Valerie: Questions about TMR4A

I don’t disagree, but then she should have said that to begin with. If instead of diving headlong into arguments about the topic she’d just said to begin with that it would be better to fully educate herself on these matters before making opinions public and quoting the material at length, I would have been completely okay with that. That would have been the best way to proceed. First educate, then pontificate.

But it seems to me that ship has already sailed. She’s been more than willing to discuss, or at least repeatedly quote and advertise the contents of the book as if it was authoritative, up until now.

I also challenged her in another thread where she was quoting the book authoritatively, to find me someplace where Sanford defines a crucial concept in a way that can be measured and quantified. Again there she stopped being willing to discuss the matter with the excuse she needs to read more. Funny how that keeps happening when the assertions she quotes get put to closer scrutiny and she’s asked to explain or substantiate things.

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I still have this saved from a review I wrote up for the person I borrowed the book from. Here you go. :slight_smile:

The curve from Kimura’s paper, where he says he left out the beneficial mutations because they blew up his model:
KimuraCurve

Sanford’s version of the curve with a teeny tiny beneficial mutation curve drawn in:
SanfordCurve

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Excellent, thank you. I love this. It even has a title.

Okay so, @thoughtful my first question is: Can you tell me what’s in the grey box?

You’re welcome. And that’s from chapter 2, so she should be able to discuss that part. :wink:

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SanfordCurve

Okay so, @thoughtful my first question is: Can you tell me what’s in the grey box?

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This would be news to creationists.

Natural Selection - Answers in Genesis

Replacing the Creator God with what he called the “war of nature,” Darwin claimed that all appearance of design in biology is the result of time, chance, struggle, and death—the process of “natural selection.” Is there any evidence that Darwin was right? Can nature select as well as man? Answer: There is considerable evidence that Darwin was indeed correct about natural selection and the “war of nature.”

In an article written by Jeanson and Purdom, expressly commissioned by Ken Ham to address natural selection, we find…

Natural selection has happened, and it continues to happen every day.

AiG positions survival of the fittest as a legitimate mechanism driving speciation within “kinds”. Even Sanford does not deny that natural selection exists, but rather
Mendel’s Accountant: A New Population Genetics Simulation Tool for Studying Mutation and Natural Selection

…the vast majority of mutations, both deleterious and favorable, are invisible to natural selection because of their small impact of overall fitness

which is of course, consistent with his graph showing selection zones. So

indeed is a faithful representation of Sanford’s position, and a necessary implication, as @Rumraket points out, is that a filtering effect on the degree of genetic variation would be expected over time. Valerie’s refusal to recognize this much at least, has resulted in this exasperating discussion where she disputes that infertility and other self evidently selectable genetic variation is culled out. The real question with Genetic Entropy is, can you have a condition - slightly deleterious mutation - which is ultimately lethal, but is not the least bit detrimental until the very point of death?

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What I was trying to describe and what Sanford says in the book is slightly different than what @rumraket is pointing out. He hasn’t read the book, so no he’s not completely representing the position faithfully. There are subtleties that are extremely important.

I’m not sure. Again, I’ll finish the book and then we can discuss.

Both of these have to be assumptions in the model. Its the model itself that has to be proved to be more useful than the current one. For example:

I’ve already seen here where others have disputed that this is the only thing required for evolution to create the complexity we see today starting with a cell.

If a front-loaded design model, with evolution happening on scales different than the current understanding works better, and models what is actually happening, then that’s what should be accepted by biologists.

God is the first cause. He is omniscient and so is the original designer and has no need to acquire knowledge. The purpose of design for us as humans is to acquire knowledge. We do acquire this knowledge by studying His designs. That’s what all of science is. It doesn’t work without a first cause that is consistent in His designs.

Wow, yet you guys are fond of criticizing “evolutionary assumptions”.

When performing phylogenetic analysis, evolutionary biologists assume common ancestry between the organisms or biomolecules being investigated. Common ancestry is assumed because it has supporting data. What is the supporting data to justify assuming frontloaded design and diversity?

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And if my grandmother had wheels and pulled a plow she’d be a tractor.

But she doesn’t, so she isn’t.

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Well, common ancestry is obviously true. It’s just how much? What we see in humans is most important. If the current data about human evolution is not compatible with common ancestry with great apes, then front-loaded design and diversity have to be assumed. This is what Sanford has been trying to show.

And it matters a lot to me, because then we also don’t share common ancestry with bacteria and viruses. We can’t assume that evolutionary processes work the exact same way on us.

