Biological Information and Intelligent Design: evolving new protein folds

You want to replace direct testing with “analyzing sequence data for nested hierarchies”? What possibly can be your justification? Are you aware that these nested hierarchies are a human construct?

E[quote=“NonlinOrg, post:131, topic:34703”]
It’s not my “satisfaction” that matters.Maybe it’s easier to see what other known bacteria are related to E.coli, yet clearly different and to analyze what makes them different. Then to look for a combination of those factors.
[/quote]

Well, common descent has already been proven to my satisfaction, and to many others’ as well. I don’t know if you can speak for anyone else’s conclusions following this experiment but your own. So yes, your satisfaction is the factor in question.

You mean known, related bacteria like salmonella? Ok. So what makes salmonella (or a different bacteria of your choice) different from E. coli?

Maybe! Depends how you define the species. Pretty sure that was @DennisVenema’s point.

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That’s fine. No one is forcing you into knowing more than you want.

@NonlinOrg

If the strain does not successfully mate with other populations equally as well as bacteria that are not of that strain … then we are half way to speciation.

Over time… just a few more changes … and voila … we have something new … that cannot reproduce with any other life other than with it’s Own Kind.

You can put that in the bank…

[quote=“NonlinOrg, post:133, topic:34703”]
Are you aware that these nested hierarchies are a human construct?
[/quote]Protons, neutrons and electrons are human constructs, too. If the human construct explains the data well, though, it is good science.

“essentially, all models are wrong, but some are useful” - George Box

Does that mean you’re not interested in defining differences between bacteria anymore?

A proper analysis will determine if a nested hierarchy is just a human construct that sort of resembles the data, or if a nested hierarchy is actually the best fit explanation for the data. But honestly I don’t know why you would need a detailed study to prove this; all you have to do is look at any number of categories of animals, like vertebrate, tetrapod, mammal, rodent, house mouse, and you see nested hierarchies. Genesis doesn’t describe why ‘mammal’ is a real category, but that doesn’t mean it’s not describing the real world.

So basically, either God created animals in nested hierarchy categories that looked like a pattern of descent, or animals all actually descended from common ancestors. This is only confirmed, and strongly, when you look at the genetic data. If you’re interested in actually looking at such a study, there was discussion of one here not long ago:

[quote=“NonlinOrg, post:133, topic:34703”]
You want to replace direct testing with “analyzing sequence data for nested hierarchies”? [/quote]
That is direct testing. Common descent makes robust predictions, not just of vague similarities.

Science!

[quote] Are you aware that these nested hierarchies are a human construct?
[/quote]No more than any other mathematical fitting of the data. Common descent predicts them, you see.

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Honestly laughed out loud when I read this. Pure entertainment.

I wonder how many Nobel Prizes have been granted for largely computational work? Their have been several. In a field adjacent to mine, most recently Karplus was awarded one in 2013: https://www.nobelprize.org/nobel_prizes/chemistry/laureates/2013/karplus-facts.html With some of the fundamental advances in machine learning, it would not be shocking if we saw a Nobel Prize for Deep Learning in our lifetime too.

Going back to the beginning (of science), Kepler and Newton were just computational researchers too.
Stepping out of mainstream science, there are a lot of ID and YEC people that do computational work. Jeff Tomkins, Todd Wood, Kirk Durston, John Sanford, etc. Given that most do not do anything at all resembling bench science, glibly rejecting computational work does not seem strategically wise.

Regardless, disparaging quality computational work is akin to disparaging math. We are the people that take intuitive notions into quantitative frameworks with mathematical principles.

The real challenge is that it is hard for non-experts to recognize the difference between quality computational simulation and poor simulation. That is the real danger here. The right response is to get more understanding, not to dismiss the whole field.

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When people say the kind of stuff that Mr @NonLinOrg has been spouting here nonstop, one loses all hope of having anything that even vaguely resembles a meaningful discussion… I guess humor is the best remedy for such feelings of hopelessness. Thank you Joshua!

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“Research parasites” is the correct term these days, I believe.

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As a computational researcher, I disagree with this. (though I do agree most fail to understand the role of computational work; and your comment is a great example of this) This is the type of things people say when they want a loop hole to reject the clear consequences of math.

