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Tricks Theists Play (Part 1)


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9 hours ago, one.opinion said:

Clearly there are fluctuations, as you have mentioned. I acknowledge this. My point is that in order to make these types of estimates, the assumption is that mutation rates, on average over long periods of time, are predictable. I agree that it is overly simplistic to state that there is one, unchanging, mutation rate. I could agree that no one believes that is true.

Not at all, I was merely extending good will to a Christian brother. It left me with an odd feeling when you responded to everything BUT that. “No worries” now ?

My point is that in order to make these types of estimates, the assumption is that mutation rates, on average over long periods of time, are predictable

It's ironic that you raised the issue of the cladograms (from a paper I provided for different reasons) when I think the cladograms provide an excellent example that the assumptions are anything but “predictable”. These distinct stories of history for the same creatures clearly demonstrates that the outcomes are entirely dependant upon the model assumptions and input parameters.

So I guess my point is that these “predictable” “estimates” are not calculated by observation over time. They are calibrated against so-called “dated” samples – where the dates themselves are logically reliant on fundamental secular assumptions. So whether or not we consider these rates to be “predictable” is entirely dependant on whether or not we accept the multiple layers of assumption underpinning two mathematical models. You won't be surprised to hear that I don't accept the assumptions of either.

So in the context of our discussion, when you claim that the mutation rates must have increased by a factor of blah,  my question is 'Increased from what?'. In order for me to accept the secular estimations, I would have to first accept the secular uniformitarian assumptions of one model (assumptions which are known to not reflect the reality of mutation rates) – a model which itself is calibrated against another mathematical model based on a foundation of more unverifiable assumptions.

Ultimately, my preferred model doesn't even need mutations to produce diversity - just Natural Selection acting on existing gene pools.

Edited by Tristen
grammar correction
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20 hours ago, Tristen said:

So I guess my point is that these “predictable” “estimates” are not calculated by observation over time.

The estimates used to calculate divergence points, etc., are based on observed mutation rates. At least this is the case for organisms that have been genetically characterized, not sure about the guppies. It's simply a matter of a distance = rate x time equation at that point. When the genetic "distance" is measured, and the "rate" can be measured (within reasonable error limits), then "time" can be calculated. Yes, assumptions are made with the "rate" part of the equation. Yes, mutation and adaptation rates can vary, and sometimes with astonishing speed, resulting in estimates that may differ significantly (40% in the case of the guppies). Yet, a young earth creation model would require that these astonishing rates of change would take place continuously for thousands of years, and not just a brief period, as described in the review - and this simply has not been observed.

20 hours ago, Tristen said:

Ultimately, my preferred model doesn't even need mutations to produce diversity - just Natural Selection acting on existing gene pools.

There is not enough genetic variability existing between any two reproductively compatible individuals to produce the genetic diversity we see today without mutations. The number of haplotypes in any gene pool precludes that possibility. Additionally, the degree of adaptation and divergence required by your model in organisms since the 8,000 kinds exited the ark in your model could not possibly have been achieved without additional mutations.

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7 hours ago, one.opinion said:

The estimates used to calculate divergence points, etc., are based on observed mutation rates. ...

The estimates used to calculate divergence points, etc., are based on observed mutation rates

Show me the study where someone has sat down and observed, and recorded, “mutation rates” of a species over time. It would have to be a multi-generational study to provide any moderately meaningful data (I would personally need at least 30 generations of full genomic data to be able to attribute any statistical meaning) – and we already know that mutation rates fluctuate, and that just because we have observed the rates over the last few generations doesn't mean those were the rates before that. With the possible exception of microbial or Drosophila fly studies, I don't think such a long-term study would be plausible. I am next to certain they wouldn't get funded.

Divergence points” in deep time logically require external calibrators; usually DNA from some fossil which has been “dated” by secular methods. All we actually observe are the current DNA differences between species. Time is then inferred based on a molecular clock calibrated to the chosen external reference.

