Antibody Enzymes and Sequence Space

Design
Science

(Mikkel R.) #81

Okay, so there’s still only nine billion more proteins to go before that breadth of samples is met in the experiment you propose. So we’re going to need another twenty million milliters of cells.

You keep confusing 1 new cell with 1 new protein. And… all the rest I wrote, all over again, about sampling depth.

The experiment you propose doesn’t actually constitute a test of the claim that the average density some particular function in protein sequence space is found at a rate of 1 in 10^10. It is nowhere near it in magnitude. You’re going to need more time. More time isn’t “unnatural”, it’s unpractical.


(Arthur Hunt) #82

The Southern corn leaf blight epidemic refutes this claim quite categorically, @Agauger.


(T J Runyon) #83

If you don’t mind, can you break this down a little?


(S. Joshua Swamidass) #84

This is a reference to Turf13.


(Arthur Hunt) #85

The breeders who developed the cmsT maize basically did the experiment @Agauger wants to see done with E. coli, and the result was an entirely new gated ion channel.


(T J Runyon) #86

I’m basically missed that whole conversation


(Arthur Hunt) #87

Here is one explanation.


(T J Runyon) #88

Thanks, Art


(Ann Gauger) #89

You are right, @Rumraket. I was thinking in terms of one bp change per protein per cell division. Iwasn’t really trying to model a comprehensive mutagenesis; despite my stupid math error, I was trying to get a handle on how many cell divisions and therefore mutational changes we could expect in a given window of time. That, however, would not make it an adequate test of the difficulty of getting beta lactamase. But you ably interrupted me to show how I was going to underestimate how long a complete sampling would take. So what does the 1 in 10^10 represent 1 in 10^10 phage screened? This must mean that the mutagenesis is very focus on a small area, so as to sample as wide a number of variants as possible in the region of substrate binding. If so, and I will go back and check the methods, that is another reason the number is so low. Fewer residues to be sampled.

I will grant–My plating 10^10 bacteria was a stupid experiment–ill-conceived–not thought through, for the reasons mentioned above. It would not test the 10^-10 number. But there has to be a way to do it if beta lactamase function is so common. Some way other than the phage experiment to confirm it. If it’s true.


(Ann Gauger) #90

@Art can you clarify for me, the breeders made the cmsT strain or they isolated it?


(Guy Coe) #91

I admire the tenor and direction of this conversation, in the name good science. I am not savvy enough to understand it all, but I do know when I see two people inching towards a better mutual understanding. Thanks for everyone working together to get to the bottom of these kinds of issues.


(Ann Gauger) #92

@Art, I checked out your article. Unfortunately your link to the original (on Panda’s Thumb?) is broken. I think I identified it though. Could you confirm this is the first post?
https://pandasthumb.org/archives/2007/05/on-the-evolutio-1.html


(Arthur Hunt) #93

That’s the one.


(Arthur Hunt) #94

It was isolated using standard breeding and selection. This line was made long before scientists knew how to manipulate DNA.


(Ann Gauger) #95

@Thanks. That’s what I thought. So do they know when the sterile trait first appeared?


(Arthur Hunt) #96

I’m sure someone does, but I don’t. I would guess in the 50’s or early 60’s. It takes time to get traits into commercial seed. Then as well as today.


(Ann Gauger) #97

@Art one last question, then good night,

Do you know if they obtained the male sterile by screening for them from existing populations, or did they mutagenize and then look for male steriles?


(Arthur Hunt) #98

For cmsT specifically, I don’t know. I have never tracked down the research from back then. It may have not been published, I don’t know.

But generally, it is possible to incite recombination in plant mitochondrial genomes using appropriate breeding (crossing) strategies. I suspect that the recombinations indicated by the molecular data arose in this way.


(Ann Gauger) #99

@Art Thanks. I don’t know much about plant genetics, but I wondered about something like that. So there’s good reason to think they know when these mutations happened?


(Arthur Hunt) #100

I would suppose so.