Tricks Theists Play (Part 1)

[Tristen]

1 hour ago, one.opinion said:

Low population size results in low diversity, and a popoluatikn size of 2 or 14 is indeed, a low population size.

“Low population size results in low diversity”

Bottlenecks certainly reduce genetic diversity, but whether the resulting diversity can be characterised as “low” is a matter of context. Individuals closer to the highly diverse ancestors would contain much higher genetic diversity than descendants arising through hundreds of successive generations including multiple rounds of environmental pressures filtering out unnecessary genes.

[one.opinion]

1 hour ago, Tristen said:

Bottlenecks certainly reduce genetic diversity, but whether the resulting diversity can be characterised as “low” is a matter of context.

Context is largely irrelevant when a bottleneck goes down to 2, 14, or 8 (in the case of humans). It doesn't matter what kind of diversity was present in the predecessors if only 2 individuals remain. In the case of canines, there would only be 4 possible versions of each gene, one on each homolog of the canid pair. There are obviously more than 4 variants in many genes in the canine gene pool. Consequently, mutation must have taken place in order to generate the additional variants. There is no way around this fact.

[Tristen]

42 minutes ago, one.opinion said:

Context is largely irrelevant when a bottleneck goes down to 2, 14, or 8 (in the case of humans). It doesn't matter what kind of diversity was present in the predecessors if only 2 individuals remain. In the case of canines, there would only be 4 possible versions of each gene, one on each homolog of the canid pair. There are obviously more than 4 variants in many genes in the canine gene pool. Consequently, mutation must have taken place in order to generate the additional variants. There is no way around this fact. 

There are four possible nucleotides for each single nucleotide locus on a chromosome, but a single gene can be comprised of thousands of nucleotides. So an individual can carry massive amounts of information in a single gene - and therefore massive potential for diversity. Then there's other complexities like the fact that there can be multiple copies of genes, and that genes can interact with other genes to influence phenotypes, and in eukaryotes, single genes can be spliced differently to make different products from the same genes, and that gene expression can be influenced by environmental factors and different protein and RNA transcription factors, and that genes can be turned on and off over generations etc. The system is so much more complex than you've imagined. And we're still discovering layers of complexity.

[one.opinion]

13 minutes ago, Tristen said:

There are four possible nucleotides for each single nucleotide locus on a chromosome, but a single gene can be comprised of thousands of nucleotides. So an individual can carry massive amounts of information in a single gene

Yes, but you are ignoring the fact that it is still one gene. And for the ark-exiting canids only 4 possible versions of each gene.

Agreed, there are certainly additional levels that complicate the actual expression of those alleles, but you are ignoring the obvious limitation of this degree of a bottleneck. The degree of genetic diversity we observe today COULD NOT have occurred without additional mutations.

This is largely a moot point anyway, since I am reasonably confident that you will admit that mutations did indeed take place, regardless of whether we can agree on their necessity.

[Tristen]

5 hours ago, one.opinion said:

Yes, but you are ignoring the fact that it is still one gene. And for the ark-exiting canids only 4 possible versions of each gene.

Agreed, there are certainly additional levels that complicate the actual expression of those alleles, but you are ignoring the obvious limitation of this degree of a bottleneck. The degree of genetic diversity we observe today COULD NOT have occurred without additional mutations.

This is largely a moot point anyway, since I am reasonably confident that you will admit that mutations did indeed take place, regardless of whether we can agree on their necessity.

Posted my first response to this hours ago - but for some reason, it didn't stick. So had to redo it.

 

"And for the ark-exiting canids only 4 possible versions of each gene"

I'm not sure how you come to this conclusion. The only level where there are only 4 possibilities is at the single nucleotide level. A single gene can be comprised of thousands of nucleotides. That leaves stupendous potential for variation in every single gene in every individual - regardless of any additional complexity.

 

"This is largely a moot point anyway, since I am reasonably confident that you will admit that mutations did indeed take place, regardless of whether we can agree on their necessity"

Of course I acknowledge that mutations occur. Whether or not mutations are necessary is relevant to your claim that my model is implausible because of the required mutation rates over such a 'short' period of time. But if diversity was designed into the created ancestors, then mutation rates are irrelevant to my model.

