Gauger and Mercer: Bifunctional Proteins and Protein Sequence Space

Design

(John Mercer) #140

That’s not true. Here was my original proposal:

You have consistently engaged in the straw man fallacy by claiming additional criteria that you didn’t include and aren’t relevant. You do so again below.

And you still don’t understand the paper:

Wow. Amazing.

That’s not how myosins work at all. Do you really not know that regular ADP causes actin binding? Do you really not know that ATP induces actin release BEFORE hydrolysis? This is really basic biochemistry.

You’ve made it perfectly clear that 25 days later, you still don’t understand the paper. You’re just reflexively deflecting. And there’s also the bifunctionality that you can’t bring yourself to acknowledge, presumably because it shows how easily evolution can slide from one function to another.

Read your claim. There’s nothing whatsoever in your claim about new or even “genuinely new” chemistries. It’s about the prevalence of functional sequences in sequence space. Period. Do you not realize that there aren’t a whole lot of different chemistries in biology?

There’s nothing in that second claim about genuinely new or new chemistries either. I’m challenging that claim, not the others. “Genuinely” is just a totally subjective criterion that you are adding so that you can redefine it to discount relevant evidence, most of which you clearly don’t want to see.

In general, of course. A percentage would be fine.

How did you measure stability?

And I marvel at how you avoid making predictions. What would you predict?


(Ann Gauger) #141

@swamidass @Mercer @T_aquaticus @Art

Last word. Since you asked me to defend this statement, I thought I would at least explain it. Sorry for the Aragorn @swamidass, it’s only been two.

https://evolutionnews.org/2018/11/in-arguments-for-intelligent-design-definitions-and-assumptions-are-important/

I can’t get the link to copy on my phone. Apologies.


(S. Joshua Swamidass) #142

I’ve been staying out of the way of this exchange, but I don’t want this to be missed.

Do you take a different position that Axe? That would be really interesting to unpack. Can you tell us more?

It seems that you are more in the “wait and see” position. I note also that your key claim is a conditional, not actually even asserting that you know what the actual case is. I think there are some problems with this argument, but it is still notable that you are taking a more measured position than Axe. It seems that (forgive imprecision):

  1. Axe argues that evolution by natural processes alone is improbable because we know that functional proteins are rare in sequence space, and different functions are isolated from one another.

  2. You seem to argue the far more restricted claim: IF proteins are rare and isolated, then evolution by natural processes alone is improbable. Are they rare and isolated? This is an open question.

Am I reading this distinction correctly? If so, you are making a far more restricted claim than Axe, that needs to be engaged in a far different way. In fact, perhaps much of this discussion is missing the point. You would not, then, even be making an ID argument per se, but merely saying the question is currently unresolved. This would put you in a middle ground position between @Mercer/@art and Axe.

Am I reading this correctly? If so, I think this discussion has really missed your point, and deserves a reset.


(Ann Gauger) #143

At least you got the point of the piece.


(Dan Eastwood) #145

@Agauger Agree or disagree, this discussion has been informative for those of us following along. Thank you for your time and effort!


(Ann Gauger) #146

That would be Axe’s 2004 paper on the prevalence of functional protein folds in sequence space? I am not responsible for that one. If you are referring to the 2011 or 2015 papers then yes I had a role to play. I agree, more citations would have saved a lot of grief. If it had been my thesis I would’ve had a whole chapter devoted to the literature. But that was not the case.

You keep saying that your myosin mutant obviates our experiment. I keep saying that it is not a sufficient catalytic change. We have a disagreement about what constitutes a sufficient change in function. We have different criteria.

As far as I can tell, you think that changes like you observed can reach all the different kinds of enzymatic activity there are in the protein universe. I dispute that. I know of only one or two examples where a single mutational change results in a completely new chemistry (there I go again – completely is not sufficiently quantitative.)

Here are our rules.

  1. A change in substrate preference from one to a similar one is not sufficient to constitute a substantial change in catalytic activity. These sorts of changes are often easily reachable by mutation and selection.
  2. A change in chemical reaction type meets our criteria. This is beyond the reach of mutation and selection. To get a change in reaction type typically takes 6 to 8 or more mutations with no functional activity in between. This is not reachable by mutation and selection.

As soon as I am able, I will look up what we said about criteria in our papers and quote them here. Right now I am on my cell phone, and maneuvering between PDFs and this site is very difficult.

