Antibody Enzymes and Sequence Space


(Arthur Hunt) #162

@Agauger, there are more pieces of data than just the abzyme field that disagree with Axe.

An excellent and challenging ID-inspired hypothesis has been staring you in the face for 15 years or so.

Just saying’ …

(Mikkel R.) #163

Since @Agauger is ducking out can someone else tell me where this number comes from? I couldn’t find anything in the catalytic antibody paper that spawned this thread that implies this ratio, though of course I could have overlooked something.

(Arthur Hunt) #164

I am guessing that there was a typo in @Agauger’s post where this was mentioned. Otherwise, the sentence makes no sense.

(Mikkel R.) #165

To be charitable I suspect she meant allergies? Problem is, though, these actually are extremely common, so that seems to fit the evolutoinary model fine at first glance.

(S. Joshua Swamidass) #166

Either way, there are ways of screening out antibodies that give rise to allergies, and self-reactive ones that give rise to auto-immune diseases. The fact we need those processes shows that it is easy to make antibodies to most proteins, so we need a system to prevent the immune system from eating us.


We have all suffered from cognitive dissonance at some point in our lives . . .

Anyway, thanks for having these discussions and I hope you find yourself back in this little corner of the internet at some point in the future.

(John Mercer) #168

This is disturbing and it makes my point for me.

Normally, when scientists disagree on something, they can at least collaborate on the design of experiment(s) to distinguish between competing hypotheses.

There’s clearly zero enthusiasm/interest from @Agauger here. She appears to be here only to debate on behalf of her tribe, not to discuss science.

It makes perfect sense biologically, if one reads the literature.

That’s a ridiculous revision.

@Guy_Coe, look carefully at the attempt here to avoid the evidence. @Agauger is now trying to pretend that I merely said that there are papers without mentioning that I pointed her to the papers on the subject from the very beginning, and that she has already literally acknowledged that I did so!

Any protein? Where did that come from? We’re not talking about finding specific proteins, we’re talking about finding activities.

(John Mercer) #169

As Swamidass points out, this makes absolutely no sense.

Far, far more. @Guy_Coe, do you see that both sides are not looking at the same evidence here?

(Ann Gauger) #170

@mercer the only reason I am here is because the system is still sending me emails. When I saw what you were up to I felt I needed to reply. First, no scientist sticks around to to work on methods when his coworkers won’t play straight. If you have a womderffulid hypothesis out with it. I already challenged you onvced to go ahead and do your own experiment. You did not.
Second, I had to leave the site completely. That includes hanging out with you guys .???
Third, this has not been fun. This has been a posse trying to corner me so as to make me change my mind on a key I’d point. There has been an unwillingness on your side to look into my concerns.
So Mercer, collegial atmosphere this ain’t and you are the prime reason why. Next post shows why.

(Mikkel R.) #171

That’s a nicely dramatic rendering. How about just trying to persuade you that you are wrong? Is there something inherently nefarious about that? Isn’t that essentially the whole basis of having a discussion in the first place? To debate and discuss ideas and, through that, if one party is wrong hopefully get them to change their mind? Are you not also here so as to at least attempt to change our minds if we are wrong?

(Ann Gauger) #172

@Guy_Coe Mercer is poisoning the well, misrepresenting and twisting what I said. This a classic tactic here. Persuade people their former friends are not trustworthy. If you contact me of site I will tell you what is going on. But please don’t believe their lies. Mercer especially


Glad to see that you’re back. :sunglasses:

From the Eagle’s song “Hotel California”

Last thing I remember, I was
Running for the door
I had to find the passage back to the place I was before
‘Relax’ said the night man,
'We are programmed to receive.
You can check out any time you like,
But you can never leave!'

(Ann Gauger) #174

You are not being honest. You know what my train of thought was and was I was talking about but you act like it made no sense. I do no want to engage in ad hominem here but stay away from attacks on my integrity as a scientist. That is underhanded, back-stabbing behavior.
Persuade me that I am wrong. Well, that was part of the problem. There was invincible confidence on your side and no willingness to listen to me.

Should Scientists Dialogue With ID, YEC, and OEC?
(Ann Gauger) #175

Good bye


See you later alligator. :sunglasses:

(Neil Rickert) #177

You can turn that off in your profile settings.

(John Mercer) #178

We’re the ones playing it straight and scientifically. You’re the one trying to discount masses of evidence. Remember, you’ve made very public, certain claims to laypeople about the prevalence of function in sequence space, and it’s clear that your claim was not made after a careful examination of the evidence.

I already did, more than once. Did you miss it?

You’re not playing it straight. You’re debating. Debate is about challenges. Science is about collaborating to do the most stringent testing of hypotheses that we can. Again, when scientists disagree on fundamentals, they work together to design experiments that resolve disagreement. They don’t issue challenges.

Of course it can’t be! You’ve been living in a bubble.

It has to be painful to try and leave it, and I admire you for doing so. What I don’t admire is a twisting of science in which it has to be one paper pit against one other paper.

We’re not cornering you. We’re pointing you to the evidence, and you’re trying to find ways to discount the evidence instead of integrating it into your conclusion.

I disagree.

None of your concerns to date have made sense, and you jump to new ones rapidly. Again, it’s not our responsibility to look into your concerns. It’s YOUR responsibility to read ALL of the relevant scientific literature before making sweeping, global claims to laypeople.

In what way, exactly, have I poisoned any well or misrepresented anything?

I am being very, very honest. If you disagree, point to any false statement you think I’ve made. I think that’s a very serious accusation and you have a serious ethical duty to document it if you believe in what you are saying.

I stand by my position that none of the off-the-cuff objections you’ve made justify ignoring a 32-year-old field of science with >5000 papers. As we’ve pointed out, your latest one ignores the functions of the immune system that select against self-reactive antibodies; failure of that system results in autoimmune diseases.

It’s your responsibility to communicate your train of thought clearly. If you really believe that your objections make sense, then stay and explain them instead of frantically grasping at one straw after another, then running away.

I certainly don’t have invincible confidence. I’ve published papers in which I have clearly stated that my previous hypothesis was wrong.

I also am certain that everyone here, including me, is willing to listen to you. Has anyone ignored any of your objections?

The problem with your position is that from the start, it ignored the vast majority of the evidence–as Art said, the evidence is not limited to catalytic antibodies.

(John Mercer) #179

Absolutely not, particularly in science.

(Ann Gauger) #180

I did. It got turned back on some how.

(S. Joshua Swamidass) #181

Her settings were wrong and I just fixed them for her.