I’m not apologetic about the term and the distinction between it and philosophical naturalism. It’s not that hard to understand.
Methodological naturalism is the analysis of the paint and the brush strokes. Philosophical naturalism is the denial that there is an Artist.
…and the insistence that nature painted itself in its entirety.
I’m watching the whole video and so far loving it. The video is worth watching just for the explanation of how DNA is compared!
BTW, along about 1:40 starts a sequence where she shreds his methodology (or rather lack thereof).
Cool. So while most antibodies aren’t catalytic, some are and sometimes that activity may be useful.
Stepping back to the broader question, I see that there is actually a substantial literature about catalysis by small peptides, which occurs quite often. For example, one paper (https://pubs.acs.org/doi/10.1021/ja0108584) reported construction of a library of octapeptides in which six amino acid positions were randomly populated from 14 amino acids. Roughly one thousand of the resulting octapeptides were tested for the specific catalytic activity they were interested in, and they found multiple ones that worked.
So there does seem to be abundant evidence that catalytic activity is not particularly rare among peptides. Now, stepping back to the original question, is there any evidence at all that such activity actually is extremely rare? Axe’s study certainly doesn’t provide it, since he was only testing variants of a single catalyst, which provides no information on the probability that unrelated proteins and peptides would have a similar activity. Why are you so confident that it’s rare?
That’s what ID proponents say, but I’ve seen no evidence that most of them actually put it into practice. Take two examples. The first is from this thread: the use of Axe’s study of beta-lactamase to justify concluding that protein function is exceedingly rare among all proteins. That conclusion is patently invalid: you cannot estimate the frequency with which any function occurs among all proteins by slightly varying a single protein and considering a single function – it’s just not logically possible. And yet, despite this obvious problem being pointed out repeatedly, ID advocates continue to cite Axe as the one source that tells us the rarity of functional protein, something on which many of their arguments hang. Has any ID proponent ever done a thorough literature search on the frequency with which functionality is found for random peptides, or on the frequency with which mutated functional proteins acquire new functions? Have you? Have you read any of the papers from the Thornton lab reconstructing ancestral proteins and the series of mutations that led to modern, divergent versions?
If you don’t know what the evidence is that needs to be explained, how can you know what the best explanation is?
The second example is one you’ve brought up previously: nonfunctional DNA. I’ve seen many ID advocates and other opponents of evolution cite the supposed recent discovery that most of the genome is functional as a successful prediction of ID and as a failure of evolutionary biology. Over the years I’ve pointed out to dozens of people that this argument is completely wrong. First, evolutionary biology doesn’t predict the existence of a lot of nonfunctional DNA, and second, there is in fact zero evidence that most of mammalian genomes does serve any function for the organism. Among all of those people (including you), not one has ever said, ‘Oh hey, I didn’t know that – I’d better rethink that argument.’ Nor has one said, ‘No, there is evidence’ and then presented valid evidence. Most tellingly, I’ve also never had a single person ask, ‘So why do biologists think most of the genome is nonfunctional, anyway?’ That last seems to me to be the way someone would respond who is looking for the best explanation for the data: first find out what the data is.
Because that’s how science works. Science explains regularities in physical phenomena in terms of other regularities in natural phenomena. It has no tools to address anything that doesn’t obey those regularities.
That’s true of specifically scientific explanations, however. I’m more interested in whether an explanation is true than whether it’s scientific. My most basic complaint about ID arguments is not that they’re unscientific arguments but that they’re bad arguments. If you have to ignore data to make your argument, or calculate the probability of the wrong thing, or cite studies that don’t support your claim, the problem is not that you’re being unscientific – it’s that you don’t have a good case. And that’s what I’ve seen over and over with ID arguments.
Methodological naturalism is not that hard to understand if and only if you come to it without any preconceived ideas about it.
Most Christians coming to these discussions, however, do have preconceived ideas about it, up to and including viewing it as an existential threat. I’ve made this point before already: when you view something as an existential threat, your fight-or-flight response is going to take over and your dispassionate, rational approach isn’t going to get a look in. Even if your view of it as an existential threat is incorrect or misguided.
So no, it may not be hard for you and me to understand it, but it is going to be hard to get our brothers and sisters in Christ to understand it. It is going to lead to misunderstandings and miscommunications, and that is why I keep saying that we need to find other, better ways to express ourselves.