I suspect you will not be satisfied by what I have said. You want me to argue why your change in function is sufficient to prove that evolution can accomplish any kind of transition. I submit that since this is your claim you need to argue it. You say the literature is replete with examples of transitions happening in one or a few amino acid changes. Well, I ask you, do those examples show a change in substrate? Is the new substrate similar in chemical structure to the first? Do they show the same reaction type taking place? In my review of the literature this is almost always the case. That does not constitute a sufficient kind of change to permit the evolution of all kinds of enzyme function. You expect me to address thousands of references? Just show me two or three that contradict me. I know I have seen one clear example of such a transition and we discuss it in our paper. And to be fair, any citations you offer should pre-date our papers, meaning before 2015. I would, however, be interested in any you can show that happened since then.

If you can show me an example or two that meet my criteria, I will be happy to say that our claims cannot be universal. In fact I would say that we do indeed need more examples from other enzymes to strengthen the case. It would be great if someone would do those experiment. Unfortunately I cannot.

One last note: you would have heard this explicit statement from me sooner if the tone of the conversation had been more collegial.

Please do not come back at me saying that I need to prove that thousands of examples in the literature are false or sufficient to negate my claim. First of all, as I have said above, my claim is not a firm universal claim. More experiments would be helpful. Second, for me to prove a negative by showing you thousands of papers don’t do this is ludicrous. You on the other hand just need to show me two were three that do. But in order to demonstrate I am wrong you need to show me two or three papers that meet my criteria. Namely, that evolution can produce all kinds of catalytic activity by mutation and selection.

Actually, I won’t make it that difficult. All you need to show me is a conversion from one type of chemical reaction to a different type. Not a shared substrate, not shared chemical reaction, instead a switch from one type of chemical reaction to a different one.


(John Mercer) #147

Are you kidding? I’ve quoted YOU several times, and you’ve just published a new one!

“When we say functional sequence is rare in sequence space, we mean a different sort of function and sequence than in ENCODE. We mean a sequence that can have the ability to carry out an enzymatic reaction.”

Note that you used the first-person plural pronoun “we” 3X there, so you clearly are responsible.

You’ve made it abundantly clear that you don’t read the literature, so this doesn’t make a lot of sense.

I’ve never said anything of the sort. I’ve said that it, and thousands of other studies, obviate your CLAIMS that are at best hasty generalization fallacies. The fatal flaws in yours and Axe’s experiments have been discussed to death.

And this isn’t just one mutant, but you clearly have no interest in any of the papers that follow this one.

Do you think that anyone reading this can’t simply scroll up and see that you are being inaccurate and fallacious?

I think that you are deliberately avoiding addressing what I am actually saying, which was clear.

Nothing I have written here would support such sophistry.

If you are conversing in good faith, why not quote me and address the actual questions, instead of inventing thoughts to put in my head?

The thought you are putting into my head is incredibly arrogant. As a scientist, I don’t make such arrogant claims. We’re talking about your arrogant and fallacious claim here. My claim is merely that our results are in no way consistent with your global and fallacious claim. Nothing more. I am challenging your claims of the prevalence of function in sequence space, and you can’t bring yourself to admit that our work, along with the work of hundreds of others, is highly relevant.

When did I say that? You’re inventing again.

I’m saying that the literature is replete with thousands of examples that show your claims about the prevalence of function in sequence space is false, but you won’t address that.

I’ll add something else here: the literature is replete with thousands of examples of de novo enzymatic activity from random sequences.

I wouldn’t do that. I’m saying that you simply don’t read the literature and you should do so before making arrogant, global claims that are only supported by the weakest of data and unfounded assumptions.

What’s ludicrous is that you are claiming a global negative without bothering to read (apparently) any of the thousands of relevant papers. One can’t prove a negative, but one can make an earnest effort to look for positives. You haven’t.

How about going more to the heart of your claim about sequence space, with thousands of papers describing novel enzymatic activities discovered in random libraries?

I’m talking about the claim you just published:
“It is our claim that proteins made from random sequence will rarely if ever have ANY sort of enzymatic activity.”
https://evolutionnews.org/2018/11/in-arguments-for-intelligent-design-definitions-and-assumptions-are-important/

You’ve set the bar at ANY enzymatic activity, and you are incredibly wrong.

Would you like to put a frequency on “rarely” before we proceed?


(Dan Eastwood) #148

TIME OUT!

We have multiple claims and accusations in play here. If Ann is on mobile it may be difficult for her to give complete replies. Everyone take a step back, consider carefully, and take just one item at a time. Please.


(Dan Eastwood) #149

I agree the wording is ambiguous, but let’s not go grammar-police.

