The Current Status of Ewert's Dependency Graph of Life

No, I don’t. Please show your work.

You need to understand that the model works with the fitness contribution of a single 100bp locus, which is taken as a proxy for function. Once the fitness gain passes the genic threshold, that is taken to be the birth of a new gene. The probability of function is necessarily subsumed by the fitness effect.

It would make no sense to include any of the numbers from Art’s pandasthumb article, as these are estimates for the probability of a particular fold with a particular function, rather than just the probability of any fitness-contributing functional gene. The latter is what de novo gene evolution from non-coding DNA would be all about, not trying to hit particular sequence-structure-function targets.

Do you understand?

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Across all population sizes, gene birth is more likely when the frequency f and average size p of beneficial mutations are higher, the size of deleterious mutations n is lower, and the DFE is more long-tailed (Fig3–Figure Supplement3).

If you are a far distance from a functional sequence the mutations are very unlikely to be beneficial. A search is required to find beneficial function and now wait times become too long.

And that is how Bill shows his work.

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And this is how Faizal eggs on a burden shift :slight_smile:

Yes @Faizal_Ali, how dare you demand that poor Bill show anything more than ‘the dog ate my homework’, it would be a terrible burden on him to actually show any real calculations. :sob:

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Sure, if. But why should we assume we are far from a functional sequence? As this shows, we are actually much closer to folding protein sequences in non-coding DNA than you would naively suspect:

As we also know from studies such as the ones I cite in this post, simply obtaining a folding protein sequence means it is likely to have a useful biological function.

I’m sorry to have to tell you Bill, but this premise you can’t seem to let go of, that function is rare in sequence space, is just wrong. There is no support for it. Once you remove the strange and unrealistic requirement for a specific target sequence or target structure with a specific target function, but allow for any fitness improving function, functions are ubiquitous and unavoidable.

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I think we have agreement that we must assume we are close to function. The discussion of why that is can be set aside.

The “any sequence will do” argument is mildly challenging :slight_smile:

I’m glad you agree with this much, at least. Perhaps there is light at the end of this tunnel after all.

And a small correction: It’s any fitness-improving functional sequence will do.

@Meerkat_SK5: I owe you a clarification.

This particular example he conducted is falsified, that doesn’t mean he (or others) could not go on testing for Dependency Graph patterns in other data. My understanding is there is also a methodological problem with this interpretation on phylogenetic data, which means it might not be a very good test, but that is not my concern. I maintain that Ewert is testing a valid scientific hypothesis.

How so?

Oh no you don’t! There are threads about this on multiple sites, here, TSZ, and Panda’s Thumb that I am aware of. I’m confident you were part of some of those discussions, and are well aware of the criticisms. Please don’t be disingenuous.

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I certainly saw criticisms but not falsification of the hypothesis he directly tested.

So… the model clearly shows how, given realistic parameters, de novo genes with useful functionality arise from non-coding stretches of DNA.

Your reply is to repeat the same assertion you were throwing around before we discussed the paper. It seems like we’ve made exactly zero progress, which is of course frustrating to all parties concerned.

It seems you have still not understood the model. Do you have a background in stochastic mathematics, Bill? I’m aware of the fact that this math is well beyond basic algebra and geometry, but it shouldn’t be beyond the capabilities of someone who has taken a few semesters of math at the university level.

Of course, not everyone has that sort of background, and maybe you are one of them? It’s not a badge of shame to not have that math background, of course. It just means that we would need to adjust expectations on both sides of the conversation to make sure we can interact productively.

Best,
Chris Falter

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The observed pattern is expected under the evolution model (something to do with deletions???). If you want to say that design looks exactly like evolution, then OK, it’s not falsified - but you would have conceded that evolution IS the designer. It may also be a useless test, again not falsified, but still useless.

I have stated before, and will repeat now: Ewert should refine his methods, test more data, and validate the results. Even if his test were clearly positive for ID, no one would accept it without repeating the experiment.

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This cannot be true. What makes you say that? You must be referring to a different model of separate creation that is from the YEC camp because it does not apply to my model or RTB’s. Or maybe the confusion is that you think I am using his model to explain the whole history of life, which I am not. I am just using the model to explain the nested hierarchical patterns that cannot be explained by HGT. That’s it.

Well, no. There is some account Baraminology that has been brought forth by YEC, but it just continues to be problematic and flawed because it is derived from a YEC perspective.

Again, I am just going off of Gunter Beuchley’s presentation of the fossil record and give you an idea of what those examples of basic types are.

Are you suggesting that basic types are nested within each other phylogenetically speaking?

I fail to see your point. Why is this the case?