Both of these things (our genetics and how they evolve and the genetics of diseases and how they evolve) have massive implications for health. At this point, I probably care equally about the origins debate as I do about how much more of jump we could gain in knowledge if we knew more about evolution if we’re understanding it wrong. It looks stalled out to me when I read articles in the news such as this one. Probably studying all the mutations of SARS-CoV-2 will help.

Valerie, you’re not reading what I wrote: you and Behe are ignoring the NATURE of the complexity. It doesn’t resemble intelligently-designed objects at all.

To see the nature of the complexity, you’d have to get into the actual evidence, not some hearsay like “Whoa, it’s really complex!”

Can you grasp that there are different KINDS of complexity (pun intended)?

Please don’t make claims about

when you’ve never bothered to look at the complexity for yourself. Words will never describe it sufficiently.

My point is that it doesn’t.

Science isn’t about arguing and accepting; it’s about testing hypotheses. If IDcreationism had any validity, those who “accept” it should be far more productive than the rest of us.

This is yet another day without anyone starting a creationist pharma or oil exploration company.

This is yet another day without a creationist Christian college or university putting millions of dollars into actual research that would show whether creationism “models what is actually happening.”

Science is much more about doing than about arguing and persuading. Why is creationist doing (scientific productivity) virtually nonexistent?

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It is. Here’s an example from this forum today; see Fig. 3 for the data. The text is not relevant to my point–this is how obvious the common ancestry of the primates is.

Why doesn’t it matter enough to induce you to leave hearsay for the evidence?

We aren’t assuming like you do and pretending to be familiar with the data. We actively do science.

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By all means inform me of those subtleties one you’ve answered my question here.

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Not really for sequences. Most tree diagrams are actually representations of the mathematical relationships between sequences without assumptions.

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OK I stand corrected on that.

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When examining them, it’s important to keep in mind that, if the root is on the left and the sequences are labeled on the right, the lengths of vertical lines are meaningless. The distances are only represented by the lengths of the horizontal lines.

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Okay so since @thoughtful is clearly not interested in even trying to answer my question, I might aswell go ahead and lay out the obvious contradiction between Sanford and Jeanson.

Jeanson dismisses the concept of the time-dependent mutation rate because it would undermine his argument that the higher pedigree mutation rates support his young-Earth timeline.

But we can understand by reason alone that there has to be a time-dependency to the rate of mutation, which I tried to explain with some obvious examples such as lethal mutations or mutations that strongly affect fertility.

The point being that there clearly are deleterious mutations of large effect that will be removed by selection, and hence the long-term rate of mutation must be lower than what shown in pedigree mutation studies.

@thoughtful tried to dismiss these arguments by saying that Sanford has shown that all deleterious mutations have such small effects that they can’t be removed by selection. They are supposedly “invisible” to selection, and hence they can accumulate in large numbers and therefore will not affect the long-term rate of mutation.

So I tried to get @thoughtful to take a look at Sanford’s actual Distribution of Fitness Effects(DFE) of mutations-figure to see that it really does contradict Jeanson. I wanted her to first show that she understands the figure by explaining what is inside the grey box (the one marked as belonging to the “no selection zone”). Those would be the mutations she spoke about, that supposedly make up the majority of mutations. The deleterious mutations of invisibly small effect that contribute to Genetic Entropy.

They are inside the zone labeled “no selection” because their effects are supposed to be so small selection can’t detect them.

The figure clearly does represent what Sanford thinks the real distribution of mutations look like. Sanford has labeled it “Correct distribution!”.

Okay good, so all the too small to select away mutations are inside the zone of no selection.

But then,
A Great Mystery

That looks like deleterious mutations outside the zone of no selection. Deleterious mutations that aren’t invisible to selection. Those deleterious mutations that would contribute to the time-dependent rate of mutation. Jeanson and Sanford can’t both be right.

The end.

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I’m sorry that maybe I didn’t understand what you were asking. His book is next on my list after Genetic Entropy. But I don’t think he dismisses time-dependent rate of mutation but instead checks against both evolutionary and creationist rates in his papers. Maybe I didn’t explain something correctly before. I’m still hazy on how these things are measured. I’m better at understanding the conceptual arguments.

Figures 1 and 2 I’m assuming are testing time-dependent rate. I think I said “de novo” before, but maybe that’s not a right explanation. Evidence Human Y Chromosome Molecular Clock | Answers Research Journal

Remember I’m a baby scientist. :slightly_smiling_face: Trying my best.

But as it turns out the current data are very compatible with common ancestry with great apes. They aren’t compatible with any alternative hypotheses, most definitely including “front-loaded design and diversity”. So now what?

Let’s hit some of the evidence again:

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