AJ Roberts: One of The Biggest Questions

Adam

(Anjeanette AJ Roberts) #1

@swamidass has stumbled upon or walked directly into one of the biggest scientific questions that needs answering for all interested parties… what is the range of adaptability and plasticity in any one organim’s genome? But he may be premature in asking that someone develop a mathematical model. We may not have the necessary data yet for comparison and we may not have the computational power yet to make the relevant comparisons.

As I think about this quite a bit there are several things that bear on this topic. Two questions worth asking (even though we may never know the exact answer) is: What did God create (what kinds of organisms) and what diversified from his creations through adaptive, secondary cause-and-effect mechanisms? But another important observation is that Linnaeus’ taxonomy was helpful but does not define real distinctions across different phyla that hold in other phyla’s subcategories. This is hard for me to articulate. But thinking about classification, not on morphologies as Linnaeus primarily did, but on genetic relatedness, the biodiversity within one ‘order’ or one ‘family’ may exceed the biodiversity within a different ‘order’ or different ‘family’ in different phyla. In other words Linnaeus’ system is a bit arbitrary. This is definitely well supported by the nearly constant reclassification of some organisms within species, genera, families, and orders that litters the scientific landscape.

The problem is first and foremost one of being able to determine through more complete genomic analyses (not just selected SNPs or gene sets) which ‘kinds of organisms’ are clearly in the same lineage. And to be able to justify those classifications through some type of experimental confirmation. A first step, no-brainer, confirmation would be reproductive compatibility. No doubt there. But a lot of ‘species’ designations and reclassifications ignore this aspect of biological reproductive compatibility. A second type of confirmation could be something like are viable offspring produced if artificial insemination is used, rather than relying on mating compatibilities or success. A third type of confirmation could be something like, are iPSCs transferred from one ‘organism’ to another ‘organism’ capable of rescuing a gene knockout in the recipient organism?

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.) Shared similarities at these levels do not necessitate the conclusion of shared ancestry unless the genomic primary sequences show a mechanistic pathway. In other words something like this: If genetic/genomic similarity is there and range of biodiversity can be shown to be ‘inclusive’ through one of the 3 suggested experimental confirmations (or another similar to those) offered above then we have identified a potential ‘created kind’. (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.)

If the genetic/genomic similarities are not there at a complete genome level and primary sequence level, if experimental confirmations of the kind above are missing and if the only data supporting a common lineage is partial genomic comparisons, shared morphologies, or phylogenomics (without traceable primary sequence pathway changes and mechanisms identified) then common descent through shared lineage is a paradigm driven conclusion and not one necessitated by the data.

This is by no means a complete summation of my thoughts or an RTB model. It is one experimental, progressive creationist thinking out loud about how one would approach delineating a model for testing and confirmation.

So please, try to understand what I’m presenting and suggesting before zeroing in on one particularity I may not understand the same way you do or to the level of sophistication that you do.

Thanks! And pax Christi, AJ


Uncommon or Common Descent?
The Creation Project Recognizes Peaceful Science
Should Scientists Dialogue With ID, YEC, and OEC?
(S. Joshua Swamidass) #2

Hey @AJRoberts, so great to hear from you. I’ll thinking more detail about your post. I really appreciate you being here. I may move this to its own thread, because it really does deserve it a deeper engagement all its own.

You seem to be advocating an OEC bariminology effort. That could be interesting.

Also, looking forward to picking up the conversation with Fuz and you soon.


(Anjeanette AJ Roberts) #3

Josh, yes, I think our way of thinking about this will parallel or benefit from some of the bariminology work by YECers. I’ve been trying to follow the thread on MdN too. And think you’re spot on and have not misrepresented my position there. Cram seems to miss the distinction between doing science and thinking about data from a philosophical position outside the bounds of MdN.


Swamidass is Inescapably a Philosophical Naturalist
(S. Joshua Swamidass) #4

It will be interesting to hear how you avoid the pitfalls that the YECs faced there.

Thanks. Now I’ll just hope you leave a note for @Ronald_Cram to read there.


(Anjeanette AJ Roberts) #5

It’s a very complex question to approach. Pitfalls are bound to occur, especially if we make wrong assumptions about range of biodiversity without one of the suggested experimental type confirmations. Or, likewise, if we make assumptions about range of adaptability in one group and extrapolate that range to another group without experimental justification that the ranges of adaptability should be or are actually similar.


(S. Joshua Swamidass) #6

The main pitfall was that they couldn’t find an objective way to group things into kinds that did not also group chimpanzees and humans together.


(Anjeanette AJ Roberts) #7

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?


Uncommon or Common Descent?
(S. Joshua Swamidass) #8

That is not how I’ve experienced science to work. With that criteria we would never be able to do any modeling because we always can wonder about more data to look at. That objection applies to just about every study ever published, it seems.


