AJ Roberts: One of The Biggest Questions

[swamidass (S. Joshua Swamidass)]

@AJRoberts

Do my responses make sense to you, even if you don’t agree with the model I’m trying to explain or formulate or think out loud about?

I’m on your side here @AJRoberts. I want to help you guys get to a solid and easily defensible model, even though I affirm evolutionary science. I’m growing more convinced it is not going to be difficult to get there.

Preparing For the Real Dialogue

I also want to state that I don’t want to go to far in public here before talking to Fuz, to hear how you guys would like to work this out. We can either do it publicly, like this, with Fuz’s participation too, or we can do it privately. I prefer public, along the lines of Winston Ewert: The Dependency Graph of Life. That has the benefit of being transparent and well document. However, given Reasons to Believe’s profile, that may not be your preferred approach. We need to have a conversation to figure out the right way to do this, to build consensus here. I don’t want to preempt that process.

As summer draws to a close, and Fuz things about reaching to me, we should have a conversation early and quickly to figure out the best way forward for you, that will balance between openness and confidentiality, as needed. With that in mind, I will briefly answer here a few points on methodology in this type of research. We don’t have to litigate this now, but I want to give you some time to think about this.

@AJRoberts

Josh, you’re asking for distinctions between the models now and that is a different question than building a model for progressive creation and testing its hypotheses, not just through computer, mathematical based algorithms, but additional evidence through experimental verification. If we build a model that matches the data and fits the data better, not just mathematically, but experimentally then you can choose between two competing theories which is best.

I need to push back on that. Mathematical fit is no different than experimental. These two concepts cannot be set up in opposition this way. All quantitation requires mathematics. Any theory that does not have QUANTitation (and is therefore QUALitative) is going to be much more debatable. It might be valid, but it puts on much weaker ground for resolving disagreements. In the conversation right now is the high reliance on QUALitative arguments, and near absence of QUANTitative models, but that can just end to unending debate.

I think we can get you stronger footing in the a QUANTitative model. That is really where the focus should be, and also on human evolution, not places there is less evidence and less theological significance. This is what you, rightfully, care about most, so lets look at it there. The strongest critique of your position is this syllogism:

1. DNA evidence is growing exponentially.
2. Evolution provides a mathematical model of origins that explains a large number of patterns in the DNA evidence, and even has even successfully predicted new evolutionary mechanisms.
3. Some patterns in the data remain unexplained and are active areas of research.
4. Critiques of evolution point to unexplained patterns, but offer no alternative mathematical model for either the unexplained or explained patterns of evolutionary science.
5. Therefore, the only known mathematical model of origins that accounts for most patterns in the DNA is evolutionary science.
6. Therefore evolution is the best explanation.

By evolution, I mean primarily the common descent of Humans with the great Apes, and evidence against a genetic bottleneck of 2. I am not making, here, an argument against God’s action. This is a positive case for evolutionary science, that is growing every day.

Respond with Model Building

This is the argument I can help you with, but your only path is stop doing #4 and produce a better model, so #5 is no longer true.

Others are trying to do this at the Discovery Institute (@Winston_Ewert and @AJRoberts) and in YEC (Jeanson, Carter, Sanford). They are no where near explain the full cohort of patterns that evolutionary science has produced, nor have they yet demonstrated they can explain any new patterns quantitative patterns. @Winston_Ewert’s work is the closest to finding a new pattern, but he isn’t there yet, and its not clear there isn’t an evolutionary explanation for the pattern either.

Nonetheless, these efforts are recognizably engaging the data. Like you, I don’t think the inference to special creation is mainstream science (because that would violate methodological naturalism). This is however legitimate scientific work that tell us how well different theological models can account for the data. One of them might even be true, whether or not it is recognized as “science.” Even if that label can’t be claimed, you still would be able to present a positive mathematical model.

The Objections to Model Building Fail

Many of your objections are not convincing.

@AJRoberts

They don’t have the necessary distinctive data yet. And these data may not be obtainable. It really could be an entirely new category of extensive research projects required to collect the necessary information. Sometimes we have to be patient to realize we don’t have the data to build the testable aspects of the model yet. Maybe? Yes?