I don’t think it has worked that well (you’ve been doing it a long time, and admirably ; - ). Unless someone has actually worked in the sciences, in practical engineering, in the field or in the laboratory, or at least has a decent understanding of how science is really done, harping on measurements does not necessarily communicate any more clearly either.
Somehow it is the conceptualization that is missing, and we obviously have not arrived yet.
98.5% is holding up fine as a reasonable ballpark number.
ID proponent Richard Bugg’s position on the human genome has shifted.
Richard Buggs: How Faith Can Improve Rigor and Creativity in Science 29:02
if we look at an evolutionary process we look at the evolutionary biology does that seem like a fair conclusion or is there but biologically we’re very similar to Apes you know our our genomes are are very similar it’s it’s our cognitive abilities it’s our minds that really set us apart
Actually - it is so.
Erica’s discussion at 1:01:51. Using Tomkin’s invalid methodology yielded the screwy 83.83% similarity comparing the same genome. The fact that Tomkin did not himself perform controls to anticipate such results discredits his work and is an indication that he is not interested in advancing science, but rather concocting YEC pseudoscience.
5 to 8 million years divergence is right in keeping with the observed differences.
Would you like to discuss irreducible complexity, which is the OP topic?
I just look at it as being the logical approach for fallen humans. It also works with the difference between agency and action: all we have to look at is the action; agency is a gut conclusion that is no longer science.
Do we want a different term, or just a better description?
I think this is a superb start for a description!
What YECs don’t get is that Christians and unbelievers can work side by side in the analysis of the paint and brushstrokes. There is no conspiracy in that work to deny the existence of the Painter!
Darwin described natural selection without any personification or deification.
It’s pretty simple.
- There is variation within a species.
- Species will reproduce geometrically until limited resources prevent additional population expansion.
- Limited resources will necessarily result in some individuals having more offspring than others.
- Variations will influence who has more offspring.
- Variations that aid in having more offspring will be passed on at a higher rate.
No personification. No deification. Just simple observations and a logical argument based on those observations.
That’s fine as an estimate of the single-base substitution rate – which is the most important one for some purposes, since it’s the only kind of mutation for which we have any kind of reasonable estimate of the mutation rate. Larger fractions of the genome differ because of insertions and deletions, including duplications of large chunks of DNA. If we’ve got two nearly identical copies of a long stretch of DNA and chimpanzees only have one (or vice versa), that represents a big difference. Why anyone thinks that sort of difference undercuts common ancestry for humans and chimpanzees is a mystery to me, however.
Even though you and I may differ in our beliefs, we both understand the limits of methodological naturalism in the very same way. Like you say, it’s not hard to understand. This is why the religious and non religious can both do science shoulder and shoulder without any issues.
@DennisVenema came up with a great way of expressing it, IMHO.
How is that making methodological naturalism any clearer?
Well, thinking further about this topic: It’s far more subtle, I think. There are catalysts that are really simple and common, like metals and many other simple molecules, like OH- etcetera. Therefore, it’s not surprising that oligopeptides can have a catalytic function.
However with regard to Axe’s study:
- If I am right, Venema confirmed the validity of his study for that specific structure
- There are more studies, generating such extreme low chances
- It might be true that it is not taken into account “that the probability that unrelated proteins and peptides would have a similar activity.”
However, if you substantially want to lower 10^-50 to 10^-30, then you need that there are 10^20 unrelated proteins and peptides that have a similar activity. Yes, we know that there are unrelated structures that can have the same activity, but numbers of 10^20, and all different from each other, is a bit high.
However, I haven’t studied Axe in very much detail. A few weeks ago, I checked the book of Stanford: Genetic Entropy . He had some statements that I didn’t believe. That check has delivered me really nice odd results.
Sorry Dale, I was going to reply more fully to this, but I’ve been too busy this evening doing science to spend any time talking about science. Here’s a photo of the side project I’ve been working on for you to enjoy:
I’ve read the data sheet for the ICL7107CPL integrated circuit, on which it is based, from cover to cover, and I haven’t found the words “methodological naturalism” in it anywhere.
Get out of there, it’s gonna blow! 
Dale noted privately that:
An algebra textbook doesn’t need to contain the word ‘algebra’ either. And as a matter of fact, that data sheet does not contain the words ‘integrated circuit’ in it anywhere.
True enough, though it’s hard to imagine an algebra text that doesn’t have the word in it!