I find it very ironic that you keep telling me that I don’t read studies and then you end up doing the very thing that you accuse me of…

“Although observed rates of acquisition of horizontally transferred genes in eukaryotes are generally lower than in prokaryotes, it appears that, far from being a rare occurrence, HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing in most lineages. Between tens and hundreds of foreign genes are expressed in all the animals we surveyed, including humans. The majority of these genes are concerned with metabolism, suggesting that HGT contributes to biochemical diversification during animal evolution.”

Sure, I think I did overstate it . What I should have said and I am saying now is that it’s unneccessary and unparsomnious to separate both fields. In other words, you are making a distinction without a difference.

As I told @Rumraket, I am simply taking the work that has been done from other experts and putting the pieces together to provide a robust theory, such as the Orch-OR theory, common design model and Winston’s model. The only aspect of my model that could be considered vague and falsifiable is the one involving Baraminology because it comes from an YEC perspective which is what I was referring to before when I said that.

I say it because words have meanings. The term “convergence” presupposes an evolutionary trajectory. Are you trying to claim that taxa were separately created and then became more similar through convergent evolution? If so, that’s not at all what Ewert’s theory postulates.

That’s not why it’s problematic, though it doesn’t hurt. It’s problematic because there is nothing supporting separate creation, and you can’t make the data work that way, no matter how hard you try.

Sadly, you have misunderstood Bechley’s video, assuming you even managed to watch the whole thing. You’re even a bad parrot.

I’m suggesting that there are no basic types, and that if there were basic types they most certainly wouldn’t be nested within other basic types. Is this unclear?

Yes, and I’m getting tired of explaining it. You just don’t understand all the papers you cite and fail to read.

That’s a different notion of what “rare” means, and I would happily argue with the authors about that. Rare events happen all the time. The fixation of a neutral mutation is a rare event, and yet a hundred or so happen in the human population every generation. I say again that 1% or less counts as rare. Why do you disagree?

That made no sense again. When you say “in other words”, what follows is commonly quite different from what you said previously. And so it is in this case.

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No, I am saying that “Convergence refers to the occurrence of identical, or nearly identical, anatomical, physiological, and/or genetic features in species of life that are unrelated or distantly related within an evolutionary paradigm. Both creationists and mainstream biologists offer explanations for convergence, but those explanations are radically different.”

Well, that is the reason why it is problematic to me and why you can’t make the data work that way.

I did watch all of it. So please tell me how I misunderstood him.

No, it’s still unclear. Tell me why there are no basic types even though there are many instances of sudden appearances in the fossil record.

Well, this is entirely subjective and arbitrary so I can’t really respond properly.

Then, you can omit the last part of what I said in order to respond better.

When you quote, you need to say where you’re quoting from. I would take issue with that statement, whoever said it.

What are you trying to say there?

Well, for one thing Bechley doesn’t appear to believe in separate creation at all. He believes in divinely guided macromutation. And he wasn’t listing “basic types” in that bit. He was listing divinely guided macromutation events.

I explained that: basic types, if they existed, should not be nested within other basic types. If somehow basic types exist, they can’t be the ones you have tried to name. (And, again, your source doesn’t think they exist either.) Sudden appearances in the fossil record are generally of individual species, closely related to previous species. So the basic types suggested by the fossil record are, if anything, individual species. But of course this contradicts the evidence, as even you agree. The solution to that is that sudden appearance in the fossil record has some other explanation than the creation of a new basic type. It instead shows how incomplete and episodic, in both space and time, the fossil record is.

Well of course you can’t respond properly. Rather than worry about what “rare” means, you should consider whether the number of HGT events postulated in that paper actually supports your claim. I’d say that 1% of genes isn’t enough to effectively counterfeit common descent. Would you agree?

The first part of what you said made no sense either. I was just pointing out an additional way that the whole thing made no sense. Just because quantum tunneling happens (supposedly) in both the origin of life and in some mutations is not a reason you can’t reasonably separate the two fields. You might as well say that metal is used in both automobiles and paper clips, so you can’t separate auto mechanics from clerical work.

I’m trying to impress upon you how bad your reasoning and scholarship have been throughout, in hopes that it will encourage you to do better. So far it has not. But do you see the possibility that some day it might?

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Biological Convergence Challenges Naturalistic Evolution Models - Reasons to Believe

Yes, I agree but remember I am defining basic types based on sudden appearances in the fossil records for my own model. But again, the morphological aspect of my model is not fully worked out yet.

Sorry, this argument has already been refuted by the data:

Absolute measures of the completeness of the fossil record | Nature

I am not qualified to say but if this is truly the case, then maybe there might be studies in the future that show how HGT was even more pervasive than reasonably expected.

Well, it is in regards to my theory and model. You cannot separate the two

You are not an expert in quantum physics. So how can you say this?