Doug Axe and Wistar II

(S. Joshua Swamidass) #1

Continuing the discussion from Is Wikipedia Fair to the Biologic Institute?:

This was originally on another thread, but it made more sense to separate this out into a new topic…

Regarding Doug Axe

Finally, I was not there, and I do not know how accurately Brooks represented the situation. However, I did carefully read the very long article and found it to be damaging for a different reason. Several of the critiques he raised of ID arguments back in 2008 appear valid, and have not been substantively engaged by ID proponents. Remember, this was written in 2008, ten years ago. For example, look at this exchange (which is germaine to Doug Axe’s work, not Ann Gauger):

Gunther Wagner congratulated Dr. Gauger on doing some great experimental work, but noted some logical inconsistencies in inference. The first is a phylogenetic comparative issue; it is necessary to know the ancestral state of the two proteins. If you are dealing with two proteins each derived separately from a common ancestor, then the experiment involves a minimum of two steps, backwards to the ancestral condition and then forwards to the alternative derived condition. It seems unlikely that you would be able to do that experimentally, especially if you have no idea of the environmental conditions under which the evolutionary diversification took place, and no idea if there were any intermediate forms that no longer survive.
https://pandasthumb.org/archives/2008/02/id-intelligent.html

This appears to be a valid critique of Axe’s inference based on the papers he has published on this. Rather then engaging this critique with better experimental design, it appears he has just ignored it. I find it concerning. As I had though I might have been the first people to raise this concern directly with him. It turns out that he had know for years that this was critique. That is a legitimate and substantive critique, offered now by several biologists. It needs to be engaged by Axe.

In this case, I know that @Agauger was the presenter, but this has become Axe’s public argument. It seems that Axe is really the one responsible for engaging this criticism. Remember, I made that same point to him directly several years ago. He has heard it now from more than one source for ten years now.

I know there is unfair treatment of ID proponents, but in my world at WUSTL we would not tolerate ignoring legitimate critique from anyone, ID or not. It is not good scientific behavior. Instead of focusing on the bias, I wonder what would happen if Axe would actually engage the legitimate and valid criticism of his work by qualified scientists, and also surprise us by retracting claims he could not defend. That would be great to see happen.

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What Theological Claims Does ID Make?
(Blogging Graduate Student) #2

Ann has replied to this point before:

https://evolutionnews.org/2012/07/on_enzymes_and/

Needless to say, I don’t find it convincing.

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Is Wikipedia Fair to the Biologic Institute?
(S. Joshua Swamidass) #3

Good point. I probably need to revise that language. But I’ll leave it for now. Ann is not the one who has written a book relying on this like Axe.

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(George) #4

Disputing ID is only necessary if a person thinks there can only be ONE WAY for God to create humans.

The arrival of Peaceful Science eliminated the Either/Or dilemma!

At last … Pax Vobiscum! God created humanity using BOTH methods of providential engagement in the Cosmos!

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(S. Joshua Swamidass) #5

@art did you ever engage him on these points?

(Arthur Hunt) #6

I don’t think so. But I believe this may be putting the cart before the horse, for me at least. Axe has yet to address the core issues I raised way back in 2007. This discussion moves pretty slowly (something once every 3-4 years), but I am not very confident that we can ever get past these problems. Certainly, it seems that, with his book, he has moved past this.

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(S. Joshua Swamidass) #7

Well he has engaged you before, and Discovery does follow Peaceful Science, for better or for worse. Perhaps invite him to a dialogue here on the points you raised. I’ll make sure it is seen by them.

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(T J Runyon) #8

A discussion with @Agauger or @bjmiller may be beneficial as well since both have questioned @Art knowledge of the subject matter. If I remember correctly, Miller even went as far as saying Hunt didn’t even really deserve a response from Axe because he isn’t an expert in protein evolution. Of course, then that would mean no one should have to respond to ID proponents because the majority of them write about things they weren’t trained in. Believe he said that on this forum

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(Arthur Hunt) #9

I would be on board for such a discussion.

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(Arthur Hunt) #10

I long ago fell out of touch with Axe. I suspect that he will learn of this discussion in due course (paging @pnelson) , and can join if he is so inclined.

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(S. Joshua Swamidass) #11

Perhaps clarify what you want to talk to him about, lay out some of the history, in a new topic?