 

It's simply a matter of a distance = rate x time equation at that point

When you can show me how a “rate” can be determined without reference to an external calibrator, I will consider the simplicity of your equation. Until then, “it's simply a matter of” accepting the assumptions used to 'date' the calibration reference, and on top of that, accepting the assumption that mutation rates are consistent over time (an assumption which we both know to be inaccurate).

 

When the genetic "distance" is measured, and the "rate" can be measured (within reasonable error limits), then "time" can be calculated

Except that the “error limits” are premised on the accuracy of the calibrator. Without assuming that accuracy, the statistical error is mathematically meaningless. The error is just a reflection of how statistically close the data points align - not how accurate the measurements are over time.

 

a young earth creation model would require that these astonishing rates of change would take place continuously for thousands of years, and not just a brief period

A “young earth creation model” doesn't “require” mutations at all. Mutation rates are irrelevant since mutations can't add new, functional, heritable genes to existing genomes (at least no mechanism to accomplish this has been observed).

 

There is not enough genetic variability existing between any two reproductively compatible individuals to produce the genetic diversity we see today without mutations

Based on what? Obviously the extant diversity levels in current generations is the outcome of thousands of years of environmental pressures filtering out obsolete genes. But that doesn't mean we couldn't have started the process from a point of high ancestor diversity. Many species have even gone through several generations of genetic bottlenecks, yet maintain enough genetic diversity to adapt and speciate into new environments.

 

The number of haplotypes in any gene pool precludes that possibility

How so? What is the number of “haplotypes in any gene pool”? Haplotypes just speak to past point mutations. There could even be multiple such mutations every generation. Over a few thousand years, there could be many thousands of haplotypes in a single species.

 

Additionally, the degree of adaptation and divergence required by your model in organisms since the 8,000 kinds exited the ark in your model could not possibly have been achieved without additional mutations

Why not? There are still many species which are highly diverse. And previously isolated populations can come back together replenishing genetic diversity in their gene pool. The genetic information system is still considered to be the most efficient information storage system in existence. I don't know why you think speciation needs so much time, and I don't know why you assume there is some upper limit to ancestor diversity.

 

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8 hours ago, Tristen said:

Show me the study where someone has sat down and observed, and recorded, “mutation rates” of a species over time. It would have to be a multi-generational study to provide any moderately meaningful data (I would personally need at least 30 generations of full genomic data to be able to attribute any statistical meaning)

These studies are fairly common in microbes, where many generations can occur in a relatively short period of time. Obviously, studies of higher eukaryotes over that many generations are pretty sparse, but I did find one study in Arabidopsis (click here). Of course, the amount of meaning derived from a single study is limited, but at least it offers something of a baseline.

8 hours ago, Tristen said:

just because we have observed the rates over the last few generations doesn't mean those were the rates before that

Yes, obviously, assumptions are made when extrapolating mutation rates far back into the past. And yes, we know that mutation rates can fluctuate. But for your model to work, mutation rates would have to be orders of magnitude higher than those that have been observed, not for a few generations, but over thousands of years. And there is simply no evidence available that supports that degree of hyper-mutation over that degree of time.

8 hours ago, Tristen said:

Divergence points” in deep time logically require external calibrators; usually DNA from some fossil which has been “dated” by secular methods.

Do you have a better method for dating fossils? I will continue to stick with these "secular methods" until there is a confirmed better methodology to accurately date them.

8 hours ago, Tristen said:

A “young earth creation model” doesn't “require” mutations at all.

Are you certain you want to stick with this statement? Even assuming that 8,000 kinds were on the ark, what we see today in the genomes of living organisms absolutely requires that mutations have taken place over the last 4,000 years. It is physically impossible for the genetic diversity we see today to have been present in the 2 (or 14) animals of each kind without any new mutations taking place since the ark exit. Altering the frequency of alleles would be inadequate to result in what we see today if you only have a maximum of 28 or 4 sets of alleles to begin with.

9 hours ago, Tristen said:

I don't know why you think speciation needs so much time

I'm not talking about new species, I'm just talking about the odd assertion you are making that a young earth model doesn't require mutations. How would a kind change over time without mutations? You are an intelligent guy, so you must mean something other than what you are actually saying.

