Gauger and Mercer: Bifunctional Proteins and Protein Sequence Space

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Where Does that Leave Us?

At this time,

  1. I am going to carefully split out some of the side trails that are important, so they are not lost in the shuffle.
  2. I’d suggest that final comments are made by everyone participating here.
  3. I’m putting a timer on this topic for it to close in 48 hours.

Remember, this not the first or the last of our exchanges. This one was somewhat bruising too. I want to emphasize that @Agauger acknowledged mistakes and was doing her best to engage. At the same there was high frustration from @mercer. Somewhat like a dam breaking, it seemed like there was a lot on his mind, in addition to a lot of frustration behind these things. I understand this too, as this is his area of expertise. He does not feel the body of work he has been working with for a career was adequately addressed. I’d agree with this, and am sympathetic to his frustration.

For that reason, I want to specifically thank both @Mercer and @Agauger for pressing through this exchange. My takeaways are:

  1. "Function" remains a fudge word that requires precise definition, and needs to be defined more precisely from the get go. No midstream changes to the definition are allowed midstream. Next time around, I suggest laying out several numbered definitions of function, and referring to them. See, for example, how we dealt with the menagerie of Irreducible Complexity arguments…Which Irreducible Complexity Argument?.

  2. There does appear to be important areas of the literature that have not been fully taken on by ID. I’ve been impressed with @Agauger’s willingness to admit where she has made mistakes reading the literature. That is good news. As she gets a chance to process it, I’m curious how it changes her view. I suggest we consider a non-argumentative thread or series of threads, where scientists here (@mercer, @T_aquaticus, @swamidass, @art) just explain the experiments and interpretations of relevant studies. For example, the work on abzymes is really important and deserves a more careful review: Gauger: Aragorn in The Last Battle. Let’s educate the public on these studies, letting @Agauger listen in, and then see how it affects her thinking in a few months.

  3. Perhaps most significantly, there seems to be a large gap between Axe and Gaugers view of the situation. Gauger seems to hold a more middle ground position. I want to know more about how she arrived at this.

Though there was a lot of heat in this conversation, do not despair. It takes time to process complex scientific topics. A lot was put out here. I know @Agauger well enough to be certain she is going to be taking this all very seriously. So, let’s wrap this up, and come back to it in time, after some contemplation.