Biological Information and Intelligent Design: Meyer, Yarus, and the Direct Templating Hypothesis

Eddie

Some of the perils of modelling selection from purely genomic studies are mentioned here. No doubt the models are continually updated, but are always vulnerable to their theoretical assumprions.

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@Eddie you are horribly misreading the paper Jon linked to. Did you even read it?

The paper starts with a history lesson with THREE misconceptions about evolution (misconceptions that are often promoted by ID advocates) associated with neo-Darwinism. This of course totally validates my consistent claim that neo-Darwinism was falsified a long time ago, and is not synonymous with modern evolutionary theory. The article prefaces these misconceptions by saying:

As a result of these gaps in knowledge, certain unrealistic views became part and parcel of the Neo-Darwinist account of natural selection, and unfortunately, many of these are still with us, at least implicitly. The following are three major areas of misconception among the Neo-Darwinists:

Here is the point. All this stuff was fixed with neutral theory (which was addressed in the next section of the paper). Then the paper instead focuses on better ways to detect positive selection when it occurs. Remember, neutral theory does not deny the importance of positive selection, but correctly recognizes that is quantitatively less important than other non-Darwinian mechanisms.

So of course it is silly when ID people argue against neo-Darwinism as if that is the position of mainstream science. That is an absurd misrepresentation of our best understanding of evolution, and fundamentally misleading to the public. It is about as sensible as arguing against the “sufficiency” of Newtonian Physics as evidence for rejecting Einstein’s Relativity. The whole argument relies on a false equivalence between neo-Darwinism and the modern understanding of evolution. As the referenced paper makes exceedingly clear, these are not the same thing.

So if ID was arguing against neo-Darwinism to correctly teach the modern theory of evolution, that would be great and welcomed. Instead, they argue against neo-Darwinism (conflating it incorrectly with the modern understanding of evolution) as if this is evidence for design. That is simply bad logic, whether or not it is intentional or ignorant misrepresentation.

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Yes Joshua

Nevertheless, Hughes complains that at the time of writing, “hundred” of papers were still being published in which the lessons of neutral theory have not been suffficiently learned, and hence the assumptions of the models used lead to badly skewed understandings of selection.

More critically, he criticises the practice of using any model that is not cross-checked against empirical data (once more suggesting that such methodological error is widely practised). He does, indeed, repeat the claim in his 2007 paper and (if memory serves) one three years later - clearly he felt the lessons were still not being learned even in 2010.

He doesn’t mention ID at all, and the context of my entire argument on this thread has not been about ID, but the limits of science with respect to contingency and complex systems, so it seems somewhat diversionary to turn Hughes’ strong critique of methodological errors within mainstream biology on to what ID people say. That wasn’t the point of the citation - nor even of Eddie’s comments on the thread.

That said, I accept the thread title is about Intelligent Design, so my whole argument about contingency is off-topic… but I think, more significant to EC than the tired old culture wars stuff.

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Information Theory is a very technical topic that is not easy for people to apply correctly or assess. I am not going to litigate this in internet comments. I’m working on some academic papers to address these issues. I’ll let you know as they are published.

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I agree.

I agree here too. That is more important, and you are starting to clarify your thoughts there. Great. If you can find a way to express it that doesn’t seem to be disputing the details of NS, you will be onto something. I’ll point out also that Francis Collins has made comments supporting your notion (he explicitly references the KT event). So you are in good company.

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Ah, but what are we to do about grasping “the details” when natural selection is no longer the sine qua non of evolution? I see that Austin Hughes actually died last year, resulting in a welter of tributes to his intellectual strength (and his orthodox Catholic faith, incidentally - his priorities were oredered, one obituary said, as “faith, family science”).

That obituary led me to a more recent (2011) paper of his, proposing that much adaptive change has nothing to do with natural selection at all but the “plasticity-relaxation-mutation” model for which he offers evidence. Rather cheekily he heads the paper with the original French version of Laplace’s saying about God, “I have no need of that hypothesis,” clearly not meaning his own.

