “kind” --> domestic dogs, wolves, coyotes, dingos, etc.) hyper-evolved into.

As you are fond of saying on your YouTube comments, will you “man up” and answer here? :slightly_smiling_face:

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You’ve yet to make any concrete arguments in this thread. You ignored the very first 2 points (well, a question and a point) I made in response to you. Not exactly an auspicious start to your PS career.

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@SFT let me assure you that YouTube comments are not how scientific issues are hashed out. I did not even attempt to explain the issues in any detail. I noted also that you didn’t seem to understand that little I did right,

You are certainly welcome to disagree with me, really you are. But that comment thread does not make your case.

For you to make your case, you’d have to start by demonstrating comprehension of some key concepts here. Even if you disagree with them, we’d have to know you understand what we are saying. Only then would any critique be possible,

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Nothing in that comment provided empirical evidence that immune genes are mutating faster in living human populations that the rest of the genome. Here’s a hint: look at studies documenting de novo mutations in pedigrees, and show that immune genes mutate more than the rest of the genome,

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If you want to understand the TMR4A work, I suggest you start here and go in without any preconceived ideas, because I think at the moment you have some misunderstandings that need correcting.

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@SFT

Yes… that would be the assumption for a YEC to make. That is granted.

But you can’t get from 1 mated pair (or 3+ mated pairs if you assume a global flood) and arrive at the genetic diversity displayed in the billions of humans alive today – unless someone has some kind of x-ray machine broadcasting in the maternity huts of humans all around the world!

It’s not enough time, or the bottleneck is too narrow, or both!

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I don’t think you question and objection takes into consideration the proper definition of an allele. An allele should be defined in terms of genetic position. These are all objections that have been answered. This is probably why Dr. Jeanson responds to those who wish to publish their responses in the AIG journal for accountability purposes as compared to endless blog wars. Like him, I do not have the patience to answer the same questions over and over again.

On pages 34-39 in my book cited in previous comments in this thread, I address your objection in regard to alleles:

“If the differences are built in from the start, generating new species is easy. As a matter of fact, the numbers of species on the planet today are far better explained by the young earth creation model.

Before we conclude this chapter, I want to note that many critics of the front-loaded DNA diversity model have used an argument that reflects a poor understanding on how to best define allele. Dr. Nathaniel Jeanson has had an extensive written debate with Dr. Stefan Frello that can be found on the Answers In Genesis website in the Answers Research Journal section. Dr. Stefan Frello has also chosen to utilize this poor argument against the created heterozygosity hypothesis. Dr. Nathaniel Jeanson addresses the argument by first pointing to where Dr. Frello has accurately represented his model:

“Let’s start by identifying where Frello’s claims and representations of Replacing Darwin are correct. In these paragraphs, he clearly and unambiguously states the genetic compartment to which he refers—the nucleus (“15 nuclear genes”). He also correctly identified my explanation for the origin of the DNA differences in this nuclear DNA compartment as, “the majority of genetic variation within families is due to original created variation.”

But then Frello’s argument commits a common genetic mistake. In his endnote, he (correctly) defines an allele as “One of two or more versions of a particular DNA position” (emphasis mine). But then he contradicts himself in the paragraph above: “a maximum of four alleles 1 of each gene could be present in this original pair” (emphasis mine). By definition, genes consist of more than one DNA position. So which is it? Is an allele a version of a particular DNA position? Or a version of a gene that contains hundreds to thousands of DNA positions? Frello can’t have it both ways.” (Most italics in this book have been added by this author)

Next, Dr. Nathaniel Jeanson points out that this argument that Dr. Stefan Frello has employed has been addressed in a prior published paper. This again goes to show that these militant critics of biblical creation fail to read the relevant literature before making an argument.

“In fact, his argument rests on his (erroneous) adoption of the second definition—that alleles are different versions of genes. Under this definition, he misrepresents my explanation for nuclear DNA differences. In fact, in one of my published papers (Jeanson and Lisle 2016) that I refer to at least 15 times in Replacing Darwin, I explicitly addressed Frello’s error:

If an allele is defined in terms of a gene unit, then generating “allelic” diversity by mutating just one gene per mutational event produces little diversity. Instead, if an allele is defined as a single genomic position, independent of its relationship to a gene, then enormous allelic diversity can be generated by mutation . . . As an aside, allelic diversity need not arise via mutation. Again, if we use the genomic position definition of an allele rather than the gene unit definition, other mechanisms besides mutation can generate allelic diversity. For example, a single gene typically spans thousands of nucleotides, and SNVs [SNVs = Single Nucleotide Variants] might be distributed throughout the gene—for example, at 90 of the nucleotides within the gene. If we allow for the genomic position definition of alleles, every single one of these 90 SNVs may have existed in a heterozygous state in each of the individuals of the pairs brought on board the Ark.