All simulations are limited and do not fully represent the world. The fundamental task of computational science is to limit the complexity of the system enough that simulation is tractable but the details important to the question at hand are reproduced well enough to be meaningful. We design the simulations to test hypothesis.

Of course, simulations can be wrong (in the same way that web lab experiments can be wrong), but we then have to make a good case for what factors we missed that might explain the deviation from reality. If possible, we then include that in the simulation to test if that re-mediates the deviation. Rinse repeat, till we can answer our question.

Of course, simulations make simplifying assumptions. But to the extent they reproduce reality, that demonstrates the complexities they lop off are not important to understand the domain of reality we are simulating. That is not a reason to disregard the whole endeavor.

Driving this process is a nearly religious commitment to falsifying our own work with good “controls.” We poke holes in our theories relentlessly, because that is how we expect to advance our modeling effort.


An Example

A great example of how this plays out in the debate is the intuitive notion that “shared function” caused by a “shared designer” can explain the similarity between life on earth, and specifically humans and chimps. That is an intuitive and satisfying theory. It is rhetorically strong. It is no surprise that many latch on to this explanation of the world

However, as scientists, we have to rigorously test it. You might be at loss on how to test this. Understandable. This is hard to do, and that is why we need clever people to work hard on it. It turns out that we did test this idea… Phylogeny vs Similarity and Function

The summary:

Shared function can explain the similarity between life to some extent (that is good news). However, it is too much of an simplification. We can explain things much better if we also infer a shared history between life (common descent).

Of course neither model explains everything, but that wasn’t the purpose of the simulation. The purpose is to discriminate these two theories of life. And the simulation is 100% successful in this. This is why we say there is strong evidence for evolution (i.e. common descent).

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We have done this. Correctly, setting up a clear experiment with clear defined targets to discriminate multiple theories. This is how science works. We are not post-hoc interpreting the data to our narrative.

There many many more tests just like this.

The key target we set ahead of time is that shared history explains the data better than other principles. That is exactly what we see time and time again.

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Someday I’d love to see someone write, “When people say the kind of stuff that Mr @NonLinOrg has been spouting here nonstop, I stop and ask myself why my religion makes this so frustratingly common.”

Try it.

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Ouch, that hurt! Haha :slight_smile: . I have actually been wondering about that and it’s one of the reasons I am contributing to BioLogos. It can be one of the means to remediate that problem somewhat.

But on top of that, it also has a lot to do with people’s individual traits that can make them more vulnerable to “alternative facts”, so to speak. I have some non- / anti-religious friends who are completely into alien visitations and one even believes in a flat earth (yes, completely flat!).

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@sfmatheson I guarrantee you this is not unique to religion. In fact (I would assert) it is not even most strongly associated with religion.

See it in “full flower” in politics and some not-to-be-named corners of academics too. Atheist scientist are not immune; just read “God Delusion” if you have doubts, or strike up a conversation about politics with a colleague. And of course there are all the non-religious pseudosciences like: irrational opposition to GMOs, anti-vaccers, anti-“chemical” sentiment, and (yes, I’m going there) the Food Babe and Dr. Oz.

Rather than blaming this on religion, it is more correct to recognize it as a fundamental feature of human nature. We are prone to delusion. There is a good helpful religious term for this too: idolatry.

That term “idolatry”, and the Christian conception of it (idolatry is ubiquitous and needs to be rejected), lies at the root of science too. See Novum Organum.

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@Swamidass

You point to the obvious fact that delusion and fact-aversion are deeply rooted in human cognition. But you did not ask yourself why your religion is so deeply addicted to falsehood. (It is. And yes there are numbers.)

I did not assert that only religion, or only your religion, makes intellectual dysfunction “so frustratingly common.” But even if I did, your response is striking in that it simply lumps adherents of your religion in with populations of “atheist” and “non-religious” in their fondness for nonsense. Even if there were no difference in the susceptibility of these populations to alternative facts (and there clearly is), your comments seem to concede that faith in the evangelical god makes no difference. That is exactly the conclusion I reached a few years ago, looking not just at evangelical credulity (which is epic) but also at evangelical conduct.