Questioned in a podcast on the article, Hughes replied: “There really isn’t all that much evidence that [natural selection] actually happens to the extent to which it would be needed to explain all of the adaptive traits of organisms.”

Well, who is qualified to answer that? Not, I imagine, the hundreds of population geneticists dutifully turning out the papers whose entire basis for recognising selection he castigates in the 2006 paper. So PRM is an adaptive mechanism in evolution, and so is adaptive selection - which is more important is a matter for scientific debate, and to treat either as beyond criticism sounds more a cultural response than anything.

But if a member of the public were to conclude that he’s been told - and is still being told in popular sources - a story-book version of an evolutionary process that is actually highly complex, highly contingent, and regarded in different and often incompatible ways by different biological specialities, then he wouldn’t be far wrong.

All being well, he’d slap them on the back and wish them well in a fiendishly difficult endeavour - but I suspect he wouldn’t be too keen to accept that evolutionary theory should have any significant impact on his view of the nature of God and his role in Creation.

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In modern scientific discourse, there is no such thing as “formal academic debate”. We resolve disagreements in the peer reviewed literature, with carefully reasoned arguments, data, and established methods.

Have no fear. I am starting to engage some of the most egregious of the ID arguments in just this way. The wheels of peer-review turn slowly. Be patient.

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We are in culture war. You are right. However, I am not seeking victory as you define it. Instead, I am seeking peace, and for the Gospel to be clearly declared in the scientific world. I do not care if people disagree with me about evolution. It just does not matter to me. They can and believe whatever they want. The Church, however, I want to see return to the message of the Gospel when they engage with scientists.

Fight on if you must. You certainly are a culture warrior. You love the fight. And warriors usually do not like those seeking peace.

@Eddie, you really love to have the last word. So go ahead and take it. I’ve made all the points I need to make for now.

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So you tempted me to respond =). I think you need a better last word than this silliness.

False. Frankly, this approaches slander.

I get along just fine with many ID, YEC, and PC people. BioLogos and RTB as a whole has exemplary relationships in the midst of disagreement. I work just fine with the anti-evolution committed Concordia Seminary. This works because I do not care if they accept EC. They do not care if I belief evolution. We find enough common ground in Jesus to work together as family. This is the peace I seek.

False. Remember, I regularly call Behe and example of a theistic evolutionist (I thought you were TE too). We disagree about the science, but the two of us get along great. The root of your confusion might be in how you see disagreement. When I express my scientific opinion I do not expect others to agree. Agreement is not the peace I seek.

I can and do admire the sacrifice of many (e.g. Behe, Gonzalez) that are actually scientists that paid a real price.

But BioLogos also is fighting against a non-teleological understanding of evolution. Our strategy just works better in science. We make the same theological point, without getting kicked out. And if this was “all that ID was asking for” we would not be having this debate. Clearly, ID wants much more than this.

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I have no problem with their objection to non-teleological evolution. I have the same objection.

Do you really want to argue that ID is equivalent to “just war”? You know that is the same thing that got us stuck in Iraq and Vietnam. Perhaps the analogy is actually quite good. ID is certainly stuck in a quagmire.

One personal objection to ID is their use of the “ways of the world” to fight this battle. Instead of seeking peace, some seem fixated on war. Instead of confident trust in scripture alone, they seek to add to it with human science. I cannot go there with them. I would rather use other means to accomplish the same purpose. I would rather pursue peace.

All the same, thanks for laying this all out. You are clearly explaining the logic of war. Before us all is this choice. Will we choose peace, or will we choose war? I choose peace.

False. Once again, this borders on slander of both EC and YEC.

I do not seek for YECs to change their mind. I just ask that we accept each other as family, as fellow members of the body of Christ. While AiG and Ken Ham refuse to do this, many YECs do. Of course, they can continue to be YECs. I do not care.

They do not have to accept evolution, but they must (if they are to follow Jesus) accept the evolutionist. And I must accept the young earth creationist too, even though I reject young earth creationism.

This is the radical call of Jesus in the creation wars.