 

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14 hours ago, one.opinion said:

These studies are fairly common in microbes, ...

 

These studies are fairly common in microbes, where many generations can occur in a relatively short period of time. Obviously, studies of higher eukaryotes over that many generations are pretty sparse, but I did find one study in Arabidopsis

Good job in finding one. I thought there might be some in microbes or insects. Didn't think of plants. But it makes sense, since some can overturn generations quickly.

Notice however that they didn't actually measure mutations over time. They observed mutations over “generations”. They could only calculate mutations over time by “assuming a generation time of one year” - so yet another assumption to add to the already over-simplistic model. That is, the assumption of a consistent of turnover of generations, when we know very well that the rate of generation turnover is not consistent over time.

And I couldn't find where they scaled their calculations to the entire population. They used “per generation per site” a lot, but they were dealing with a very limited sample size. Whatever rates they calculate from their observations have to be scaled to the size of the entire population. Double the sample size and you double the potential for mutations (and therefore mutation rate estimates). I don't think I've ever seen a model that accounts for population size changing over time. So there's another assumption to add into the mix.

Nevertheless, I am prepared to moderate my language. Apart from rare exceptions, molecular clocks are overwhelmingly calibrated by external references - references which themselves incorporate their own sets of assumptions.

Studies using molecular clock methods are not “sparse”. So the point I've been making is still abundantly true for the overwhelming majority of cases (despite the existence of occasional exceptions). But even in those rare cases, I am still expected to accept ridiculously oversimplified assumptions about very complex systems.

 

Yes, obviously, assumptions are made when extrapolating mutation rates far back into the past. And yes, we know that mutation rates can fluctuate

You don't seem to understand the magnitude of this logical weakness. Its the same logic weakness in all dating methods. The outcome of the method is fundamentally, logically, mathematically, 100% dependant on the truth of the assumptions. So if any of those assumptions untrue, the outcome is completely meaningless – as in utterly, logically useless. Here you express that you know the assumption of the method is not true, yet you somehow fail to comprehend how that logically bankrupts the method.

The common knee-jerk reaction is to claim we can reasonably assume its correct most of the time, but until there's a way to independently test which ones are or aren't correct, that's just another assumption on top of all the others. How can we know which dates are correct and which aren't? They could all be equally wrong. And if there's a way to independently confirm the accuracy of proposed dates, lets use that method, instead of those containing such overt logic weaknesses.

 

But for your model to work, mutation rates would have to be orders of magnitude higher than those that have been observed, not for a few generations, but over thousands of years. And there is simply no evidence available that supports that degree of hyper-mutation over that degree of time

My model doesn't require consistent mutation rates of any kind.

 

Do you have a better method for dating fossils? I will continue to stick with these "secular methods" until there is a confirmed better methodology to accurately date them

So a wrong date is better than no date?

How does one confirm the quality of a dating method without a time machine? If there's a way to do so without relying on a set of questionable assumptions, then lets use that method.

I am happy for you to “stick with” whatever you decide. But there is so much scope for logical error built into those methods that critical thinking obligates me to dismiss them as lacking credibility. This is only relevant to our conversation because much of much of your argument assumes I accept several layers of assumptions – which I obviously don't accept.

 

Are you certain you want to stick with this statement? Even assuming that 8,000 kinds were on the ark, what we see today in the genomes of living organisms absolutely requires that mutations have taken place over the last 4,000 years. It is physically impossible for the genetic diversity we see today to have been present in the 2 (or 14) animals of each kind without any new mutations taking place since the ark exit. Altering the frequency of alleles would be inadequate to result in what we see today if you only have a maximum of 28 or 4 sets of alleles to begin with

You're going to have to qualify that statement. Hand-wavy assertions about what is “physically impossible” aren't convincing to me. I look at the fact that most domestic dog breeds have only arrived in the past couple of centuries – meaning that the massive phenotypic diversity in dog breeds arose from a pool of highly diverse ancestors (i.e. mongrels) in the last few hundred years. I think perhaps you are underestimating the complexity of genes.

