Confessing to the Evidence

https://www.pnas.org/content/96/18/10254.full

Study: Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place.

My comment. “Common ancestor” is an a priori assumption and not warranted by the science involved. In actuality, what this study has probably found is a common genetic creation template from which both primates and humans were constructed – or fashioned by God.

Study: In theory, the species distribution of a set of known integration sites can be used to construct phylogenetic trees in a manner similar to restriction fragment length polymorphism (RFLP) analysis.

My comment. Removing the unsupported claim of a common ancestor, the phylogenetic trees are simple pictographs representing genetic change over time within created animal kinds.

Study: Second, as with other sequence-based phylogenetic analyses, mutations in a provirus that have accumulated since the divergence of the species provide an estimate of the genetic distance between the species.

Comment. “Divergence” is an a priori assumption and not warranted by the science involved. In actuality, what the study has probably found is a means to estimate the genetic distance that both primates and humans have moved from the original creation template .

Study: To estimate the age of each provirus the human/chimpanzee distances from each tree were used to calibrate the rate of molecular evolution at each locus. The most recent common ancestor of humans and chimpanzees lived approximately 4.5 million years ago.

My comment. Removing the unsupported claim of a common ancestor, and substituting molecular “change” for “evolution”, this study attempted to identify an historical date for the animal/human creation event – specifically, the time before current that God brought forth primates and humans from a common genetic creation template . (The 4.5 mya figure is likely in question and warrants further research.)

@noUCA is very prolific. I think this dialogue diserves a @moderators split into a new thread.

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I still don’t see where the varve article has been addressed, or have I missed it?

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Please stand by - I lost a post that ought to lead this thread.

Hi @noUCA -

I want to suggest a framework for obeying Proverbs 18:17 (have you looked it up yet?) and having a productive discussion about evidence:

  1. Show you understand the evidence being discussed.
  2. Show how those who disagree with you interpret the evidence.
  3. Show an arguably better interpretation of the evidence.

I will try to model the desired behavior by analyzing Gould’s punctuated equilibrium hypothesis:

1. THE EVIDENCE. The fossil record contains examples of both slow/steady evolution (eohippus to horse) and rapid evolution (Cambrian explosion; rapid evolution of mammals after K-P boundary 66MYA). Gould states that the prevailing model prior to his writing in the 1970s, gradual change, did not explain the evidence sufficiently. He postulated that evolution at a grand scale occurred in punctuated equilibria.

2. AN INTERPRETATION OF THE EVIDENCE. YEC scientists argue that

  • The dearth of transitional fossils in large-scale changes demonstrates that the large-scale changes simply did not occur.
  • Uniformitarianism, a necessary part of evolutionary theory, is defeated by the hypothesis of punctuated equilibrium.

3. A BETTER INTERPRETATION. Biologists disagree with YEC reasoning on several grounds:

  • Many large-scale changes that were not documented by transitional fossils when Gould was writing have subsequently been filled by important fossil discoveries. Examples include the evolution of tetrapods (lobe-finned fishes -> early amphibians (e.g., Tiktaalik) -> amphibians -> reptiles), the evolution of cetaceans from artiodactyla, and the evolution of birds from dinosaurs.
  • Many large-scale changes that are not well-documented by fossils have been documented after Gould’s writing by other kinds of evidence that were not available to him at the time. This evidence includes:
    • The application of mathematics to genomic evidence, which yields nested hierarchies that traverse the fossil gaps.
    • The recapitulation of large-scale changes during developmental stages. Ancestral structures appear for a time, but later are transformed due to different regulatory gene networks. An example is the appearance of pharyngeal arches in human pre-born infants, which later become the bones of the ear and jaw. In fish, the pharyngeal arches develop into gills. This discipline of biology is referred to as “evo-devo.”
  • Uniformitarianism of processes was discarded a long time ago in biology. Some phenotypic changes happen incrementally, but others (driven by changes in regulatory genes, sudden changes in selection pressures, or a final mutation after the accumulation of drift) can happen quickly. For example, orthologous HOX genes show how the basic proteins and designs in limbs can be expressed differently across various taxa of chordates.