I have no qualification in biochemistry, but it seems that 6-8 mutations of type 1) might result in a change of reaction type as in 2). Am I asking a silly question? Is it a reasonable possibility??

These questions are aimed at keeping the discussion on track. If they do not help in that respect, feel free to ignore them.


(John Mercer) #150

There’s no ambiguity and it’s not grammar policing. It’s her claim, but she’s been trying for weeks to pretend that I am challenging a different claim of hers.

Easily, but it depends on how one defines “reaction type.” Has she defined it? Do you see her rhetorical strategy here?

That doesn’t make sense, as your questions are aimed at Dr. Gauger’s straw man.

I am challenging both of the premises of her claim:

Our work is relevant to both premises. It shows that a functional sequence not found in nature was easy to find, one substitution away. In addition, we gave one of the most complex enzymes known to man an additional substrate specificity (allowing us to manipulate it in cells without disrupting any of the other myosins), without losing any of its many original functions. This last point, which Dr. Gauger can’t seem to acknowledge, provides additional support for the hypothesis that functional sequences are clustered together and shows how a single sequence can evolutionarily bridge a new function to an existing function.

None of this would have been possible if her claim is correct.

She keeps pretending that I am challenging a different claim that contains the strategically undefined rhetorical escape hatches “genuinely new,” “fold,” and now “reaction type.”


(Dan Eastwood) #151

@Mercer I am only capable of asking stupid questions about biochemistry. You could be entirely right - but I can’t make that judgement. My goal here is to ask some obvious questions to draw out basic definitions.

If Ann is on a mobile device, she deserves a chance to clarify. Please allow her that chance. I know this is frustrating. But one problem at a time, please.

@Agauger, I can see where John may have some valid complaints too. There is considerable disagreement about what “reaction type” means, even to my level of understanding.

I don’t how to help the situation except by asking stupid questions until I hit on something useful. :wink:


(John Mercer) #152

Good luck with that!!!

Dan, I’m still on my original point, which Ann has yet to address. I’m merely offering to move the discussion forward by instead addressing a claim she seems far more interested in discussing.

Indeed, at all levels of understanding. :smile: Note that neither of my challenges to those claims is dependent on any way on those ill-defined terms.


(Dan Eastwood) #153

Please keep this civil. Slowing things down is a good way to do that. Right or wrong, it’s difficult to address multiple issues all at once. I see Ann is working on a reply, let’s see what she has to say…

It’s difficult for me to step into the middle of a discussion. I know I’m not giving your point priority, but I’m doing what I can to facilitate a difficult discussion.

Meanwhile, try reading this instead of making my day harder. :slight_smile:


(Ann Gauger) #154

You are a biochemist, right? And you work with proteins, right?

Reaction type: The comprehensive enzyme information system BRENDA, on the page labeled enzyme classification https://www.brenda-enzymes.info/ecexplorer.php?browser=1

Fold: SCOP Structural Classification of Proteins http://scop.berkeley.edu/statistics/ver=2.07

These are not undefined terms.

There are lots of papers that modify substrate specificity by enlarging the active site. Hundreds. In Mercer’s paper the new substrate was a modified ADP analog of the naturally occurring ADP. And the change to the active site allowed the analog to bind; the chemistry for unmodified ADP was unchanged, it was still the same as for the original reaction. In other words, it still bound ADP in the modified binding pocket, and myosin could still facillitate actin filament motility. The new chemistry with the artificial substrate was not functional, however. The modified ADP, when present, prevented actin filament movement. If you doubt me read the abstract of his paper.

Here’s the abstract.
http://www.jbc.org/content/274/44/31373.abstract

Note the abstract says

Several of these N 6-modified ADP analogs were more than 40-fold more potent at inhibiting ATP hydrolysis by Y61G than wild-type myosin-Iβ; in doing so, these analogs locked Y61G myosin-Iβ tightly to actin. N 6-(2-methylbutyl) ADP abolished actin filament motility mediated by Y61G, but not wild-type, myosin-Iβ.

So tell me how promoting the binding of an artificial ADP to the mutant myosin helps evolution, if the result is that actin filament motility mediated by the mutant myosin was abolished.

Here you go. You want me to say how your paper shows I am wrong when I say

So unless functional sequences are easy to find (very common), and/or are clustered together (easily reachable from one functional island to another), explaining current protein diversity without design is impossible.