 

I'm just talking about the odd assertion you are making that a young earth model doesn't require mutations. How would a kind change over time without mutations? You are an intelligent guy, so you must mean something other than what you are actually saying

I can assure you I meant what I said. Your paradigm requires a mechanism for adding diversity to the genome. If you start from a simple common ancestor, then diversity can only arise through an additive mechanism such as mutation. But when you start from a point of high diversity designed into each kind of creature, then genetic diversity filters down over time through environmental pressures. Like filtering out the diversity in a poodle from a mongrel ancestor, creatures become less diverse over time. No mechanism for increasing diversity is required. So the diversity observed within kinds is simply a less intense version of what we have artificially done with dog breeds.

 

 

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1 hour ago, Tristen said:

So the diversity observed within kinds is simply a less intense version of what we have artificially done with dog breeds.

So quick question... do you think that all dogs are genetically identical to whatever dog-kind came off the ark, or do you think some mutations occurred that contributed to their diversity?

I keep trying to give you the opportunity to rephrase, please take advantage of it this time. Please fix “Ultimately, my preferred model doesn't even need mutations to produce diversity”.

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56 minutes ago, one.opinion said:

So quick question... do you think that all dogs are genetically identical to whatever dog-kind came off the ark, or do you think some mutations occurred that contributed to their diversity?

I keep trying to give you the opportunity to rephrase, please take advantage of it this time. Please fix “Ultimately, my preferred model doesn't even need mutations to produce diversity”. 

do you think that all dogs are genetically identical to whatever dog-kind came off the ark, or do you think some mutations occurred that contributed to their diversity

I think your question is a false dichotomy. Apart from genetic twins, I don't think any dog is “genetically identical” to any other dog. I don't think genetic mutations are logically necessary to explain phenotypic variation in dogs.

 

I keep trying to give you the opportunity to rephrase, please take advantage of it this time. Please fix “Ultimately, my preferred model doesn't even need mutations to produce diversity”.

Nope, I'm sticking with what I said. Maybe you're reading something into my words that I didn't intend, but I don't have any problem with that statement as it stands.

 

 

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Alright, let me try this from a different angle to hopefully clear up some confusion. Do you think it is possible that the modern dogs we see today could have arisen from the dog-kind that exited the ark without mutation? If so, how do you account for the genetic diversity?

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8 hours ago, one.opinion said:

Alright, let me try this from a different angle to hopefully clear up some confusion. Do you think it is possible that the modern dogs we see today could have arisen from the dog-kind that exited the ark without mutation? If so, how do you account for the genetic diversity?

Do you think it is possible that the modern dogs we see today could have arisen from the dog-kind that exited the ark without mutation?

Yes – I think extant dog diversity could exist without mutations, though I don't exclude the possibility that some loss-of-information mutations may have contributed in some part to dog diversity. But mutations are not a logical requirement of diversity across kinds – i.e. diversity doesn't necessitate mutations unless the models starts from a point of low diversity.

 

If so, how do you account for the genetic diversity?

High genetic diversity was designed into the created ancestors of dogs (presumably so that they would be able to adapt to the different environments they'd encounter). As offshoots of the original population became isolated, over time and generations, local environmental pressures selected out of the gene pool those genes which were not beneficial to their fitness in that environment (i.e. reducing genetic diversity in the daughter populations with every iteration of this scenario). More recently, breeders realised they could take a nondescript type of dog, and breed out undesirable genes from that particular lineage. Individual breeds are therefore the result of selecting out almost all genetic diversity – so that when they reproduce, the offspring have only the desired characteristics. Different breeds result from repeating this process for different characteristics.

Individual breeds therefore have very low genetic diversity. But the genetic diversity across the dog kind remains high – resulting in high phenotypic diversity in dogs.

 

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8 minutes ago, Tristen said:

diversity doesn't necessitate mutations unless the models starts from a point of low diversity.

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

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