[JohnD]

Have you ever approached Ken Ham to debate?

 

 

[one.opinion]

5 hours ago, Tristen said:

Whether or not mutations are necessary is relevant to your claim that my model is implausible because of the required mutation rates over such a 'short' period of time.

Well ok...

5 hours ago, Tristen said:

I'm not sure how you come to this conclusion.

If there were two canids that exited the ark, and each canid was heterozygous for a particular gene, then there were 4 different versions of that gene remaining in the gene pool, one on each homologs of each surviving canid. For an edible kind, there would originally be 28 potential versions, but there would likely be some homozygosity that would reduced that number somewhat.

But back to canids, of course there would be the recombination that would occur between homologs during meiosis, but this is a form of a mutation since it is a “heritable change in DNA”. Additionally, the variety of phenotype that would result after the emergence of the canid pair would require significant mutation (whether directly in genes heavily influencing phenotype, or in modifying genes tweaking phenotype, or in regulatory genes that influence extent of expression of other genes).

Over the last several posts regarding the canids, I have not (yet) argued that the mutation rate was insufficient to produce the canid diversity we see today. What I have been attempting to argue against is the odd (and demonstrably false) notion that modern diversity could have arisen without mutation.

[Tristen]

9 hours ago, one.opinion said:

Well ok...

If there were two canids that exited the ark, and each canid was heterozygous for a particular gene, ...

“If there were two canids that exited the ark, and each canid was heterozygous for a particular gene”

Heterozygosity does not define the limit of genetic variation for a gene. Genetic variation is defined at the nucleotide level – so by how many permutations of 4 nucleotides are possible for the DNA-sequence length of the gene. Obviously, most of those permutations would be nonsense, but the topic at hand is the theoretical limits of genetic diversity. Even leaving aside the real-life complexity of gene interactions, that limit is certainly not restricted to 4 for every gene (in two individuals).

 

“of course there would be the recombination that would occur between homologs during meiosis, but this is a form of a mutation since it is a “heritable change in DNA””

That's a bit of a Wow!!! statement. If “mutation” includes “recombination” “during meiosis”, then mutations occur in the production of every gamete. I'd wager that exactly none of the mutation rate papers have factored recombination into their mutation rate equations.

 

“Additionally, the variety of phenotype that would result after the emergence of the canid pair would require significant mutation (whether directly in genes heavily influencing phenotype, or in modifying genes tweaking phenotype, or in regulatory genes that influence extent of expression of other genes)”

I don't know what this means. Recombinations would only be producing alternate versions of working genes. No modification-by-mutation required. If the new version provided less fitness than the other versions, it would ultimately be selected out of the population by environmental pressure.

 

“Over the last several posts regarding the canids, I have not (yet) argued that the mutation rate was insufficient to produce the canid diversity we see today. What I have been attempting to argue against is the odd (and demonstrably false) notion that modern diversity could have arisen without mutation”

You are trying to generate gotchas by confusing statements of potential with truth statements. According to my model, extant diversity “could have arisen without mutation”. That is a statement of theoretical potential. You can't claim a statement of potential to be “demonstrably false” unless you have proved it to be mathematically impossible. Now, if I was to claim that diversity necessarily happened “without mutation”, that would be a truth statement. But I only ever claimed that diversity doesn't require mutations, NOT that mutations have never contributed to diversity.

Unless I've misunderstood, you have been trying to argue that - to achieve the observed diversity from a starting population of two individuals, the mutation rates would have had to be sustained for thousands of years at an implausibly high rate – a rate which is not congruent with current observation. I argued that extant diversity doesn't require mutations if starting form a point of high diversity – so mutation rates are irrelevant to my model. I then used an example of a species whose radical diversity has only arisen over the past two-or-so centuries – where we know exactly how that diversity was attained. It was accomplished by taking ancestor dogs and breeding genes out of each lineage till only the desired characteristics remained. This extensive diversity was NOT accomplished by generating new characteristics by mutations. All of that diversity we see in dogs today already existed only a few centuries ago in the handful of ancestor breeds (i.e. genetically diverse mongrel breeds) from which the new breeds were bred.