(Guy Coe) #9

Well, the other side of the equation is to try to determine what the Hebrew text requires of us to find, at a minimum. That is, when and where is Hebrew idiom at play, and when does it intend to be understood more literally, what is its meaning, what implications does that have for our model building, what are the evidentiary “surprises” to deal with, given our current favored interpretation(s), etc. It really is a specialty subject that may not quickly yield all its secrets, as you say, A.J.


#10

I don’t quite understand how testing breeding capabilities would provide much useful information for the bigger picture of relationships at ‘higher taxonomic’ levels above the ‘mating compatibility’ concept for species. Further, mating incompatibility can occur as a continuum in populations with being readily inter-fertile and being completely non-compatible at the extremes.


(Jon Garvey) #11

I agree with this, and tend to suppose that baraminology tends to do the reverse of what Genesis is trying to say by “kinds”, especially if one takes into account the sequential viewo f Genesis 1 (such as mine), where the creation account presents the first creation, in its completed entirety, as a backdrop to the ensuing drama Eden.

And so, in order to show God’s faithfulness and constant provision, the text tells us that all the living things God made reproduce true. This is orthogonal to evolution, as the “kinds” in question would be “all the stuff you see around that God has made”.

But baraminology treats “kinds” in a special way as a limited number of original types, which then don’t breed true, but diversify in the distant past. Lo, the simple point of the naartive is lost in reconstructive science.


(S. Joshua Swamidass) #12

Except it doesn’t say “reproduction limited to kinds”. It says “many kinds”.


(Jon Garvey) #13

Actually Josh remarkably few kinds, on land three, to be precise - but broad and functionally orientated as livestock, wild carnivores and wild herd animals.


(Anjeanette AJ Roberts) #14

That’s the no-brainer bit and obviously only applies to the most specific level… but it is ignored in redesignations of species today in much of the scientific literature, so it complicates the landscape. I’m trying to specify a landscape. 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. The other suggested experimental confirmations are applicable in a much wider contexts and are meant to give a range of potential experimental verifications when diversification within kind results in failure of immediate or IVF-facilitated reproduction.


#15

Mating is hard to test and doesn’t really give many answers to the questions the taxonomists and biologists are asking. Measurements of gene flow and statistical indicators of reproductive isolation are the metrics they use to study population relationships and variability.


(S. Joshua Swamidass) #16

So Homo sapiens and Neanderthals are the same species and kind?

On a similar note, why can’t God created different species designed so they might hybridize? How could we possibly tell the difference between Sapiens and Neanderthals specially created separately to interbreed, or created from a common ancestor?


(Anjeanette AJ Roberts) #17

I didn’t say it would be easy to get the data. Just pursuing easy data clouds the complexity of the system and ignores the questions we’re trying to formulate and address. And they are asking different questions with a different paradigm in place, aren’t they?

But again mating data is the simplest as the other experimental verifications require IVF technologies, and gene KOs and iPSC experiments, respectively.


(Anjeanette AJ Roberts) #18

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.

If you recall, my Dabar response was you can always fit the data to a model. The common descent model requires a lot of paradigm driven, just-so fillers… the muddy middle layer of mechanism.

I really wonder if it’s possible to rethink this question from outside your (and the vast majority of scientists’) paradigmatic starting point. An inability to think completely from a new starting point with new assumptions about the data alone creates problems, for one, that of seeing another model for what it is without importing problems based on the model and assumptions of which one is trying to step outside.

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 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… 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. Kind of like people could have argued God sure set it up to look like the earth stood still and the sun moved… until we had a better model and better data. (I’m not saying this to push buttons but to help us see different paradigmatic starting points lead to different critiques and different questions.)

To the second, God may have refurbished a pre-existing hominid to form modern humans and pushed the genomic changes necessary… sounds a lot like Ann Gauger’s model if I understand hers correctly. And maybe some progressive creationists would think of it this way too. 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.

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?


(S. Joshua Swamidass) #19

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.

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.

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

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.

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.

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).

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

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

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.

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

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

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,

  1. The approximate timeline of the Genesis account genealogies.
  2. Flexibility to move Adam and Eve whereever you think is best in history.
  3. Connecting the Fall to the rise of civilization and agriculture.
  4. 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.


(S. Joshua Swamidass) #20

I also want to reiterate @kkeathley cautious optimism about the Genealogical Adam. I believe he is on the Reasons to Believe board, right @AJRoberts? Have you seen his comments here? Ken Keathley: Notes from Dabar and a Baptist's Hope



I am curious if Reasons to Believe is going to accept this among their stable of acceptable options. I hope you do, as at least one option among the many you are working on. It might be even be one of the preferred ones, especially if you can hash out plausible ways the larger population was created.

Of course, I want to look at your existing model too. There is no reason to limit ourselves to a single option. For that matter, a more ancient Adam should be on the table too.

If you guys could come to solid scientific grounding here, that would be a real game changer for the conversation.