My quote says “unless functional sequences are easy to find”. Your mutant myosin is not functional–it cannot move actin in the presence of the modified ADP. That’s myosin’s function. If the mutant can’t do that it is not functional. That’s a non-starter. The mutant can perform the original function and move actin in the presence of ADP, but that does not move evolution forward either, because that is not a new function. The first requirement of evolution of a new function is to be functional along the way. Your mutant myosin can accommodate a new substrate, but that new substrate wrecks its function.

The only thing I conclude is that by modifying the binding site you have made a tool that is useful for studying myosins, but that is useless as a demonstration of explaining functional evolution, or protein diversity.


(S. Joshua Swamidass) #155

Thanks @Dan_Eastwood, @Art, @Mercer, and @Agauger. Let me see if I can summarize where things stand…

@Mercer’s Paper on Myosin

There was some history here:

Part of what happened was picking up this very old and important conversation. @mercer felt his work was not accurately represented. I’ve had some of the same frustration when IDist have responded that cancer evolution merely “gums up the works.” So I understand @Mercer’s frustration.

Ann apologized for misreading the paper.

This has been a charged conversation. It is very common to just dig in our heels in conversations like this. @Agauger did not. This is to be commended. The issue then is…

@mercer explains…

The Claims About Reading the Literature

I want to point out that that fairly rough accusations like this:

Are very common among scientists. This is how we talk to each other, for better or worse. I just reviewed some grants this last weekend, and wrote nearly the same thing in my reviews. This is partly a culture gap. We are often assessing one another this way, and stating it as such. This is especially true when a non expert makes a comment about our field. It pisses us off if they get important things wrong, and we don’t hold back.

I acknowledge also that this sounds very accusatory, more accusatory than it actually is in scientific culture. I’ve been called out in the same on this regularly. Most recently, on the work I did on population genetics. I’m no geneticist, so this was the general assumption experts had when they heard my surprising claims. Then they read my paper, saw how I answered questions, and realized that I knew what I was talking about. So these charges are possible to answer. They do seem rude, but this is how the testosterone driven world of science works.

Of note, what I think is going on here is that @Agauger didn’t carefully read @Mercers paper at the time, as she has already explained. The issue is not that she didn’t ready any literature or a lot of literature, but that she missed something material to the argument to she was making.

Mistakes happen. She has already owned up to this (see the apology above), so I’m thinking the real question is how this new information (for @Agauger) alters her view. There, also, is other new information that arises here too…

How Tolerant are Proteins to Mutation?

Unfortunately, this conversation has not been well focused. Another line of followed this:

I have to admit that it is very hard to follow this exchange and how we arrived at this. I’m usually able to follow exchanges, but in this case a lot of ambiguous pronouns switching between several lines of argumentation leave me confused on precisely how we arrived here.

I’d be cautious about picking on this too much though, as I sense a On the Spot Fallacy here…On the spot fallacy - RationalWiki

What is Function?

Astute readers will notice we have already been discussing function in several squish ways. @Agauger clarifies here, and I think this is important.

I must say, however, as a person who works in computational biology in precisely this space, this is not a well-formed definition. I do not know how to, from this, write an algorithm to determine of two reactions are of a “particular catalytic activity” or not. I think the ambiguity here is creating an immense amount of confusion.

@mercer is pointing ot changes in catalytic activity, but @Agauger is saying that these are a not significant changes. However, significance is not well-defined in this context, so it seems to be a large frustrating miss. We really need a clear definition of what is a significant change or not, and it is not clear we are getting it from here.

So for me, I"m still lost on what “genuinely” means in this:

What exactly is genuinely new? How do we determine this? Without some more substance here, I am not sure what to make of this. I would wonder the same as @Mercer on this:

So this is how @Agauger tries to clarify:

This is not clear enough for me to make sense of here. I’ve read Axe’s papers too. It is not clear what would or wouldn’t qualify.

@agauger helps me out a bit here:

Not undefined, but certainly subjective. Those classifications are blurry.

Axe’s Argument

It is important to remember that @Agauger seems to have real disagreements with Axe. She seems to call this an open question, while I am sure Axe would not grand this. As an aside, this point by @Art is very important, and needs to be picked up in a different discussion…

Regardless, I think we will be splitting much of the exchange with @Art into another thread to simplify things here…

The important point, hwoever, is that @Agauger is at least currently making a different argument than her 2015 paper with Axe…

I think this is an important distinciton. I’d like to explore why and how @Agauger ended up taking a different position on this than Axe, though that might have to wait to a later date.