 

[one.opinion]

I'm going to keep this post real short because you don't seem to be understand the reality of what you are claiming.

14 minutes ago, Tristen said:

Heterozygosity does not define the limit of genetic variation for a gene.

Not usually, no. But a bottleneck of two individuals would have their diversity limited to a maximum of four possible alleles at a particular gene. Is this true or false?

You also seem to be misunderstanding what I have been trying to do for days - I have been attempting to bring to a point of realization that mutations had to have occurred in order to result in today's observable genetic diversity.

22 minutes ago, Tristen said:

Unless I've misunderstood, you have been trying to argue that - to achieve the observed diversity from a starting population of two individuals, the mutation rates would have had to be sustained for thousands of years at an implausibly high rate

Earlier in the thread, we were debating about rates of mutation, until you claimed that your model didn't require any mutations. And when pressed, you double-down on this claim. Let me be real clear about what I am currently attempting to explain - mutations must have occurred to go from the 2-member population of canids from the time they exited the ark to bring about the variety of canids we see today. Claiming past genetic diversity is meaningless when a population drops to 2 members. Any sort of previous diversity is lost through the bottleneck.

[Tristen]

3 hours ago, one.opinion said:

I'm going to keep this post real short because you don't seem to be understand the reality of what you are claiming ...

“you don't seem to be understand the reality of what you are claiming”

First you label my assertion as “odd”, and now you say this. We appear to be departing from courteous debate to the 'you don't know what you are talking about' phase of our discussion.

 

“But a bottleneck of two individuals would have their diversity limited to a maximum of four possible alleles at a particular gene. Is this true or false?”

I think you are using terminology strangely. In a simplified model where one gene contributes to one trait, and there is only one copy of that gene carried by each individual, “two individuals” could have a maximum of four different versions of the same gene existing in those two individuals. But because of the potential for genetic recombination (a non-mutational process operating on existing genetic information), there is enough information in those four genes to generate perhaps hundreds or more different versions of that same gene.

 

“You also seem to be misunderstanding what I have been trying to do for days - I have been attempting to bring to a point of realization that mutations had to have occurred in order to result in today's observable genetic diversity”

I'm not “misunderstanding”, I'm disagreeing that mutations were necessary to produce the levels of high diversity we observe today. That is not to claim that it hasn't happened, but it is to claim that mutations are not logically, mathematically necessary to achieve such high levels of genetic diversity. I am certain that loss-of-information mutations have contributed in small part to genetic diversity, but high levels of extant diversity do not require these to have occurred. Therefore, claims about mutation rates (which assume mutations are a requirement of diversity) are not relevant to my model.

 

“Earlier in the thread, we were debating about rates of mutation, until you claimed that your model didn't require any mutations. And when pressed, you double-down on this claim”

And now I'm about to triple-down on the same claim.

 

“Let me be real clear about what I am currently attempting to explain - mutations must have occurred to go from the 2-member population of canids from the time they exited the ark to bring about the variety of canids we see today. Claiming past genetic diversity is meaningless when a population drops to 2 members. Any sort of previous diversity is lost through the bottleneck.. ”

I have perfectly understood your position all along. But you are simply incorrect. Most of the phenotypic diversity we see in dogs arose only over the past two hundred years – not since the flood, but during the last two to two-and-a-half centuries. Since we know how that diversity arose (i.e. through artificially filtering out existing genes, and not mutating new genes), we know that the genetic diversity between extant breeds was all carried by their two-or-so hundred year old ancestors. Those ancestors carried high genetic diversity in their genomes – and that diversity is now reflected in the diversity the descendant breeds.

Nevertheless, many pure breeds are at the end of their genetic pathways. If two poodles reproduce, there is not enough genetic diversity between them to make anything other than another poodle. But if two mongrels reproduce, the outcome is unpredictable, because they each contain much more genetic diversity (and are therefore much healthier in terms of the adaptive capacity of their descendants).