Expanding this single gene example across the entire genome reveals a tremendous potential for allelic diversity on the Ark. In just two diploid individuals, four genome copies exist. Since only four DNA base-pairs exist, virtually every possible genomic position allele (i.e., far more than 4–28 gene unit alleles) could have been present at the time of the Flood, if the individuals were heterozygous. (Jeanson and Lisle 2016, 99) [emphases in original paper]

In other words, every single one of the nuclear DNA differences in Frello’s graph could have existed in a heterozygous state in the felid ancestor on board the Ark—because my model defines alleles in terms of DNA position, not individual genes. Thus, Frello’s (apparent) claim—that a maximum of four versions of each gene could be present in this original pair—is incorrect.

Conversely, my model has no need for the mutation rates that Frello claims; in fact, in theory, it has no need for mutations in this example at all. Frello has made a common genetic error, which nullifies his conclusion.” Source: Jeanson, Nathaniel T. 2018. “Response to ‘No Replacement of Darwin: A Review of Replacing Darwin—The New Origin of Species’.” Answers Research Journal 11: 63–83.

I encourage the reader to analyze both sides of the written exchange between Dr. Stefan Frello and Dr. Nathaniel Jeanson. I genuinely believe it is a prime example as to why the evolutionary community is only capable of grasping at straws. As I have stated before, the critics of biblical creation have nothing left to offer. “

No they haven’t been answered. All you do is keep repeating the same unsupported assertion “genetic diversity was BUILT IN during Creation”. That’s the thing you need to support with positive evidence, not just keep regurgitating “read this Creationist book!”.

Why not just admit your claim doesn’t fit the Ark scenario instead of all this silly tap dancing and question dodging?

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I was referring to the comments in regard to the molecular clock data found in the non-combining/uni-parentally-inherhited DNA. This is where us young earth creationists look to first since the mechanism for the origin of DNA differences in these DNA compartments (mtDNA and Y chromosome) are namely mutations. With the autosomes, we are looking at a combination of sorting of the created DNA differences and also mutations. This makes things a little more messy and complicated. This is also why Dr. Jeanson is having fascinating results in his active research program in regard to the mtDNA and the Y chromosome. I feel you simply hand waved the molecular clock data away in the comment section without addressing anything. And that is fine. I am not going to reiterate it all here. Luckily, you linked the video at the top of this post and I pinned the comment thread and therefore, people can read it for themselves. I think it is rather obvious that the population genetics issues are resolved with what I have stated above, created nuclear heterozygosity, small population followed by rapid and exponential population growth with any declines in population size being short-lived. Thanks and God bless.

LOL I think we can all see who is the one dodging.

Once again, here you go:

Before we conclude this chapter, I want to note that many critics of the front-loaded DNA diversity model have used an argument that reflects a poor understanding on how to best define allele. Dr. Nathaniel Jeanson has had an extensive written debate with Dr. Stefan Frello that can be found on the Answers In Genesis website in the Answers Research Journal section. Dr. Stefan Frello has also chosen to utilize this poor argument against the created heterozygosity hypothesis. Dr. Nathaniel Jeanson addresses the argument by first pointing to where Dr. Frello has accurately represented his model:

“Let’s start by identifying where Frello’s claims and representations of Replacing Darwin are correct. In these paragraphs, he clearly and unambiguously states the genetic compartment to which he refers—the nucleus (“15 nuclear genes”). He also correctly identified my explanation for the origin of the DNA differences in this nuclear DNA compartment as, “the majority of genetic variation within families is due to original created variation.”

But then Frello’s argument commits a common genetic mistake. In his endnote, he (correctly) defines an allele as “One of two or more versions of a particular DNA position” (emphasis mine). But then he contradicts himself in the paragraph above: “a maximum of four alleles 1 of each gene could be present in this original pair” (emphasis mine). By definition, genes consist of more than one DNA position. So which is it? Is an allele a version of a particular DNA position? Or a version of a gene that contains hundreds to thousands of DNA positions? Frello can’t have it both ways.” (Most italics in this book have been added by this author)

Next, Dr. Nathaniel Jeanson points out that this argument that Dr. Stefan Frello has employed has been addressed in a prior published paper. This again goes to show that these militant critics of biblical creation fail to read the relevant literature before making an argument.

“In fact, his argument rests on his (erroneous) adoption of the second definition—that alleles are different versions of genes. Under this definition, he misrepresents my explanation for nuclear DNA differences. In fact, in one of my published papers (Jeanson and Lisle 2016) that I refer to at least 15 times in Replacing Darwin, I explicitly addressed Frello’s error:

If an allele is defined in terms of a gene unit, then generating “allelic” diversity by mutating just one gene per mutational event produces little diversity. Instead, if an allele is defined as a single genomic position, independent of its relationship to a gene, then enormous allelic diversity can be generated by mutation . . . As an aside, allelic diversity need not arise via mutation. Again, if we use the genomic position definition of an allele rather than the gene unit definition, other mechanisms besides mutation can generate allelic diversity. For example, a single gene typically spans thousands of nucleotides, and SNVs [SNVs = Single Nucleotide Variants] might be distributed throughout the gene—for example, at 90 of the nucleotides within the gene. If we allow for the genomic position definition of alleles, every single one of these 90 SNVs may have existed in a heterozygous state in each of the individuals of the pairs brought on board the Ark.

