Side Comments on Gauger and Mercer


(S. Joshua Swamidass) #21

I think this is a non sequitur. Ancient genome sequencing has little to do with ancestral protein inference. What am I missing?

(John Mercer) #22

You’re right. I mentally filled in “reconstruction experiments,” such as Thornton’s, after “ancient genome sequencing.” That clearly was what Dr. Gauger was talking about.

Also, there are ones from before 2011!

(Nathan H. Lents) #23

Hi everyone - I am not ducking out of these conversations. I am on the road this week for some book events and only have time here and there, which is mostly spent catching up on work stuff. Also, we’re now entering the really busy part of the semester which will continue through the holidays. I really do want to engage here again and I hope to get the time soon!

(Dr. Patrick Trischitta) #24

Here we go. Common on. Have a scientific exchange. Seek to be understood as well as to understand.

Gauger and Mercer: Bifunctional Proteins and Protein Sequence Space
(Ann Gauger) #25

I did. Tell that to him.

(Dr. Patrick Trischitta) #26

Was this what you were trying to post?

@Agauger Let me be as nice and gracious to you as possible - this makes no sense.


Sure, let’s ignore scientific research. You ok with that @Agauger?

(John Mercer) #29

No, we’re seeing if Dr. Gauger actually reads the literature, as she claims to do. From my perspective, her obsessive dragging everything back to discussing her own papers appears to be a defense mechanism to cover up her failure to read the relevant scientific literature.

As I said, I was challenging her global claims about sequence space. She is clearly ignoring most of the relevant data, of which our paper represents literally only one of thousands.


That is a completely different claim than one which suggests that her papers are not relevant to the discussion. I would like to hear whether you think that her papers are not relevant.

And if you agree that they are relevant, I’d like to know how you view their relevance.

(Timothy Horton) #31

What papers published by her in the peer-reviewed primary scientific literature do you consider relevant? Keep in mind that the DI’s self-published Bio-Complexity is not recognized as a legitimate peer-reviewed journal.

(John Mercer) #32

They are only barely relevant. The papers have massive conceptual and technical holes in them, so the numbers could be orders of magnitude off. Even if they were sound, the sample size is insufficient to make the global claims she makes. Those who offer global hypotheses should be eager to test them globally, don’t you think?

Dr. Gauger’s responses to me have been formulaic. She hasn’t asked a single question that might help her to understand the paper despite her lack of understanding. She has shown zero interest in the papers that followed this one. She misrepresents the facts (not the interpretation) of the paper I offered (to her credit, her misrepresentations have been progressively less severe), then dismisses it as irrelevant to her claim that I didn’t cite, but doesn’t address her claim that I did cite. This is not how scientists behave.

Now, let me ask you.

Let’s take the claim she repeatedly and falsely accused me of challenging–that “genuinely new” activities are rare in sequence space.

Now, would what we know from a method in which scientists start with tiny snippets of random sequence and develop completely novel enzymes be relevant to that claim?

Would it even be MORE relevant to that claim than anything she or Doug Axe have ever done?