Of course, this is exactly what is happening all around the country. I just gave a talk to a church full of YECs this last Tuesday about evolution. They did not agree with me, but respectfully heard me out. I did not try to change them, but to explain my position. We accepted each other as family. Fondly, many of them prefaced their comments by saying, “first, let me emphasize that I think you (a TE) are a Christian.” So I certainly object to you calling all YECs totalitarian. This is just false.

I think YECs can and should teach their own kids whatever they want at home and church. I would oppose any legislation that threatens this. I do not think that religious teaching belongs in public high school biology classes. Most of them (even AiG!) agree.

BioLogos is a big tent too. It has the admiration of atheist scientists, and also includes Open Theists and reformed providentialism. Even though you specifically oppose Open Theism and attack BioLogos relentlessly for including them. This is actually a pretty common sentiment among ID people. Apparently, in ID land, you can work with the Unification Church and Muslims, but not a Christian who thinks differently about God’s providence. Somehow, a variant of Christianity that affirms the Resurrection (Open Theism) is a more unacceptable heresy than the Unification Church, Hinduism and Islam.

Go figure.

I am not an Open Theist, and in science I work with people of all faiths including Hinduism and Islam, but let’s be real. Every social/political movement tolerates disagreement on many issues. All you are saying here is that you “fit” in ID. Partly because they reject some of the same people you think are heretics.

And I would point out that ID cannot tolerate my position either, even though I believe in God’s providential control of all things. I agree God designed us. I agree that evolution has purpose. I agree the evidence points this way. However, because I disagree with the famous ID arguments I am often doubted and attacked. It is too bad. I could be your friend.

Science is NOT inclusive. It is not the Church.

It is privileged to be part of the scientific community, an earned right, and none of us (certainly not me) decide who is included. Why would you expect atheist scientists to be fair to you?

I am empathetic and respectful of their plight. But these things are not the same.

The difference is that the Church is inclusive, in a way that science never can be. No one has authority to exclude EC/TE from the Church because it is Jesus who grants us our seat here. He pays for it and gives it to all who trust in HIm. The peace I seek only requires we live in accordance with this Truth.

Moreover, it silly to say that this is “all that ID is requesting”. You know better than that.

I totally support them in this. They should read nature however they want. Of course, since they reject the rules of mainstream science, I am not scientifically convinced. But they can do whatever they want. No one is stopping them from this. Scientists, however, do put their foot down when ID people claim the authority of “science” to make their point.

I know you make light of these demarcation issues. But this is the center of the conflict. No one is thought policing here. Rather, the authority of science is buing guarded from those that do not do science.

In principle, I would support the tenure of people that disagree with evolution. And so do many of my colleagues. Just look at James Tour. He has done pretty well (even as he has faced discrimination). Regardless, 3 dozen peer-reviewed publications is not enough for tenure at WUSTL (my institution) so I’m not sure what to make of your counterfactual any ways.

Yup, some individuals. I’m making friends all the time with the non-combative ones. The combative ones (which appears to include many at the DI, though not all) seem to be in the positions of power. Go figure.

Well, it doesn’t include atheists. Given that most scientists are atheists, they are better described as trying to unify all the theists in warful opposition with mainstream science. This, of course, is almost an exact restatement of the ID strategy.

Like it or not, the most pluralistic of the camps is mainstream science. It is more ecumenical than any of the creation camps. Shocker. I know. And it is rough to be excluded by the most open-minded, largest, and most powerful of all the campus. So I see why ID is upset. Maybe they should have been trying to find a way to peace with mainstream science, instead of trying to overturn it.

I am not asking them to capitulate. I am asking them to confidently seek peace. A book quite relevant here was just published by my colleague John Inazu,

I would say ID is a great example and product of the culture wars. It is not that I “accused you of being a culture warrior”. You took that label on yourself, and invoking “just war” as the reasoning for the ID movement. In my view, this is an extremely insecure response to the challenges of secular society. For many (of course not all), ID is a defensive response to fear of secular science.