Yes, there are unexplained patterns. Yes, there is more data to get. This has 0 relevance to the argument above. There is just a massive amount of data that evolutionary science can quantitatively account for, and no one else can. You have do deal with what we know. Look at the syllogism above? It is not impacted by this argument one bit

@AJRoberts

If organisms are capable of biological reproduction then they should not be reclassified as separate species, and then obviously of the same lineage and same kind.

You are falling into precisely the same trap as bariminology in the YEC world. If that is true, then your position on Homo sapiens and Neanderthals is inconsistent. With this argument, if it is true, it has invalidated your current Reason to Believe model. Is that really what you want to do? Don’t loose sight of the ball. You have to be more consistent than that. In your current model, this is just not a sensible way determining two species are the same kind.

If you go with @Agauger back to 2 million years ago, you have a different problem. But we can get into that later.

Moreover, we know for a fact that we can observe speciation events in nature by apparently natural processes. So that is direct evidence that seems to falsify this criteria for determining evolutionary boundaries.

@AJRoberts

Shared similarities at these levels do not necessitate the conclusion of shared ancestry unless the genomic primary sequences show a mechanistic pathway.

Except DNA analysis has now demonstrated the ability to start from an explained and characterized pattern in DNA, to infer a biochemical mechanism (hertofore unknown), and demonstrated it in vitro to be real. This is such an established fact that your argument doesn’t work. Rather we look for a pattern with modeling, then have reliably been able to go determine biochemical mechanisms that explain that pattern. This is one way evolutionary models of DNA are leading the way in increasing biological knowledge. Given this reality, and the complexity of biology, we see a new pattern and there is no a prior reason yet to think it is not an unknown mechanism.

@AJRoberts

I actually think the modeling done in phylogenomics could shed much insight into common design models. (I actually think this is what is being detected in phylogenomics where the relatedness of proteins that share similar functions but no, or extremely little, sequence similarities at nt or aa levels point to the common forms or blueprints God used in creating the various forms.)

Except phylogenomics is not about similarities, nor is about nested clades. Phylogenomics starts with the assumption of common descent, then tries reconstruct the history of common descent. And it is immensely powerful. No one has been able to merge that with OEC yet in a quantitative way (though I have a proposal at the bottom).

@AJRoberts

(I think the created kinds are likely at a phyla or class level of classification. But again, this could vary from phyla to phyla where the created kind boundaries fall. It could be at the ‘order’ level in some phyla. Or in our order, it could be at the species or genera level.)

That is far far outside the scientific streetlight. Given what we have already observed, the ambiguity here will likely never be resolved with new evidence. That is why OECs are always going to disagree on these boundaries.

This also is one of the pitfalls of baraminology. There is no clear boundaries between kind. Therefore there will be always be disagreement between baraminologists about where the clear boundaries really are. The argument itself ultimately demonstrates that there are no clear boundaries. So the endeavor becomes self-defeating, even as it begs the question. Not a good direction. It is a sure recipe for failure.

Why Theology Becomes Critical

@AJRoberts

I see this creeping into some of your critiques of how we at RTB think about things. One is that you keep saying why would God set it up to look like common descent is true if it isn’t? Another is that progressive creationism requires God start with some pre-human hominid and refashion it to produce modern humans.

To be clear, that is not what I’ve said. The precise language is important here. I did not say it was God’s intention. Rather I’m stating at a bare fact that DNA appear to tell us that common descent was God’s design principle. Maybe God intended something else, but it the cold hard reality you face for the coming decades (even if the situation ultimately changes) is that it really looks like Common Descent.

Perhaps there is a fingerprint of God here (human exceptionality), but there is no fingerprint of special creation we have seen, even when we have looked.

I like that you present to options…

Option 1: Better Progressive Creation Model To Be Discoverdd

@AJRoberts

To the first, we can only say that the data, with all the presumed, unevidenced (actual progressive mechanistic pathways), is compatible with a complex set of evolutionary postulates and placeholders . We can’t possibly begin to say if that is the best model; only perhaps, the best model available today…

That is true. We cannot say common descent is the best model across all possible models. In fact we can be certain our current understanding it is not the best model, which is why we are improving it all the time. However, science only cares to focus on the best model available today. You have to produce a better model, or sit down and get back to work.