Expanding this single gene example across the entire genome reveals a tremendous potential for allelic diversity on the Ark. In just two diploid individuals, four genome copies exist. Since only four DNA base-pairs exist, virtually every possible genomic position allele (i.e., far more than 4–28 gene unit alleles) could have been present at the time of the Flood, if the individuals were heterozygous. (Jeanson and Lisle 2016, 99) [emphases in original paper]

In other words, every single one of the nuclear DNA differences in Frello’s graph could have existed in a heterozygous state in the felid ancestor on board the Ark—because my model defines alleles in terms of DNA position, not individual genes. Thus, Frello’s (apparent) claim—that a maximum of four versions of each gene could be present in this original pair—is incorrect.

Conversely, my model has no need for the mutation rates that Frello claims; in fact, in theory, it has no need for mutations in this example at all. Frello has made a common genetic error, which nullifies his conclusion.” Source: Jeanson, Nathaniel T. 2018. “Response to ‘No Replacement of Darwin: A Review of Replacing Darwin—The New Origin of Species’.” Answers Research Journal 11: 63–83.

I encourage the reader to analyze both sides of the written exchange between Dr. Stefan Frello and Dr. Nathaniel Jeanson. I genuinely believe it is a prime example as to why the evolutionary community is only capable of grasping at straws. As I have stated before, the critics of biblical creation have nothing left to offer. “

That is directly refuted by the actual genetic data. Remember it’s not enough for you to hand-wave human DNA. You need to explain the genetic diversity of ALL species which supposedly arose from the single pairs of “kinds” on the Ark only 4500 years ago.

Here’s an mt genomic analysis of a hominin found in Spain and dating to 300,000 years ago. It confirmed this species is ancestral to both the Neanderthals, Denisovans, and extant humans.

A mitochondrial genome sequence of a hominin from Sima de los Huesos

Your explanation is…?

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Once again we see the questions being dodged and the same regurgitated Creationist non-answer offered instead. I detect a pattern here… :slightly_smiling_face:

And those sequenced have been from all over the planet including the Americas, Australia, East Asia, and Africa. We now know human migration from all over Europe, Asia and the Americas. Remember GAE is based on genealogy not genomics. GAE is a theological construct and is purposely made to be invisible to markers in ancient DNA, human history, and all scientific inquiry. Therefore, anytime anyone uses science or even probability modeling to analyze GAE, they will far short. GAE is a miracle by God, therefore has a probability of 0 of have happened when investigated by science.

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@sft

Oh for goodness sake…

Break out a box of LEGO’s and make Adam’s alleles and Eve’s alleles.

If you “front load” dozens of alleles into either or both lego strands … where do they disappear to in subsequent generations? In the modern generation … we find NOBODY with dozens and dozens of inactive alleles as you describe.

A string of mutations to delete “used alleles” is just as unlikely as a string of mutations to ADD alleles.

Your “mental model” does not correspond to physical reality.

Hi all, just want to chime in since I’m the aforementioned “Dr. Dan”. I’m an evolutionary biologist; my degree is in molecular genetics and microbiology and my thesis work was on viral evolution.

I too have asked SFT these questions and have not gotten answers any more satisfactory than you see here.

This seems like a really nice place for discussions, going to try to stick around.

Cheers.

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In theory there is a maximum possible four nucleotides at each locus, and Adam/Eve between them could have all four since they have a total of four genomes. Thus all existing alleles can be generated by recombination. This doesn’t work for the Y chromosome or mDNA, obviously, but that’s a technical detail that can be ignored.

This also ‘works’ for the mated pairs on the ark.

It may even be a confirmed biblical prediction, since we didn’t know until recently how many different nucleotides were used in DNA/RNA. That there are four nucleotides (C, G, A, U/T) and four copies of the human genome in a mated pair fits perfectly. If DNA or RNA had three base-pair options, or organisms only carried one copy of the genome, that would have refuted biblical genetics.

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In theory, yes, intragenic recombination could potentially explain a great deal of diversity, given four initial alleles that are sufficiently different. This is basically what Jeanson argues in “Replacing Darwin”, as far as I can tell. But, correct me if I’m wrong, intragenic recombination is relatively uncommon, compared to recombination events with break points in intergenic regions, and intraexonic recombination is rarer still.

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Exactly, and this is what @swamidass has shown in his TMR4A work - accounting for recombination rates and locations, human genetic diversity coalesces to 4 alleles around 500,000 years ago, not 6000.

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Not indels, duplications, inversions, and such, though.

Doesn’t work for the X chromosome either. And of course anything can be ignored, if you really want to ignore it.

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