I instead look to peace through confident pluralism. I hope that we could all (no matter our beliefs about origins) move to confident faith within our scientific world.

Now @eddie, if you have it in you, try again at your last word. Please do not slander me in the process.

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Joshua has just responded to this, and I fully agree with him. I am a strong proponent of teleology in evolution, (as I hope to be able to prove to you shortly. See Joshua’s previous comment about the slow turning of the peer review wheels). Some ECs are less sure about teleology, or are less interested in it. But all of us (I think it is fair to say) agree that biology, much like the entire cosmos is designed. I have heard Deb Haarsma, Dennis Venema and others state this. And here is the critical point.

The existence of Design does NOT contradict Darwinian evolution.

Yes, Darwin stated that his theory made teleology and the need for design moot, and Dawkins says that evolution proves that the apparent design in biology is simply that - apparent. But no evolutionist has ever claimed to have proven the absense of design, whether intelligent, divine, or accidental. The atheists hold the philosophical view that since there is no God, and no need for God or God’s intervention at any point in the history of life, then all appearances of design are simply artefacts of the power of natural selection in shaping biology. The EC argument says that one way or the other (and the details of what way precisely are not specified) God IS the designer as well as the Creator of everything, including life.

I believe that God might very well intervene during the evolutionary process, but as you might have seen in the latest Hump post, I believe such interventions are not scientifically detectable. But that isnt important, what is important is that the EC quarrel with ID is not about the existence of design, nor about the existence of teleology, but about what ID claims.

And here is the problem, Yes, Denton limits his claims. (I havent changed my positive view of Denton’s book, as described back in February here). But other IDers claim that design negates evolution. It is a negative argument. And in fact we now find ourselves returning to the original topic of this thread and the blog post by Dennis. Meyer and Nelson had published a paper that attacked the work of Yarus. While I agree with a good deal of their points, I also pointed out previously (as Dennis mentioned) that their attack included some statements that criticized Yarus for things he never said.

If we retain the metaphor of a struggle, I dont think its fair to say ID is the innocent victim of EC attacks. Almost all of ID theory is based on a negative assessment of evolutionary theory. I agree (with Jon, often) that ID has some valid points about the role of contingency and the insufficiency of strict neo Darwinist views, but many ECs (as Joshua has pointed out) feel the same way. So in fact do quite a few non theistic evolutionists.

I think Joshua’s point about not wanting to be a warrior is extremely important. As scientists (or as those who view science as valuable, which I assume you do) we must make peace over our shared vision of science as one of the gifts we have been given to understand our world. As Christians, we should should be striving to find peace in our shared vision of the glory of our Creator, and joy in Christ’s message of love. I think it is time, and you yourself have said as much very often in this forum, for ECs, IDs, and everyone else who share the human quest for knowledge to focus on what we agree on, how we can move forward in our understanding, and try to de-emphasize the importance of our disagreements.

I know this isnt easy to do. But as Joshua said, our enemies are not evil, they are just wrong ):wink: So lets keep talking, until we all find the truth.

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Secular universities should discriminate against those who think that mere notions are sufficient. Develop the notion into a testable hypothesis and test it.

The idea that universities should not discriminate against those who refuse a priori to actually do science and produce new knowledge is absurd.

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That’s high-school debate. How often would such debates be held?

[quote=“Eddie, post:211, topic:5784”]
That is sophistry. In publishing “carefully reasoned arguments” against the positions of one’s colleagues, one is engaged in “formal academic debate.”[/quote]
Where are the judges you specified above?

I don’t think that Swamidass mentioned a stage.

[quote]It’s still a debate if in competing journal articles and books evolutionary biologists oppose one another’s views on evolutionary mechanism.
[/quote]You clearly stated that there needed to be judges for the debate to be properly formal. Who are they?

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Hi Joshua,

In the midst of your wonderful essay, you committed a typo that changes your intended meaning. I think you meant something like:

“Since they have rejected the rules of mainstream science, I am not scientifically convinced.”

Blessings,
Chris

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