More Confusion on Function…

This seems to be the problem of fuzzy definitions of function. All of a sudden there was a “code switch”, it seems, with this…

Now I am confused entirely. Or maybe not. I think I know the sourcee fo the problem. We’ve changed definitions of "function. This is a reference to the initial starting biological function of the protein, which might be changed with a mutation. This seems to be a totally different than the enzymatic function that we were previously discussion.

@Agauger can you make sense of why this could possibly matter? I hope you are not putting this forward as a serious objection.


(S. Joshua Swamidass) #156

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.


(Dan Eastwood) #157

@swamidass That summary was amazing! Thank you.

I was working on one more comment when work called me away, I’ll go ahead and post it as my final comments here.

@Agauger A refinement on my earlier question, and apologies if this is stupid

Is it possible to define frequencies of “easy” changes, such as those that might found in similar substrates, and compare this to the frequency of changes in type of chemical reaction? I don’t even know how to define a common denominator for comparison here, but that might lead to a basis for comparison.

Is it further possible to name certain mutations and roughly rank them in order of probability? This would be a tough question simply as a statistical problem, and perhaps it is not reasonable to ask?

Given the vagueness of my questions, vague answers are acceptable. Any way you can enlighten me here is helpful. - Thanks! :slight_smile:


(Ann Gauger) #158

@swamidass

@Swamidass. Now I am confused entirely. The biological function of an enzyme is to be an enzyme, and carry out its chemistry. The initial starting chemistry of Beta-lactamase is to break down penicillin. That’s its function. If you introduce a mutation into beta-lactamase most of the time it will still break down penicillin (a beta-lactam class antibiotic). It will still have the same function. What if a single mutation to one of the catalytic amino acids takes place? It will no longer break down penicillin. It will be functionless.

What if we should be so lucky (sarcasm here) as to have a mutation occur that allows a modified version of penicillin to be broken down? Has its function changed? In one sense yes, in another no. Its function is still to break down beta-lactams. It just breaks down a slightly modified one. What if a mutation was introduced that caused a modified penicillin to bind very strongly to beta-lactamase. It would be functionless as far as the new modified penicillin is concerned. It might still break down penicillin just fine, but be inhibited by the new antibiotic.

So now to myosin. Its function is to facilitate the movement of actin filaments by ATP hydrolysis. A mutation occurs which changes the substrate profile of myosin. It can now bind ADP and a modified ADP. Its function is still to facilitate the movement of actin filaments. When in the presence of ADP it still does. It retains that function. In the presence of the modified ADP it cannot facilitate the movement of actin filaments anymore. It is functionless in the presence of the modified ADP.

If this were an attempt to move myosin along the path to a new function (i.e. something other than its existing function), it would be a failure. What new function is there? You can’t claim a new substrate preference, because the new substrate blocks myosin’s function and does not introduce a new one. If you are looking for the evolution of a new trait this is not the way to go about it.

Swamidass, to say that BRENDA and SCOP are not definitive is ridiculous. That’s their purpose–to define and catalog. BRENDA is a catalog of enzyme catalytic activity, broken down into reaction type, progressively. SCOP is a catalog of protein structures, starting with folds and progressively being more specific. Fold is the highest level classification. These are basic terms. If Mercer excoriates me for not knowing about catalytic antibodies, then I have to say to not know about these things is equally shocking.

@Swamidass, you are not stupid. Neither is @Mercer. This is word gaming, and not on my part.

For the record, I object to much of the characterization that @Swamidass has written. Mercer was not the only one frustrated here. From my perspective it was obtuseness and obfuscation on Mercer’s part. I don’t have to go through and make a line by line rebuttal. You gave Mercer all the slack, and the only positive things you said about me were that I apologized and I stuck with it.


(S. Joshua Swamidass) #159

Not really. We are getting in to my area of study. These reactions are far more squishing and subjective at their boundaries than you might think. There are only really a few basic mechanisms in enzymatic reactions. Much of the differences in BRENDA types is merely about shape differences, not fundamental chemistry.

Even then, there are surprising things that can happen. In P450 systems, which are built around a harnessed iron ion, both reductions and oxidations (the opposite!) can happen in the same basic structure. So can conjugation reactions and more. All this in the same active site, and it is often easy to tune enzymes to favor particular reaction over the others.

It is not absurd. It is just non-intuitive.

I know. It is surprising. But the weirdness of biology grows when engaging with small molecules. I’ve spent my whole career engaging that question. I know what I am talking about on this one.


(S. Joshua Swamidass) #160

Absolutely, you were frustrated too. And you handled it without returning. Thank you. I did not mean in any way to suggest you were not frustrated.