@AJRoberts

And if a progressive creationist model, complex as it may be to develop and test, is actually better, then we could say, God didn’t set it up to look that way (like common descent was true) but it just looked that way until we had better data and a better model

Sure. That is a possible end point, but we are no where near there. Right now, from our point of view, it really looks like common descent. It appears like common descent. Maybe there is a better model, but someone needs to buckle down and produce it. It will not be an easy task.

I can estimate it somewhat. If there is a major investment of a highly disciplined computational biology effort (minimum cost would be probably several million per year), it is possible you might get something interesting within the next twenty years. That is about the scale of effort that will take, I would estimate, if you are lucky enough to be right. It could all be a wash too. And it would have to be an immensely disciplined effort, steering away from polemics, to get the science right.

I am not OEC, but if that happens, I would consult for you all, and help you get there. I want to know the truth too. I would be fair.

Option 2: Refurbished Human

@AJRoberts

To the second, God may have refurbished a pre-existing hominid to form modern humans and pushed the genomic changes necessary…

That is not @Agauger’s view, but it is @Guy_Coe’s. I can see why that won’t work terribly well in Reasons to Believe. I’m not sure your base happy with that.

Option 3: De Novo Human

@AJRoberts

But it need not be that way. God could have common elements (think building blocks like DNA, protein, lipids) and common elements or archetypes in mind (language of analogy employed… not suggesting God has a physical brain) and then instantiates a new creature, the one envisioned by God as unique and in his image. Here there is no use of a pre-existing ancestor, and no unbroken chain that would be impossible to distinguish from evolutionary creationism. There would be real divisions of kinds, including modern homo sapiens sapiens.

Sure. That is exactly what I have been arguing. However, you then have a major theological challenge to explain in your current model. If God is tarting from scratch, why the heck did he make this de novo person so similar to everything that came before? Why was it even possible that viable offspring could be produced between Adam and Neanderthals? It seems to directly contradict the basic assumption of your inquiry that there is evidence for special creation, and that Sapiens are a distinct species.

As currently explained, it makes little sense in your theological system. I do not think this is coherent with your theology, unless you can give a reason for it.

The Genealogical Adam

That is where a de novo Adam in a larger population outside the Garden helps you. If you look over my Dabar paper again, I laid down the theological ground work to make your model coherent. The key thing is looking at interbreeding as intentional. We know that not from Scripture, but from the natural theology of observing hybrids.

God could have made Adam and Eve very different, unable to interbreed, but He didn’t. Not because he wanted to make hybrid beast-men, but because Adam and Eve were the same kind, created with the purpose to interbreed with those outside the garden. This is just taking your logic about defining kinds by interbreeding forward into human biology.

I showed from here how you can recover all the key doctrines you care about,

1. Sole-progenitorship from an original couple
2. Special creation of Adam and Eve
3. Original Sin through one couple

and also to give you back even more you see in Scripture, and might have given up on a long time ago,

4. The approximate timeline of the Genesis account genealogies.
5. Flexibility to move Adam and Eve whereever you think is best in history.
6. Connecting the Fall to the rise of civilization and agriculture.
7. A good inerrantist account that competes well with YEC

Where did the population outside the Garden come from? You have several options. Perhaps:

1. Evolutionarily created population outside the Garden in God’s Image
2. Supernatural refurbishment of evolutionarily created population outside the Garden in God’s Image
3. Special creation of population outside the Garden in God’s Image

All these things work, though perhaps #2 has the same problems as your current position. One intriguing possibility is to extrapolate a Genealogical Adam back as a mechanism for introducing genetic novelty into evolution at times. Perhaps God regularly intervened in Creation by de novo creating animals to interbreed with existing animals, giving rise to better forms.

That seems like a model that might fit OEC creationism’s bedrock assumptions, but be entirely consistent with the evidence. If we can see that pattern in humans, why not wonder if it happened with animals? The only thing you would have to give up, however, is the oppositionalism to evolutionary science. I wonder though if that is important for your base. At least its good work it out so those that want to be less confrontation have a way forward.

Where Now?

So that was a lot. I’m taking your work really seriously @AJRoberts. When it makes sense, please run this thread by Fuz. I’ll look forward to hearing from you end of the summer. I’m looking forward to serving you here. Any further thoughts or reflections you can give me in the mean time are greatly appreciated. You are always welcome here.