Gauger: Answering Art Hunt on Real Time Evolution

Design

#99

"A model is a lie that helps you see the truth" - Howard Skipper (biochemist/oncologist)


#100

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(S. Joshua Swamidass) #101

Then please restate them the way you think is appropriate.


(Ann Gauger) #102

@swamidass. @T_aquaticus. @Patrick. @Art
You are all smart people. When we set things up in the lab we do everything possible to maximize the chances of success. Nasvall did th same . The only deck they did not stack was the vector they used, which was very low copy. Would this work in the wild? Under the right selections and fortuitous regulatory mutations yes.
What about Schmidt and OSBS? I am less sanguine because of the very low level of expression

Νοw, I see no point in continuing. I have said what I wanted to,since you seem determined not to understand…(Good bye).


(S. Joshua Swamidass) #103

So you think this will work in the wild, in the right circumstances great. I’m just left wondering how the initial objections could be salien then.

Perhaps this is just example of conceding without conceding?


(Tiberius Claudius Caesar Augustus Germanicus) #104

A “noncession”?


(Arthur Hunt) #105

Absolutely not. Properly done, experiments are designed to get answers, not “maximize the chances of success” (which, in @Agauger’s eyes in this case, is the production of enzymes with differing functionalities) . Nasvall designed their experiments to ask three questions, NOT to optimize their chances to generate enzymes with differing functionalities. Their hypotheses could very well have been wrong, and their experiments would have been successful.


(Faizal Ali) #106

Really? Is that what you and Doug Axe did in your experiments? Maximized the “chances of success”? i.e. That the functions you were investigating would be as likely as possible to arise thru mutations?

I don’t think so.


(Ben Kissling) #107

Even Darwin understood the difference between artificial selection and natural selection. It’s been 150 years, and you guys still haven’t gotten as far as him. Strange.


(Ben Kissling) #108

You should change your name to the Evangeleical Atheist.


(S. Joshua Swamidass) split this topic #109

2 posts were split to a new topic: Welcoming Ben Kissling


(S. Joshua Swamidass) split this topic #110

2 posts were merged into an existing topic: Welcoming Ben Kissling


#113

@Agauger
I agree with all of this. What we were scratching our heads over was the initial criticism that lab experiments don’t count. We thought that was a bit strange, and there is always the chance that we misread your criticisms.

Can random mutations switch HisA activity to TrpF activity if the gene is being expressed and in the right environment? Yes. Would we expect the same to happen in the wild if the same conditions are met? Yes. If we can agree on these points, I think we could move on to more general questions about protein evolution.


#114

I tend to view ‘getting good answers’ as what a ‘successful’ experiment does.


Welcoming Ben Kissling
#115

In that sense every experiment is a success.


#116

In my view . . .

A successful experiment is one where you get a strong yes or a strong no. The unsuccessful experiments are the ones where you get a maybe, or a “can’t tell”.


#117

Did they show that the mutations were random with respect to fitness as they had defined fitness for the purpose of the experiment?


#118

Given the rate at which these mutants appear, it would be consistent with random mutation. If you had 1 million bacteria and 500,000 of them had the mutation after one generation then that would certainly cast doubt on random mutation. However, if you only see one positive mutant out of billions or trillions of bacteria, that supports the conclusion of random mutations.


(Curtis Henderson) #119

Not really, I have personally done quite a few experiments that didn’t give good answers (one way or the other) and needed to be tweaked and repeated - often numerous times.

Ditto.


#120

You are now using a different definition of random mutation than the one you gave in your OP on random mutation.