(Arthur Hunt) #12

I will see what I can come up with. In the meantime, if any of the principals mentioned here care to jump in, feel free…

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(Herculean Skeptic) #13

I was wondering if you could explain why you don’t find her response convincing. I read it and it seemed to make sense and to be logical. It seems that what @Agauger is saying is that there was a sequence that once went from A to Z, step by step, from letter to letter… So, as an experiment, some folks looked to see how difficult it would be (or challenging) to replicate the step from X to Y, for instance. They found that it was quite challenging. The critique seems to be that in order to set up a truly significant experiment, one must begin at step A and not some other point in between.

Is it that the step from X to Y within the lab would have been more challenging there than it would have been in nature? Apologies in advance for my simplistic version of the issue. I’m merely hoping that I might be able to better understand the issue from my own elementary perspective.

(Blogging Graduate Student) #14

It’s not that a sequence went from A to Z letter by letter, it’s that a sequence started at A, then diverged into B1 and B2, and then each of the 2 lineages continued towards Z1 and Z2 through C1, D1, E1… and C2, D2, E2… etc.

What Axe and Gauger did was to try and convert Z1 into Z2, whereas a more realistic experiment to recapitulate the process that gave rise to Z1 and Z2 would have been to infer the sequence of A, then try and evolve it stepwise into Z1 and Z2.

Ann’s response to this criticism is to say that it’s still interesting that it’s so hard to directly convert Z1 into Z2, because that implies functional changes are hard in general. But this is a strawman of evolution, because no one thinks that all possible transitions are readily accessible under realistic selection regimes - sequence space is constrained. Ann mentions this constraint (quoting McBride), but doesn’t really rebut the point, she just hand-waves along the lines of: “well, if it’s constrained how did so much complexity manage to evolve?”

As you say, there are also additional things to consider too, for example it could be that there were different selected functions along the way to the modern functions of Z1 and Z2. It’s feasible that literally every step along the way was selectively advantageous, making the paths from A to Z1 and Z2 very easy to travel in nature, wheras a lab experiment selecting specifically for the functions of Z1 and Z2 from A would find lots of neutral steps were required.

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(Herculean Skeptic) #15

Thanks very much for that thorough explanation! I really appreciate it and it makes sense.

So, would you say that the only viable (as in scientifically significant) experiment in this case would be the A to Z1 into Z2? Is there any value or anything significant to be learned from the experiment that was performed (from one letter to the next?)

I’m trying to determine whether your ideal experiment would be significantly more telling, or instead that there is really no value in replicating this single letter step at all? Would the experiment that you suggest have been feasible for them to complete instead? Would it have been (or should it have been) the obvious choice in experiments for them rather than the one that was performed?

Again, thanks very much. Your explanation was very helpful!

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(George) #16

@evograd & @swamidass

ID and Evolutionists should operate under a TRUCE in this list! How are we supposed to get to the business of integrating Special Creation with God-Guided Evolution if FIRST… we SOLVE tge dispute of “Science proving Design”?

Since BOTH sides agree to design in general, I think we will find that, over time, the ID dispute means less and less in terms of the Big Picture!

#17

In science the quest for truth is more important than making fake truces. Let the facts and arguments speak for themselves, and let a consensus develop as to what is true and what isn’t.

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(Ashwin S) #18

George is not talking about Science… He is talking about theological discussions…

Its more or less established that Science doesn’t directly address the question of Design as of now.

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(George) #19

@Patrick,

Typical bombast.

There is s difference between a Fake TRUCE and a Temporary Truce!

#20

The word of the day is “epistasis”. This is where mutations have different effects in combination than they do individually. In other words, mutations interact with each other.

The best analogy I have come across is the game of Jenga. If you have ever played the game of stacking blocks ever and ever higher you will have noticed an interesting phenomena: if a block can’t be removed at one point in the game it is possible that it can be removed later in the game. As weight shifts around and different patterns of blocks emerge it change the pressure on the blocks below. If you remove a block at one point of the game the stack will collapse, but if you remove the block later the stack doesn’t fall. Mutations can act in the same way. A mutation or specific amino acid may be vital at one stage, but through mutations elsewhere in the protein it can lose its importance.

This means that if you are going to model the evolution of a protein you need to start with the ancestral sequence because the interactions between mutations can be very important. Continuing with our Jenga analogy, if you start with two identical Jenga games and then let people play them in parallel you will end up with different Jenga stacks after a while. Even though they started out the same there will be blocks that are vital in one stack that are not vital in the other stack. The same situation exists in proteins. Therefore, you can’t use contemporaneous proteins to model the historical evolution of just one lineage.

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