Biological Information and Intelligent Design: evolving new protein folds

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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Then we are in agreement, and if so I don’t understand the uproar from you and everyone else.

I will review your paper, but can’t understand why you would reject my proposal off hand as if more and direct testing hurts.

Sorry, what exactly have I been “spouting here nonstop” that is not to your liking?

If you have a choice between a model and the actual data, which one do you chose? I am proposing a feasible test. Any problems?

No one here is disparaging quality work. Why do you insist?

You got the wrong straw man. I am an expert in computer modeling, hence am not dismissing the whole field. But between the output of a computer simulation and actual field data, you should always chose the field data. I am proposing a test to provide real field data rather than a computer simulation. Any problem?

Sorry, what has your religion to do with anything I said?

When did this turn into a discussion on religion?

Direct testing is great, but the study I pointed to is direct testing too. I take exception to the notion that there is only one way to directly test this.

The problem is that you are experimental is approach is problematic for three main reasons:

  1. The standard for declaring “success” is subjective and poorly defined. We can make things more objective and precise, and those sorts of studies have been done for a while, but that leaves us with another problem.

  2. The standards for “success” you gravitate to (generation of large amounts of different morphological differences) are usually predicted by evolution theory to be impossible on lab-observable time scales. If we were successful by your standards in this experiment, it would contradict much of what we know of evolution. So it ends being an attempt to test “straw-man” version of evolution that we do not agree is plausible.

  3. Even when we can show the emergence of complexity in the lab, the experiment produces data that leads you to dismiss it as “just microevolution, not macro”. When we can recapitulate the emergence of complexity (e.g. evolution of multicellularity), in these cases (because it is in the lab) we can often decompose the pathway that evolution took. Knowing the simple pathway, you can reject it as easy because there was a pathway. Well yes, but the point is that we think there is a pathway to most everything we see, and the fact that we found a pathway encourages us, even though you take it as evidence that we are wrong.

So in the end, this experiment is not possible to clearly define, and nor does it discriminate the theory. We both predict the experiments you want to do will not work.

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Hi Nonlin -

If you have to choose between the theory of photons and the Michelson-Morley data, which one do you choose?

If you have to choose between the general theory of relativity and observations of the procession of Mercury’s orbit, which one do you choose?

What I’m getting at is that you can’t erect arbitrary walls between scientific theory and scientific data. A good scientific theory both explains the data and predicts future data. That’s what the theory of photons does, it’s what the general theory of relativity does, and it’s what the theory of evolution does.

Best,

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The problem is not so much your opinion (although I do strongly disagree with it), but the completely overblown confidence with which you state it. You are consistently dismissive of other people’s work as you make sweeping statements about evolutionary theory. As @BradKramer said, this attitude discredits you and your ideas.

If you want specific examples, here is a small selection. I have added some of my expressions of disbelief as I read your stuff:

Wait, so thousands of scientists around the world are doing stuff that is not science? A guy with a blog gets to determine what qualifies as science instead? The whole world makes more sense now.

So studies of morphological change are dismissed? Don’t bother with the scientific literature, ignoring it is much easier. Better spend your time teaching those scientists what actual science is about.

WOW. If you think that’s how biologists have gone about this… You might need to reboot your reality checker.

Touché!

It’s not useful to separate these two topics. Evolutionary theory is crucial for making sense of genetics and genetics provides strong tests of evolutionary theory.

Thanks for rejecting whole swathes of scientific work. After years of computational modelling I finally realize it is all based on… bovine feces.

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