So I would like to offer you the opportunity to put this 3-step process into action. I present to you a research paper that applies mathematical techniques to a certain kind of genomic data in order to discover latent ancestry structures among apes. Here’s the paper:

Can you read the paper, then follow the 3 steps? I do not necessarily expect you to agree with the authors or with me. What I’m hoping for is an actual discussion of evidence, with due consideration for the mathematical basis of phylogenetic models, even if you ultimately disagree.

Thanks,
Chris Falter

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Hi noUCA,

I appreciate that you read the paper, and that we are talking about actual evidence. It’s progress.

Your understanding of the paper fell a little short. You also made some assertions that do not seem to comport with the evidence. Let’s take a look.

It’s not.

EVIDENCE:

  • The use of DNA analysis in forensic science and human genealogy studies provides an incredibly strong, empirical foundation for these principles:
    • Common mutations indicate common ancestry
    • Greater similarity in mutations indicates more recent common ancestry
    • Less similarity in mutations indicates more distant common ancestry
  • Genomic studies across the primate order show that the occurrence and inheritance of mutations works basically the same as it does in humans.

When forensic scientists and genealogy researchers see the identical mutation in the identical locus in two individuals, they conclude that the two individuals share a common ancestry. Why are you discarding this empirically-justified practice?

Based on the testimony of Scripture, I agree that God has fashioned all of creation.

However, you have not explained how a YEC model would lead to the prediction that non-transcribed, generally non-functional DNA sequences that result from retrovirus insertions would be found at identical locations in species that do not share common ancestry.

How does a retrovirus insertion that has no function represent a template?

Biologists know from genomic studies that the same DNA sequence can have the same effect even if it occurs in a different locus. In other words, the same template need not occur in the same location. Assuming in arguendo that the non-functional retrovirus insertions are templates, why would they occur in the identical locus?

You have leaped to a conclusion, but you haven’t provided any evidence or reasoning that would help your readers understand why you made the leap. It seems like you have concluded, a priori, that there must be a YEC-compatible explanation. Your words skip directly to that conclusion without leading a reader along the path from the evidence to the conclusion.

Moreover, you have not taken into account the fact that the a priori foundations of the study are based on empirical observations, rather than mere opinion.

Again, you have not understood the paper. The pictogram is based on math. The math is based on the following empirical observations:

  • Common mutations indicate common ancestry
  • Greater similarity in mutations indicates more recent common ancestry
  • Less similarity in mutations indicates more distant common ancestry

Biologists have applied these indisputable, empirical principles in RFLP studies, and then Johnson and Coffin applied the same principles in a mathematical way in the ERV study.

The rest of your analysis follows the same approach, so I think I’ll stop here.

I hope that you have found this feedback helpful.

Best,
Chris

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Does empiricism rest with your starting point only? Not at all. Your empiricism does not just speak on your behalf; it also declares that there is no “common ancestor”. God would have employed the same genetic creation template used for primates when specially creating Man. YECs would believe those creation events to be separated by one day. Progressive creationists would believe them to be separated by gaps in the hundreds of thousands, perhaps millions, of years.

And my answer will also apply to all of your objections. I will only be repeating myself if I continue. I’m sorry, but you simply have no recourse in this matter.

Consider this: you and your side do not own the science. What you are discovering is fascinating, but it can really only back-up Creation, not evolution.

God owns the science. Methodological naturalism is neutral.

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That’s a nice fat assertion. Why, and how do you know?

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Empiricism starts with factual observations.