So my simple challenge is not “defend your religion” or “defend your god” but: ask yourself the hard questions. Ask yourself whether that religion makes a difference.

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The gloves come off! Haha. Just had a post along these lines censored, so I will attempt to tread lightly. In any case, a religion cannot be addicted to anything. People, on the other hand …

The problem is that Christianity is diverse, and so are its adherents. If we want to talk strictly about American evangelicalism, then I would say that your observation has much truth to it. Belief that does not translate into action is dead. Too many people have forgotten the warning of James, the Lord’s brother:

What good is it, my brothers and sisters, if someone claims to have faith but has no deeds? Can such faith save them? Suppose a brother or a sister is without clothes and daily food. If one of you says to them, “Go in peace; keep warm and well fed,” but does nothing about their physical needs, what good is it? In the same way, faith by itself, if it is not accompanied by action, is dead.

“The Christian ideal has not been tried and found wanting. It has been found difficult; and left untried.” – G.K. Chesterton

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This is a good question to ask. It’s far afield from the original topic, but a good question.

Here I have to disagree with you. I think you have a bias (not a prejudice, but a bias) based on your intimate familiarity with one particular group within one particular religion, along with a relative lack of familiarity with other similar groups in other cultural contexts.

I lived almost 5 years among Muslims in West Africa. Trust me, American evangelicals are not doing worse in understanding science.

Also, evangelicals in non-American contexts (Britain, for example) seem to be doing much better than American evangelicals. British evangelicals are Christians, are they not?

Furthermore, non-evangelical American Christians do not seem to have the same problem with science that American evangelicals have. American Methodists and Catholics are Christians, are they not?

Thus I think the problem you have identified is not inherent to Christianity, per se. It is most certainly a big problem in the American, evangelical flavor of Christianity.

Moreover, I would imagine that the problems in that flavor of Christianity impacted you personally, since you taught biology at an American, evangelical college. I’ve had some problems dealing with the intellectual dysfunction at my church, but I always have the option of just lying low for a while. You did not have that option. You had to stand in front of the formation without flinching, where the bullets are flying fastest and most furiously. You no doubt suffered injuries in the battle. If I knew what you experienced, I would no doubt grieve in my spirit for what you unjustly suffered.

If you ever feel like sharing that experience, feel free to start another thread. It would be very painful for your readers, but if it helped you make sense of what happened, I’m sure we would do our best to help you in any way we can.

Best,
Chris Falter

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Ick, no, I’m really sorry that I gave that impression. To me, there is a big difference between saying “give some thought to whether your god makes any difference” and saying, I don’t know, “your god is a monster and your religion is toxic.” The latter would be “gloves off” and I tried hard not to say it.

I thought I made it pretty clear that I was talking about evangelicalism. But I disagree that this is not relevant to the validity or overall social value of Christianity. If those Brits and Methodists and Catholics are all Christians (not my call to make), and if they share the god of the evangelicals of 2016 America, then you all have a pretty big problem that you oughtn’t (IMO) dismiss as some quirky aberration. Does this god do anything?

I am sorry that I have given the impression that I left Christianity solely because I lived and worked among people who were made worse, and not better, by that god. That’s just too simple a story, but I hear it regularly, as if it is axiomatic among believers that people leave because they were “hurt by the church.” For so many of my friends who have chosen unbelief, the final common pathway was about whether the god made credible claims about anything. About making people kind, or about saving people from plane crashes, or about making them live longer, or about growing any of the fruits of the spirit in any detectably higher quantity or, perhaps most importantly in my case, about making people more inclined to at least try to tell the truth. Once I was willing to ask the question, it broadened into “does this god do anything at all?”

You are generous and kind to offer to help me. I am pleased to say that this is not necessary. I have made sense of what happened. And I gained freedom as a result.

Now, I will ask that we close this part of the discussion. It’s my fault for raising the topic of god’s credibility, so I do not resent anyone’s responses at all. And I understand why, as Christians, you are pained and worried that I have renounced faith. But I didn’t join the BL forums to attack belief or to tell my personal story. I came as a friend, first of science and second of those who do science no matter what crazy supernatural stuff they claim to believe. I have friends here, and would be glad to find more.

Peace.

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All good. Welcome, friend.

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