Here are the factual observations I thought we were dealing with in this discussion:

  1. The use of DNA analysis in forensic science and human genealogy studies provides an incredibly strong, empirical foundation for the following principles:
    a. Common mutations indicate common ancestry
    b. Greater similarity in mutations indicates more recent common ancestry
    c. Less similarity in mutations indicates more distant common ancestry
  2. Genomic studies across the primate order show that the occurrence and inheritance of mutations works basically the same as it does in humans.
  3. Biologists have identified hundreds of thousands of ERV insertions in primate genomes.
    a. The sequences are typically non-functional–i.e., they are not functional templates
  4. There is no empirical reason to expect that non-functional sequences inserted by retroviruses would be discovered at identical loci in species not related by common ancestry (see #1 above)
  5. There is empirical reason to expect that non-functional sequences inserted by retroviruses would be discovered at identical loci in species actually related by common ancestry (see #1 above, especially 1a)

You have not even begun to deal with any of these facts. Your assertion of “creation templates” assumes functionality, but your assertion is not empirical. In fact, your assertion is completely contrary to empirical studies of the DNA sequences in question.

You have not even attempted to infer conclusions from observed facts. You have merely asserted that somehow (we do not know how) there must be a (hidden, unexplained) YEC-compatible way of interpreting the alignment pattern of ERVs across the primate order. How am I supposed to agree with your statement when you do not provide even the slightest path from the data to your conclusion?

Somehow, you think that you can ignore obvious questions like the ones I posed:

Until you can provide coherent answers to these empirical questions, how can you assert that the facts point to your conclusion?

I hope this feedback helps you.

Thanks,
Chris Falter

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The use of DNA analysis in forensic science and human genealogy studies provides an incredibly strong, empirical foundation for the following principles:
a. Common mutations indicate common design
b. Greater similarity in mutations indicates more recent common design
c. Less similarity in mutations indicates more distant common design

That’s #1

Where did your choice of word “template” come from? What does this mean that they are not “functional templates”?

I hope not from me. I did not use the word in that manner.

There is empirical reason to expect that non-functional sequences inserted by retroviruses would be discovered at identical loci in species actually related by common design via common creation template (see #1 above, especially 1a)

That’s #5

This is not correct. Phylogeny is not determined by “greater similarity” but by fit of data to trees, for example by invoking the principle of parsimony to minimize required homoplasy. The empirical observations are the presence or absence of the insertions. And we can observe that those insertions fit a nested hierarchical structure. What we need to explain is not just similarity but that hierarchical structure.

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Why would there be any non-functional sequences in a common design? What is that empirical reason?

You should also note that it’s not just one set of species you need to consider but the entire multi-level nested hierarchy of species within primates. How can one explanation of “common design” fit all those levels simultaneously? How can it explain ERVs shared by humans and chimps alone and also ERVs shared by humans, chimps, and gorillas?

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All I did at the start was to substitute “common genetic creation template” for “common ancestor”. So you questions should also be directed to yourself.

We both have the same starting point, don’t we. Mine is via creation template, yours via common ancestor.

What I’m trying to point out is that the substitution can’t actually work. There are multiple common ancestors of various taxa, but a common genetic creation template can only explain at most one of those supposed ancestors. You can’t have creation templates at multiple levels. You can’t explain a nested hierarchy by common design.

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Hi noUCA. A couple of quick questions:

If “common design” is true then why do we see four completely different “designs” for wings in birds, bats, insects, and pterosaurs?

Why do sharks have vertical tails while dolphins have horizontal tails?

How does “common design” explain the temporal sequences of transitional fossils known from the fossil record?

What would falsify your “common design” hypothesis?

And the most important one:

When did ID-Creationists establish the occurrence of ANY “design”, let alone “common design”?

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I did not say this. You did. I said from the beginning I made the substitute of common genetic creation template. All the data your experiments return will be returned identically from my starting point. But be sure, if the data does not return identically from my starting point, then neither can it return identically from yours.

Please cease with the common design. My starting point is a common genetic creation template. It is a full substitute of your common ancestor. It replaces your common ancestor.